From f103ba5bff408b0360db8b31f677ec0e67a056f2 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 8 Mar 2024 16:24:26 +0100 Subject: [PATCH 01/59] Prepare release 3.0.0 --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 93b011f556f..86bcb471976 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -23,7 +23,7 @@ jobs: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: - cli: python3 ./build/cloud/docker/docker-build.py push --images base,init + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build.outputs.version }} secrets: inherit deploy-python: From e518ee89f2de10a29ac0d8b94d06c5542fc45ad1 Mon Sep 17 00:00:00 2001 From: pfurio Date: Fri, 22 Mar 2024 14:43:18 +0100 Subject: [PATCH 02/59] catalog: return array of projects in Organization, #TASK-5922 --- .../db/mongodb/ProjectMongoDBAdaptor.java | 14 +++++-- .../iterators/CatalogMongoDBIterator.java | 22 +++++++++++ .../OrganizationCatalogMongoDBIterator.java | 21 +++++++++- .../managers/OrganizationManagerTest.java | 38 +++++++++++++++++++ 4 files changed, 91 insertions(+), 4 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java index 17bf24e8d39..e40ad419d11 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java @@ -543,8 +543,12 @@ public OpenCGAResult get(Query query, QueryOptions options, String user @Override public OpenCGAResult nativeGet(Query query, QueryOptions options) throws CatalogDBException { + return nativeGet(null, query, options); + } + + public OpenCGAResult nativeGet(ClientSession clientSession, Query query, QueryOptions options) throws CatalogDBException { long startTime = startQuery(); - try (DBIterator dbIterator = nativeIterator(query, options)) { + try (DBIterator dbIterator = nativeIterator(clientSession, query, options)) { return endQuery(startTime, dbIterator); } } @@ -570,11 +574,15 @@ public DBIterator iterator(ClientSession clientSession, Query query, Qu @Override public DBIterator nativeIterator(Query query, QueryOptions options) throws CatalogDBException { + return nativeIterator(null, query, options); + } + + public DBIterator nativeIterator(ClientSession clientSession, Query query, QueryOptions options) throws CatalogDBException { QueryOptions queryOptions = options != null ? new QueryOptions(options) : new QueryOptions(); queryOptions.put(NATIVE_QUERY, true); - MongoDBIterator mongoCursor = getMongoCursor(null, query, queryOptions); - return new ProjectCatalogMongoDBIterator<>(mongoCursor, null, null, dbAdaptorFactory, options, null); + MongoDBIterator mongoCursor = getMongoCursor(clientSession, query, queryOptions); + return new ProjectCatalogMongoDBIterator<>(mongoCursor, clientSession, null, dbAdaptorFactory, options, null); } @Override diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/CatalogMongoDBIterator.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/CatalogMongoDBIterator.java index 50666864c1d..11327f86e39 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/CatalogMongoDBIterator.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/CatalogMongoDBIterator.java @@ -185,4 +185,26 @@ protected QueryOptions createInnerQueryOptionsForVersionedEntity(QueryOptions op return queryOptions; } + protected boolean includeField(QueryOptions options, String field) { + if (options.containsKey(QueryOptions.INCLUDE)) { + List currentIncludeList = options.getAsStringList(QueryOptions.INCLUDE); + for (String include : currentIncludeList) { + if (include.startsWith(field)) { + return true; + } + } + return false; + } else if (options.containsKey(QueryOptions.EXCLUDE)) { + List currentExcludeList = options.getAsStringList(QueryOptions.EXCLUDE); + for (String exclude : currentExcludeList) { + if (exclude.equals(field)) { + return false; + } + } + return true; + } + + return true; + } + } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java index b5aef39398c..0063f764e30 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java @@ -2,12 +2,16 @@ import com.mongodb.client.ClientSession; import org.bson.Document; +import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.commons.datastore.mongodb.GenericDocumentComplexConverter; import org.opencb.commons.datastore.mongodb.MongoDBIterator; import org.opencb.opencga.catalog.db.api.OrganizationDBAdaptor; import org.opencb.opencga.catalog.db.mongodb.MigrationMongoDBAdaptor; import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory; +import org.opencb.opencga.catalog.db.mongodb.ProjectMongoDBAdaptor; +import org.opencb.opencga.catalog.exceptions.CatalogDBException; +import org.opencb.opencga.core.response.OpenCGAResult; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -20,9 +24,11 @@ public class OrganizationCatalogMongoDBIterator extends CatalogMongoDBIterato private final String user; private final QueryOptions options; + private final QueryOptions projectOptions; private final Queue organizationListBuffer; - private MigrationMongoDBAdaptor migrationDBAdaptor; + private final MigrationMongoDBAdaptor migrationDBAdaptor; + private final ProjectMongoDBAdaptor projectMongoDBAdaptor; private final Logger logger; @@ -33,9 +39,12 @@ public OrganizationCatalogMongoDBIterator(MongoDBIterator mongoCursor, super(mongoCursor, clientSession, converter, null); this.options = options != null ? new QueryOptions(options) : new QueryOptions(); + this.projectOptions = createInnerQueryOptionsForVersionedEntity(this.options, OrganizationDBAdaptor.QueryParams.PROJECTS.key(), + true); this.user = user; this.migrationDBAdaptor = dbAdaptorFactory.getMigrationDBAdaptor(); + this.projectMongoDBAdaptor = dbAdaptorFactory.getCatalogProjectDBAdaptor(); this.organizationListBuffer = new LinkedList<>(); this.logger = LoggerFactory.getLogger(OrganizationCatalogMongoDBIterator.class); @@ -78,6 +87,16 @@ private void fetchNextBatch() { internal.put("migrationExecutions", migrationRuns); } + if (includeField(options, OrganizationDBAdaptor.QueryParams.PROJECTS.key())) { + OpenCGAResult openCGAResult = null; + try { + openCGAResult = projectMongoDBAdaptor.nativeGet(clientSession, new Query(), projectOptions); + } catch (CatalogDBException e) { + logger.warn("Could not fetch projects for organization."); + } + organizationDocument.put(OrganizationDBAdaptor.QueryParams.PROJECTS.key(), openCGAResult.getResults()); + } + organizationListBuffer.add(organizationDocument); } } diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java index cf2779c97de..babb1ddfc07 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java @@ -11,6 +11,7 @@ import org.opencb.opencga.core.models.organizations.Organization; import org.opencb.opencga.core.models.organizations.OrganizationConfiguration; import org.opencb.opencga.core.models.organizations.OrganizationUpdateParams; +import org.opencb.opencga.core.models.project.Project; import org.opencb.opencga.core.testclassification.duration.MediumTests; import java.util.Arrays; @@ -76,6 +77,43 @@ public void updateAuthOriginTest() throws CatalogException { assertEquals(authOrigin.getAlgorithm(), organization.getConfiguration().getAuthenticationOrigins().get(0).getAlgorithm()); } + @Test + public void organizationInfoTest() throws CatalogException { + Organization organization = catalogManager.getOrganizationManager().get(organizationId, QueryOptions.empty(), ownerToken).first(); + assertEquals(3, organization.getProjects().size()); + for (Project project : organization.getProjects()) { + assertNotNull(project.getFqn()); + assertNotNull(project.getName()); + assertNotNull(project.getCreationDate()); + } + + QueryOptions options = new QueryOptions(QueryOptions.INCLUDE, "name"); + organization = catalogManager.getOrganizationManager().get(organizationId, options, ownerToken).first(); + assertNull(organization.getProjects()); + + options = new QueryOptions(QueryOptions.EXCLUDE, "projects"); + organization = catalogManager.getOrganizationManager().get(organizationId, options, ownerToken).first(); + assertNull(organization.getProjects()); + + options = new QueryOptions(QueryOptions.INCLUDE, "projects.fqn"); + organization = catalogManager.getOrganizationManager().get(organizationId, options, ownerToken).first(); + assertEquals(3, organization.getProjects().size()); + for (Project project : organization.getProjects()) { + assertNotNull(project.getFqn()); + assertNull(project.getName()); + assertNull(project.getCreationDate()); + } + + options = new QueryOptions(QueryOptions.EXCLUDE, "projects.name"); + organization = catalogManager.getOrganizationManager().get(organizationId, options, ownerToken).first(); + assertEquals(3, organization.getProjects().size()); + for (Project project : organization.getProjects()) { + assertNotNull(project.getFqn()); + assertNull(project.getName()); + assertNotNull(project.getCreationDate()); + } + } + @Test public void migrationExecutionProjectionTest() throws CatalogException { Organization organization = catalogManager.getOrganizationManager().get(organizationId, null, ownerToken).first(); From f50bf22779301da559eb97c05cc748ef822bdd0c Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 25 Mar 2024 12:21:55 +0100 Subject: [PATCH 03/59] catalog: ensure projects are shown to authorised users, #TASK-5922 --- .../catalog/db/api/OrganizationDBAdaptor.java | 6 ++-- .../mongodb/OrganizationMongoDBAdaptor.java | 30 +++++++++++-------- .../db/mongodb/ProjectMongoDBAdaptor.java | 16 ++++++++-- .../OrganizationCatalogMongoDBIterator.java | 12 ++++++-- .../catalog/managers/OrganizationManager.java | 2 +- .../managers/OrganizationManagerTest.java | 24 ++++++++++++++- 6 files changed, 67 insertions(+), 23 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java index e1eadaf0a93..5f478d5ab89 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java @@ -92,9 +92,9 @@ public static QueryParams getParam(String key) { // OpenCGAResult insert(Organization organization, QueryOptions options) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException; -// -// OpenCGAResult get(String userId, QueryOptions options) throws CatalogDBException; -// + + OpenCGAResult get(String userId, QueryOptions options) throws CatalogDBException; + OpenCGAResult get(QueryOptions options) throws CatalogDBException; // // OpenCGAResult incrementCurrentRelease(long projectId) throws CatalogDBException; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptor.java index 4185bc06560..ece41671fb0 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptor.java @@ -97,11 +97,24 @@ Organization insert(ClientSession clientSession, Organization organization) return organization; } + @Override + public OpenCGAResult get(String user, QueryOptions options) throws CatalogDBException { + return get(null, user, options); + } + @Override public OpenCGAResult get(QueryOptions options) throws CatalogDBException { - return get(null, options); + return get(null, null, options); + } + + OpenCGAResult get(ClientSession clientSession, String user, QueryOptions options) throws CatalogDBException { + long startTime = startQuery(); + try (DBIterator dbIterator = iterator(clientSession, user, options)) { + return endQuery(startTime, dbIterator); + } } + @Override public OpenCGAResult update(String organizationId, ObjectMap parameters, QueryOptions queryOptions) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException { @@ -234,13 +247,6 @@ private UpdateDocument getValidatedUpdateParams(ClientSession clientSession, Obj return document; } - OpenCGAResult get(ClientSession clientSession, QueryOptions options) throws CatalogDBException { - long startTime = startQuery(); - try (DBIterator dbIterator = iterator(clientSession, options)) { - return endQuery(startTime, dbIterator); - } - } - @Override public OpenCGAResult delete(Organization organization) throws CatalogDBException { return null; @@ -248,12 +254,12 @@ public OpenCGAResult delete(Organization organization) throws Cata @Override public DBIterator iterator(QueryOptions options) throws CatalogDBException { - return iterator(null, options); + return iterator(null, null, options); } - public DBIterator iterator(ClientSession clientSession, QueryOptions options) throws CatalogDBException { + public DBIterator iterator(ClientSession clientSession, String user, QueryOptions options) throws CatalogDBException { MongoDBIterator mongoCursor = getMongoCursor(clientSession, options); - return new OrganizationCatalogMongoDBIterator<>(mongoCursor, clientSession, organizationConverter, dbAdaptorFactory, options, null); + return new OrganizationCatalogMongoDBIterator<>(mongoCursor, clientSession, organizationConverter, dbAdaptorFactory, options, user); } private MongoDBIterator getMongoCursor(ClientSession clientSession, QueryOptions options) { @@ -269,7 +275,7 @@ private MongoDBIterator getMongoCursor(ClientSession clientSession, Qu } public List getOwnerAndAdmins(ClientSession clientSession) throws CatalogDBException { - Organization organization = get(clientSession, OrganizationManager.INCLUDE_ORGANIZATION_ADMINS).first(); + Organization organization = get(clientSession, null, OrganizationManager.INCLUDE_ORGANIZATION_ADMINS).first(); List members = new ArrayList<>(organization.getAdmins().size() + 1); if (StringUtils.isNotEmpty(organization.getOwner())) { members.add(organization.getOwner()); diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java index e40ad419d11..e9be9ac6563 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java @@ -556,8 +556,13 @@ public OpenCGAResult nativeGet(ClientSession clientSession, Query quer @Override public OpenCGAResult nativeGet(Query query, QueryOptions options, String user) throws CatalogDBException, CatalogAuthorizationException { + return nativeGet(null, query, options, user); + } + + public OpenCGAResult nativeGet(ClientSession clientSession, Query query, QueryOptions options, String user) + throws CatalogDBException, CatalogAuthorizationException { long startTime = startQuery(); - try (DBIterator dbIterator = nativeIterator(query, options, user)) { + try (DBIterator dbIterator = nativeIterator(clientSession, query, options, user)) { return endQuery(startTime, dbIterator); } } @@ -595,11 +600,16 @@ public DBIterator iterator(Query query, QueryOptions options, String us @Override public DBIterator nativeIterator(Query query, QueryOptions options, String user) throws CatalogDBException, CatalogAuthorizationException { + return nativeIterator(null, query, options, user); + } + + public DBIterator nativeIterator(ClientSession clientSession, Query query, QueryOptions options, String user) + throws CatalogDBException, CatalogAuthorizationException { QueryOptions queryOptions = options != null ? new QueryOptions(options) : new QueryOptions(); queryOptions.put(NATIVE_QUERY, true); - MongoDBIterator mongoCursor = getMongoCursor(null, query, queryOptions, user); - return new ProjectCatalogMongoDBIterator<>(mongoCursor, null, null, dbAdaptorFactory, options, user); + MongoDBIterator mongoCursor = getMongoCursor(clientSession, query, queryOptions, user); + return new ProjectCatalogMongoDBIterator<>(mongoCursor, clientSession, null, dbAdaptorFactory, options, user); } // private MongoDBIterator getMongoCursor(ClientSession clientSession, Query query, QueryOptions options, String user) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java index 0063f764e30..0e9f57ad912 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java @@ -1,6 +1,7 @@ package org.opencb.opencga.catalog.db.mongodb.iterators; import com.mongodb.client.ClientSession; +import org.apache.commons.lang3.StringUtils; import org.bson.Document; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; @@ -10,6 +11,7 @@ import org.opencb.opencga.catalog.db.mongodb.MigrationMongoDBAdaptor; import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory; import org.opencb.opencga.catalog.db.mongodb.ProjectMongoDBAdaptor; +import org.opencb.opencga.catalog.exceptions.CatalogAuthorizationException; import org.opencb.opencga.catalog.exceptions.CatalogDBException; import org.opencb.opencga.core.response.OpenCGAResult; import org.slf4j.Logger; @@ -90,9 +92,13 @@ private void fetchNextBatch() { if (includeField(options, OrganizationDBAdaptor.QueryParams.PROJECTS.key())) { OpenCGAResult openCGAResult = null; try { - openCGAResult = projectMongoDBAdaptor.nativeGet(clientSession, new Query(), projectOptions); - } catch (CatalogDBException e) { - logger.warn("Could not fetch projects for organization."); + if (StringUtils.isNotEmpty(user)) { + openCGAResult = projectMongoDBAdaptor.nativeGet(clientSession, new Query(), projectOptions, user); + } else { + openCGAResult = projectMongoDBAdaptor.nativeGet(clientSession, new Query(), projectOptions); + } + } catch (CatalogDBException | CatalogAuthorizationException e) { + logger.warn("Could not fetch projects for organization.", e); } organizationDocument.put(OrganizationDBAdaptor.QueryParams.PROJECTS.key(), openCGAResult.getResults()); } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java index ef37a9509be..1cb1d7cc6a8 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java @@ -131,7 +131,7 @@ public OpenCGAResult get(String organizationId, QueryOptions optio OpenCGAResult queryResult; try { - queryResult = getOrganizationDBAdaptor(organizationId).get(options); + queryResult = getOrganizationDBAdaptor(organizationId).get(userId, options); } catch (CatalogException e) { auditManager.auditInfo(organizationId, userId, Enums.Resource.ORGANIZATION, organizationId, "", "", "", auditParams, new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError())); diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java index babb1ddfc07..bc9b375143e 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java @@ -78,7 +78,7 @@ public void updateAuthOriginTest() throws CatalogException { } @Test - public void organizationInfoTest() throws CatalogException { + public void organizationInfoIncludeProjectsTest() throws CatalogException { Organization organization = catalogManager.getOrganizationManager().get(organizationId, QueryOptions.empty(), ownerToken).first(); assertEquals(3, organization.getProjects().size()); for (Project project : organization.getProjects()) { @@ -114,6 +114,28 @@ public void organizationInfoTest() throws CatalogException { } } + @Test + public void organizationInfoProjectsAuthTest() throws CatalogException { + Organization organization = catalogManager.getOrganizationManager().get(organizationId, QueryOptions.empty(), ownerToken).first(); + assertEquals(3, organization.getProjects().size()); + + organization = catalogManager.getOrganizationManager().get(organizationId, QueryOptions.empty(), orgAdminToken1).first(); + assertEquals(3, organization.getProjects().size()); + + organization = catalogManager.getOrganizationManager().get(organizationId, QueryOptions.empty(), studyAdminToken1).first(); + assertEquals(2, organization.getProjects().size()); + assertArrayEquals(Arrays.asList(projectFqn1, projectFqn2).toArray(), + organization.getProjects().stream().map(Project::getFqn).toArray()); + + organization = catalogManager.getOrganizationManager().get(organizationId, QueryOptions.empty(), normalToken1).first(); + assertEquals(1, organization.getProjects().size()); + assertEquals(projectFqn1, organization.getProjects().get(0).getFqn()); + + organization = catalogManager.getOrganizationManager().get(organizationId, QueryOptions.empty(), noAccessToken1).first(); + assertEquals(1, organization.getProjects().size()); + assertEquals(projectFqn1, organization.getProjects().get(0).getFqn()); + } + @Test public void migrationExecutionProjectionTest() throws CatalogException { Organization organization = catalogManager.getOrganizationManager().get(organizationId, null, ownerToken).first(); From 538b73416398dc8ab0aa679b0ad88f9e72e2ce5a Mon Sep 17 00:00:00 2001 From: pfurio Date: Tue, 9 Apr 2024 15:09:51 +0200 Subject: [PATCH 04/59] catalog: move secretKey to token, #TASK-5923 --- .../v3_0_0/OrganizationMigration.java | 17 ++++-- .../AuthOriginSimplificationMigrations.java | 58 ++++++++++++++++++ .../CatalogAuthenticationManager.java | 21 ++++--- .../LDAPAuthenticationManager.java | 7 ++- .../azure/AuthenticationFactory.java | 14 +++-- .../authorization/AuthorizationManager.java | 3 +- .../CatalogAuthorizationManager.java | 17 ++++-- .../catalog/db/api/OrganizationDBAdaptor.java | 2 + .../db/mongodb/UserMongoDBAdaptor.java | 2 +- .../OrganizationCatalogMongoDBIterator.java | 44 +++++++++++++ .../catalog/managers/CatalogManager.java | 15 +---- .../catalog/managers/OrganizationManager.java | 32 ++++++++-- .../opencga/catalog/managers/UserManager.java | 14 ++--- .../catalog/managers/CatalogManagerTest.java | 23 +++++++ .../managers/OrganizationManagerTest.java | 42 +++++++++---- .../core/config/AuthenticationOrigin.java | 39 ++---------- .../OrganizationConfiguration.java | 18 ++++-- .../organizations/TokenConfiguration.java | 61 +++++++++++++++++++ .../core/models/user/UserUpdateParams.java | 14 +---- 19 files changed, 325 insertions(+), 118 deletions(-) create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigrations.java create mode 100644 opencga-core/src/main/java/org/opencb/opencga/core/models/organizations/TokenConfiguration.java diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java index 3ea84a6f204..c2f9efa57f8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java @@ -377,17 +377,22 @@ protected void run() throws Exception { if (configuration.getAuthentication() != null && CollectionUtils.isNotEmpty(configuration.getAuthentication().getAuthenticationOrigins())) { for (AuthenticationOrigin authenticationOrigin : configuration.getAuthentication().getAuthenticationOrigins()) { if (authenticationOrigin.getType().equals(AuthenticationOrigin.AuthenticationType.OPENCGA) - && authenticationOrigin.getId().equals(CatalogAuthenticationManager.INTERNAL)) { + && "internal".equals(authenticationOrigin.getId())) { continue; } - authenticationOrigin.setAlgorithm(algorithm); - authenticationOrigin.setSecretKey(secretKey); - authenticationOrigin.setExpiration(3600); - authOrigins.add(convertToDocument(authenticationOrigin)); + Document authOriginDoc = convertToDocument(authenticationOrigin); + authOriginDoc.put("algorithm", algorithm); + authOriginDoc.put("secretKey", secretKey); + authOriginDoc.put("expiration", 3600L); + authOrigins.add(authOriginDoc); } } } - authOrigins.add(convertToDocument(CatalogAuthenticationManager.createRandomInternalAuthenticationOrigin())); + Document authOriginDoc = convertToDocument(CatalogAuthenticationManager.createOpencgaAuthenticationOrigin()); + authOriginDoc.put("id", "internal"); + authOriginDoc.put("algorithm", algorithm); + authOriginDoc.put("secretKey", secretKey); + authOriginDoc.put("expiration", 3600L); // Set organization counter, owner and authOrigins orgCol.updateOne(Filters.eq("id", organizationId), Updates.combine( diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigrations.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigrations.java new file mode 100644 index 00000000000..de0cba37442 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigrations.java @@ -0,0 +1,58 @@ +package org.opencb.opencga.app.migrations.v3_1_0; + +import com.mongodb.client.model.Filters; +import com.mongodb.client.model.Projections; +import com.mongodb.client.model.UpdateOneModel; +import com.mongodb.client.model.Updates; +import org.apache.commons.collections4.CollectionUtils; +import org.apache.commons.lang3.StringUtils; +import org.bson.Document; +import org.bson.conversions.Bson; +import org.opencb.opencga.catalog.db.api.OrganizationDBAdaptor; +import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory; +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; +import org.opencb.opencga.core.common.PasswordUtils; + +import java.util.List; + +@Migration(id = "add_organizations", description = "Add new Organization layer #TASK-4389", version = "3.0.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20231212) +public class AuthOriginSimplificationMigrations extends MigrationTool { + + @Override + protected void run() throws Exception { + Bson query = Filters.exists("configuration.token", false); + Bson projection = Projections.include("_id", "configuration"); + migrateCollection(OrganizationMongoDBAdaptorFactory.ORGANIZATION_COLLECTION, query, projection, (orgDocument, bulk) -> { + Document configuration = orgDocument.get(OrganizationDBAdaptor.QueryParams.CONFIGURATION.key(), Document.class); + if (configuration != null) { + String secretKey = null; + List authenticationOrigins = configuration.getList("authenticationOrigins", Document.class); + if (CollectionUtils.isNotEmpty(authenticationOrigins)) { + for (Document authenticationOrigin : authenticationOrigins) { + if (authenticationOrigin.getString("type").equals("OPENCGA")) { + secretKey = authenticationOrigin.getString("secretKey"); + if (authenticationOrigin.getString("id").equals("internal")) { + authenticationOrigin.put("id", "OPENCGA"); + } + } + authenticationOrigin.remove("secretKey"); + authenticationOrigin.remove("algorithm"); + authenticationOrigin.remove("expiration"); + } + } + secretKey = StringUtils.isNotEmpty(secretKey) ? secretKey : PasswordUtils.getStrongRandomPassword(32); + Document token = new Document() + .append("secretKey", secretKey) + .append("algorithm", "HS256") + .append("expiration", 3600L); + configuration.put("token", token); + bulk.add(new UpdateOneModel<>( + Filters.eq("_id", orgDocument.get("_id")), + Updates.set("configuration", configuration))); + } + }); + } + +} diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/CatalogAuthenticationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/CatalogAuthenticationManager.java index 18cd03bb2af..37c12c23f65 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/CatalogAuthenticationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/CatalogAuthenticationManager.java @@ -26,7 +26,6 @@ import org.opencb.opencga.catalog.exceptions.CatalogException; import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.core.common.MailUtils; -import org.opencb.opencga.core.common.PasswordUtils; import org.opencb.opencga.core.config.AuthenticationOrigin; import org.opencb.opencga.core.config.Email; import org.opencb.opencga.core.models.user.AuthenticationResponse; @@ -43,19 +42,24 @@ */ public class CatalogAuthenticationManager extends AuthenticationManager { + // TODO: Remove INTERNAL field and its usages after several releases (TASK-5923) + @Deprecated public static final String INTERNAL = "internal"; + public static final String OPENCGA = "OPENCGA"; private final Email emailConfig; private final DBAdaptorFactory dbAdaptorFactory; - public CatalogAuthenticationManager(DBAdaptorFactory dbAdaptorFactory, Email emailConfig, String secretKeyString, long expiration) { + public CatalogAuthenticationManager(DBAdaptorFactory dbAdaptorFactory, Email emailConfig, String algorithm, String secretKeyString, + long expiration) { super(expiration); this.emailConfig = emailConfig; this.dbAdaptorFactory = dbAdaptorFactory; - Key secretKey = this.converStringToKeyObject(secretKeyString, SignatureAlgorithm.HS256.getJcaName()); - this.jwtManager = new JwtManager(SignatureAlgorithm.HS256.getValue(), secretKey); + SignatureAlgorithm signatureAlgorithm = SignatureAlgorithm.valueOf(algorithm); + Key secretKey = this.converStringToKeyObject(secretKeyString, signatureAlgorithm.getJcaName()); + this.jwtManager = new JwtManager(signatureAlgorithm.getValue(), secretKey); this.logger = LoggerFactory.getLogger(CatalogAuthenticationManager.class); } @@ -136,12 +140,9 @@ public OpenCGAResult resetPassword(String organizationId, String userId) throws return result; } - public static AuthenticationOrigin createRandomInternalAuthenticationOrigin() { + public static AuthenticationOrigin createOpencgaAuthenticationOrigin() { return new AuthenticationOrigin() - .setId(CatalogAuthenticationManager.INTERNAL) - .setType(AuthenticationOrigin.AuthenticationType.OPENCGA) - .setAlgorithm("HS256") - .setExpiration(3600L) - .setSecretKey(PasswordUtils.getStrongRandomPassword(32)); + .setId(CatalogAuthenticationManager.OPENCGA) + .setType(AuthenticationOrigin.AuthenticationType.OPENCGA); } } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/LDAPAuthenticationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/LDAPAuthenticationManager.java index 58eae214538..516a54702c2 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/LDAPAuthenticationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/LDAPAuthenticationManager.java @@ -66,7 +66,7 @@ public class LDAPAuthenticationManager extends AuthenticationManager { private String host; private boolean ldaps; - public LDAPAuthenticationManager(AuthenticationOrigin authenticationOrigin, String secretKeyString, long expiration) { + public LDAPAuthenticationManager(AuthenticationOrigin authenticationOrigin, String algorithm, String secretKeyString, long expiration) { super(expiration); this.logger = LoggerFactory.getLogger(LDAPAuthenticationManager.class); this.host = authenticationOrigin.getHost(); @@ -107,8 +107,9 @@ public LDAPAuthenticationManager(AuthenticationOrigin authenticationOrigin, Stri logger.info("Init LDAP AuthenticationManager. Host: {}, env:{}", host, envToStringRedacted(getDefaultEnv())); - Key secretKey = this.converStringToKeyObject(secretKeyString, SignatureAlgorithm.HS256.getJcaName()); - this.jwtManager = new JwtManager(SignatureAlgorithm.HS256.getValue(), secretKey); + SignatureAlgorithm signatureAlgorithm = SignatureAlgorithm.valueOf(algorithm); + Key secretKey = this.converStringToKeyObject(secretKeyString, signatureAlgorithm.getJcaName()); + this.jwtManager = new JwtManager(signatureAlgorithm.getValue(), secretKey); } protected static String envToStringRedacted(Hashtable env) { diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/azure/AuthenticationFactory.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/azure/AuthenticationFactory.java index 6057144f9a3..0bcdd18688f 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/azure/AuthenticationFactory.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authentication/azure/AuthenticationFactory.java @@ -39,6 +39,11 @@ public void configureOrganizationAuthenticationManager(Organization organization Email email = new Email(); Map tmpAuthenticationManagerMap = new HashMap<>(); + + long expiration = organization.getConfiguration().getToken().getExpiration(); + String algorithm = organization.getConfiguration().getToken().getAlgorithm(); + String secretKey = organization.getConfiguration().getToken().getSecretKey(); + if (organization.getConfiguration() != null && CollectionUtils.isNotEmpty(organization.getConfiguration().getAuthenticationOrigins())) { for (AuthenticationOrigin authOrigin : organization.getConfiguration().getAuthenticationOrigins()) { @@ -46,15 +51,16 @@ public void configureOrganizationAuthenticationManager(Organization organization switch (authOrigin.getType()) { case LDAP: tmpAuthenticationManagerMap.put(authOrigin.getId(), - new LDAPAuthenticationManager(authOrigin, authOrigin.getSecretKey(), authOrigin.getExpiration())); + new LDAPAuthenticationManager(authOrigin, algorithm, secretKey, expiration)); break; case AzureAD: tmpAuthenticationManagerMap.put(authOrigin.getId(), new AzureADAuthenticationManager(authOrigin)); break; case OPENCGA: - tmpAuthenticationManagerMap.put(authOrigin.getId(), - new CatalogAuthenticationManager(catalogDBAdaptorFactory, email, authOrigin.getSecretKey(), - authOrigin.getExpiration())); + CatalogAuthenticationManager catalogAuthenticationManager = + new CatalogAuthenticationManager(catalogDBAdaptorFactory, email, algorithm, secretKey, expiration); + tmpAuthenticationManagerMap.put(CatalogAuthenticationManager.INTERNAL, catalogAuthenticationManager); + tmpAuthenticationManagerMap.put(CatalogAuthenticationManager.OPENCGA, catalogAuthenticationManager); break; default: logger.warn("Unexpected authentication origin type '{}' for id '{}' found in organization '{}'. " diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/AuthorizationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/AuthorizationManager.java index c4b6f63d6d4..0b2661baa46 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/AuthorizationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/AuthorizationManager.java @@ -16,6 +16,7 @@ package org.opencb.opencga.catalog.auth.authorization; +import org.opencb.opencga.catalog.exceptions.CatalogAuthorizationException; import org.opencb.opencga.catalog.exceptions.CatalogException; import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.core.api.ParamConstants; @@ -118,7 +119,7 @@ default boolean isOpencgaAdministrator(JwtPayload payload) throws CatalogExcepti return isOpencgaAdministrator(payload.getOrganization(), payload.getUserId()); } - boolean isOpencgaAdministrator(String organization, String userId) throws CatalogException; + boolean isOpencgaAdministrator(String organization, String userId) throws CatalogAuthorizationException; default void checkIsOpencgaAdministrator(JwtPayload payload) throws CatalogException { checkIsOpencgaAdministrator(payload, null); diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java index ec490e3acda..247fe6b41dd 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/auth/authorization/CatalogAuthorizationManager.java @@ -83,12 +83,11 @@ public void checkCanEditProject(String organizationId, long projectId, String us } @Override - public void checkCanViewOrganization(String organizationId, String userId) throws CatalogException { + public void checkCanViewOrganization(String organizationId, String userId) throws CatalogAuthorizationException { if (isOpencgaAdministrator(organizationId, userId)) { return; } - // Check user belongs to organization - dbAdaptorFactory.getCatalogUserDBAdaptor(organizationId).checkId(userId); + checkUserExists(organizationId, userId); } @Override @@ -218,11 +217,11 @@ public void checkCanCreateUpdateDeleteVariableSets(String organizationId, long s } @Override - public boolean isOpencgaAdministrator(String organization, String userId) throws CatalogException { + public boolean isOpencgaAdministrator(String organization, String userId) throws CatalogAuthorizationException { if (ParamConstants.ADMIN_ORGANIZATION.equals(organization) || userId.startsWith(ParamConstants.ADMIN_ORGANIZATION + ":")) { // Check user exists in ADMIN ORGANIZATION String user = userId.replace(ParamConstants.ADMIN_ORGANIZATION + ":", ""); - dbAdaptorFactory.getCatalogUserDBAdaptor(ParamConstants.ADMIN_ORGANIZATION).checkId(user); + checkUserExists(ParamConstants.ADMIN_ORGANIZATION, user); return true; } return false; @@ -1012,6 +1011,14 @@ public void removePermissionRule(String organizationId, long studyId, String per ==================================== */ + private void checkUserExists(String organizationId, String userId) throws CatalogAuthorizationException { + try { + dbAdaptorFactory.getCatalogUserDBAdaptor(organizationId).checkId(userId); + } catch (CatalogException e) { + throw new CatalogAuthorizationException("User '" + userId + "' not authorized to see Org '" + organizationId + "'.", e); + } + } + /** * Retrieves the groupId where the members belongs to. * diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java index e1eadaf0a93..89122cdc65c 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java @@ -27,6 +27,8 @@ enum QueryParams implements QueryParam { INTERNAL_MIGRATION_EXECUTIONS("internal.migrationExecutions", OBJECT, ""), CONFIGURATION("configuration", OBJECT, ""), CONFIGURATION_AUTHENTICATION_ORIGINS("configuration.authenticationOrigins", OBJECT, ""), + CONFIGURATION_AUTHENTICATION_ORIGINS_OPTIONS("configuration.authenticationOrigins.options", OBJECT, ""), + CONFIGURATION_TOKEN("configuration.token", OBJECT, ""), CREATION_DATE("creationDate", DATE, ""), MODIFICATION_DATE("modificationDate", DATE, ""), PROJECTS("projects", OBJECT, ""), diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java index 37a182217ca..425f72c3924 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java @@ -433,7 +433,7 @@ public OpenCGAResult nativeGet(Query query, QueryOptions options) throws Catalog public OpenCGAResult update(Query query, ObjectMap parameters, QueryOptions queryOptions) throws CatalogDBException { Map userParameters = new HashMap<>(); - final String[] acceptedParams = {QueryParams.NAME.key(), QueryParams.EMAIL.key(), QueryParams.ORGANIZATION.key()}; + final String[] acceptedParams = {QueryParams.NAME.key(), QueryParams.EMAIL.key()}; filterStringParams(parameters, userParameters, acceptedParams); if (parameters.containsKey(QueryParams.INTERNAL_STATUS_ID.key())) { diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java index b5aef39398c..def6f2a0fcf 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java @@ -1,6 +1,8 @@ package org.opencb.opencga.catalog.db.mongodb.iterators; import com.mongodb.client.ClientSession; +import org.apache.commons.collections4.CollectionUtils; +import org.apache.commons.lang3.StringUtils; import org.bson.Document; import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.commons.datastore.mongodb.GenericDocumentComplexConverter; @@ -78,10 +80,52 @@ private void fetchNextBatch() { internal.put("migrationExecutions", migrationRuns); } + // TODO: Remove this code after several releases (TASK-5923) + recoverSecretKeyTask5923(organizationDocument); + organizationListBuffer.add(organizationDocument); } } + // TODO: Remove this method after several releases (TASK-5923) + /** + * This method should only be necessary in order to be able to run the migration for TASK-5923 because OpenCGA looks for the config. + * This configuration was changed in TASK-5923, therefore, OpenCGA would be unable to initialise without it. + * Once the migration is run, this code will do nothing, so it should be removed in the future. + * + * @param organizationDocument Organization document. + */ + private void recoverSecretKeyTask5923(Document organizationDocument) { + Document configuration = organizationDocument.get(OrganizationDBAdaptor.QueryParams.CONFIGURATION.key(), Document.class); + if (configuration != null) { + String secretKey = null; + String algorithm = null; + long expiration = 3600L; + List authenticationOrigins = configuration.getList("authenticationOrigins", Document.class); + if (CollectionUtils.isNotEmpty(authenticationOrigins)) { + for (Document authenticationOrigin : authenticationOrigins) { + if (authenticationOrigin.getString("type").equals("OPENCGA")) { + secretKey = authenticationOrigin.getString("secretKey"); + algorithm = authenticationOrigin.getString("algorithm"); + Number expiration1 = authenticationOrigin.get("expiration", Number.class); + expiration = expiration1 != null ? expiration1.longValue() : expiration; + +// authenticationOrigin.put("id", "OPENCGA"); + } + } + if (StringUtils.isNotEmpty(secretKey)) { + Document token = configuration.get("token", Document.class); + if (token == null || StringUtils.isEmpty(token.getString("secretKey"))) { + token = new Document("secretKey", secretKey) + .append("algorithm", algorithm) + .append("expiration", expiration); + configuration.put("token", token); + } + } + } + } + } + private boolean obtainMigrations() { if (options.containsKey(QueryOptions.INCLUDE)) { List currentIncludeList = options.getAsStringList(QueryOptions.INCLUDE); diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/CatalogManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/CatalogManager.java index 5c8034661bc..ec266229aa8 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/CatalogManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/CatalogManager.java @@ -38,14 +38,10 @@ import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.core.common.PasswordUtils; import org.opencb.opencga.core.common.UriUtils; -import org.opencb.opencga.core.config.AuthenticationOrigin; import org.opencb.opencga.core.config.Configuration; import org.opencb.opencga.core.config.Optimizations; import org.opencb.opencga.core.models.JwtPayload; -import org.opencb.opencga.core.models.organizations.Organization; -import org.opencb.opencga.core.models.organizations.OrganizationConfiguration; -import org.opencb.opencga.core.models.organizations.OrganizationCreateParams; -import org.opencb.opencga.core.models.organizations.OrganizationUpdateParams; +import org.opencb.opencga.core.models.organizations.*; import org.opencb.opencga.core.models.project.ProjectCreateParams; import org.opencb.opencga.core.models.project.ProjectOrganism; import org.opencb.opencga.core.models.study.Study; @@ -268,13 +264,8 @@ private void privateInstall(String algorithm, String secretKey, String password, catalogIOManager.createDefaultOpenCGAFolders(); OrganizationConfiguration organizationConfiguration = new OrganizationConfiguration( - Collections.singletonList(new AuthenticationOrigin() - .setId(CatalogAuthenticationManager.INTERNAL) - .setType(AuthenticationOrigin.AuthenticationType.OPENCGA) - .setAlgorithm(algorithm) - .setExpiration(3600L) - .setSecretKey(secretKey)), - new Optimizations()); + Collections.singletonList(CatalogAuthenticationManager.createOpencgaAuthenticationOrigin()), + new Optimizations(), new TokenConfiguration(algorithm, secretKey, 3600L)); organizationManager.create(new OrganizationCreateParams(ADMIN_ORGANIZATION, ADMIN_ORGANIZATION, null, null, organizationConfiguration, null), QueryOptions.empty(), null); diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java index a58532c9544..93eea686cb3 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java @@ -131,8 +131,11 @@ public OpenCGAResult get(String organizationId, QueryOptions optio OpenCGAResult queryResult; try { + ParamUtils.checkParameter(organizationId, "organization id"); authorizationManager.checkCanViewOrganization(organizationId, userId); - queryResult = getOrganizationDBAdaptor(organizationId).get(options); + QueryOptions optionsCopy = ParamUtils.defaultObject(options, QueryOptions::new); + queryResult = getOrganizationDBAdaptor(organizationId).get(optionsCopy); + privatizeResults(queryResult); } catch (CatalogException e) { auditManager.auditInfo(organizationId, userId, Enums.Resource.ORGANIZATION, organizationId, "", "", "", auditParams, new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError())); @@ -177,6 +180,7 @@ public OpenCGAResult create(OrganizationCreateParams organizationC // Fetch created organization queryResult.setResults(result.getResults()); } + privatizeResults(queryResult); // Add required authentication manager for the new organization authenticationFactory.configureOrganizationAuthenticationManager(organization); @@ -264,12 +268,10 @@ public OpenCGAResult update(String organizationId, OrganizationUpd } internal = true; // Set id to INTERNAL - authenticationOrigin.setId(CatalogAuthenticationManager.INTERNAL); + authenticationOrigin.setId(CatalogAuthenticationManager.OPENCGA); } ParamUtils.checkIdentifier(authenticationOrigin.getId(), authOriginsPrefixKey + ".id"); ParamUtils.checkObj(authenticationOrigin.getType(), authOriginsPrefixKey + ".type"); - ParamUtils.checkParameter(authenticationOrigin.getSecretKey(), authOriginsPrefixKey + ".secretKey"); - ParamUtils.checkParameter(authenticationOrigin.getAlgorithm(), authOriginsPrefixKey + ".algorithm"); if (authenticationOriginIds.contains(authenticationOrigin.getId())) { throw new CatalogException("Found duplicated authentication origin id '" + authenticationOrigin.getId() + "'."); } @@ -290,6 +292,7 @@ public OpenCGAResult update(String organizationId, OrganizationUpd OpenCGAResult queryResult = getOrganizationDBAdaptor(organizationId).get(options); result.setResults(queryResult.getResults()); } + privatizeResults(result); } catch (Exception e) { Event event = new Event(Event.Type.ERROR, organizationId, e.getMessage()); result.getEvents().add(event); @@ -329,7 +332,11 @@ private void validateOrganizationForCreation(Organization organization, String u } else { organization.getConfiguration() .setAuthenticationOrigins(Collections.singletonList( - CatalogAuthenticationManager.createRandomInternalAuthenticationOrigin())); + CatalogAuthenticationManager.createOpencgaAuthenticationOrigin())); + } + if (organization.getConfiguration().getToken() == null + || StringUtils.isEmpty(organization.getConfiguration().getToken().getSecretKey())) { + organization.getConfiguration().setToken(TokenConfiguration.init()); } organization.setAttributes(ParamUtils.defaultObject(organization.getAttributes(), HashMap::new)); } @@ -355,4 +362,19 @@ public List getOrganizationIds(String token) throws CatalogException { authorizationManager.checkIsOpencgaAdministrator(tokenPayload, "get all organization ids"); return catalogDBAdaptorFactory.getOrganizationIds(); } + + private void privatizeResults(OpenCGAResult result) { + if (CollectionUtils.isNotEmpty(result.getResults())) { + for (Organization organization : result.getResults()) { + if (organization.getConfiguration() != null) { + organization.getConfiguration().setToken(null); + if (CollectionUtils.isNotEmpty(organization.getConfiguration().getAuthenticationOrigins())) { + for (AuthenticationOrigin authenticationOrigin : organization.getConfiguration().getAuthenticationOrigins()) { + authenticationOrigin.setOptions(null); + } + } + } + } + } + } } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java index 96098fedcff..2e28c4104f5 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java @@ -144,7 +144,7 @@ public OpenCGAResult create(User user, String password, String token) thro throw new CatalogException("Unknown authentication origin id '" + user.getAccount().getAuthentication() + "'"); } } else { - user.getAccount().setAuthentication(new Account.AuthenticationOrigin(CatalogAuthenticationManager.INTERNAL, false)); + user.getAccount().setAuthentication(new Account.AuthenticationOrigin(CatalogAuthenticationManager.OPENCGA, false)); } if (!ParamConstants.ADMIN_ORGANIZATION.equals(organizationId) || !OPENCGA.equals(user.getId())) { @@ -210,7 +210,7 @@ public JwtPayload validateToken(String token) throws CatalogException { String authOrigin; if (ParamConstants.ANONYMOUS_USER_ID.equals(jwtPayload.getUserId())) { - authOrigin = CatalogAuthenticationManager.INTERNAL; + authOrigin = CatalogAuthenticationManager.OPENCGA; } else { OpenCGAResult userResult = getUserDBAdaptor(jwtPayload.getOrganization()).get(jwtPayload.getUserId(), INCLUDE_ACCOUNT); if (userResult.getNumResults() == 0) { @@ -590,7 +590,7 @@ public OpenCGAResult update(String userId, ObjectMap parameters, QueryOpti userId = getValidUserId(userId, payload); for (String s : parameters.keySet()) { - if (!s.matches("name|email|organization|attributes")) { + if (!s.matches("name|email|attributes")) { throw new CatalogDBException("Parameter '" + s + "' can't be changed"); } } @@ -771,7 +771,7 @@ public AuthenticationResponse login(String organizationId, String username, Stri auditManager.auditUser(organizationId, username, Enums.Action.LOGIN, username, new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS)); String userId = authenticationFactory.getUserId(organizationId, authId, response.getToken()); - if (!CatalogAuthenticationManager.INTERNAL.equals(authId)) { + if (!CatalogAuthenticationManager.OPENCGA.equals(authId) && !CatalogAuthenticationManager.INTERNAL.equals(authId)) { // External authorization try { // If the user is not registered, an exception will be raised @@ -782,7 +782,7 @@ public AuthenticationResponse login(String organizationId, String username, Stri .get(0); user.setOrganization(organizationId); // Generate a root token to be able to create the user even if the installation is private - String rootToken = authenticationFactory.createToken(organizationId, CatalogAuthenticationManager.INTERNAL, OPENCGA); + String rootToken = authenticationFactory.createToken(organizationId, CatalogAuthenticationManager.OPENCGA, OPENCGA); create(user, null, rootToken); } @@ -809,7 +809,7 @@ public AuthenticationResponse loginAnonymous(String organizationId) throws Catal throw CatalogAuthenticationException.userNotFound(organizationId, ParamConstants.ANONYMOUS_USER_ID); } - String token = authenticationFactory.createToken(organizationId, CatalogAuthenticationManager.INTERNAL, + String token = authenticationFactory.createToken(organizationId, CatalogAuthenticationManager.OPENCGA, ParamConstants.ANONYMOUS_USER_ID); return new AuthenticationResponse(token); } @@ -837,7 +837,7 @@ public AuthenticationResponse refreshToken(String token) throws CatalogException break; } catch (CatalogAuthenticationException e) { logger.debug("Could not refresh token with '{}' provider: {}", entry.getKey(), e.getMessage(), e); - if (CatalogAuthenticationManager.INTERNAL.equals(entry.getKey())) { + if (CatalogAuthenticationManager.OPENCGA.equals(entry.getKey())) { exception = e; } } diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java index 07edb4610b7..df58d773ed2 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java @@ -480,6 +480,29 @@ public void testAssignPermissions() throws CatalogException { assertTrue(acls.stream().map(x -> String.valueOf(x.get("member"))).collect(Collectors.toSet()).contains("@group_cancer_some_thing_else")); } + @Test + public void getUserInfoTest() throws CatalogException { + OpenCGAResult result = catalogManager.getUserManager().get(organizationId, orgOwnerUserId, QueryOptions.empty(), ownerToken); + assertEquals(1, result.getNumResults()); + assertNotNull(result.first().getProjects()); + assertEquals(2, result.first().getProjects().size()); + + result = catalogManager.getUserManager().get(organizationId, orgAdminUserId1, QueryOptions.empty(), orgAdminToken1); + assertEquals(1, result.getNumResults()); + assertNotNull(result.first().getProjects()); + assertEquals(2, result.first().getProjects().size()); + + result = catalogManager.getUserManager().get(organizationId, studyAdminUserId1, QueryOptions.empty(), studyAdminToken1); + assertEquals(1, result.getNumResults()); + assertNotNull(result.first().getProjects()); + assertEquals(2, result.first().getProjects().size()); + + result = catalogManager.getUserManager().get(organizationId, normalUserId1, QueryOptions.empty(), normalToken1); + assertEquals(1, result.getNumResults()); + assertNotNull(result.first().getProjects()); + assertEquals(1, result.first().getProjects().size()); + } + /** * Project methods *************************** */ diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java index 9cbcb43c091..2e4ab35811f 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java @@ -17,6 +17,7 @@ import org.opencb.opencga.core.models.organizations.Organization; import org.opencb.opencga.core.models.organizations.OrganizationConfiguration; import org.opencb.opencga.core.models.organizations.OrganizationUpdateParams; +import org.opencb.opencga.core.models.organizations.TokenConfiguration; import org.opencb.opencga.core.models.study.Group; import org.opencb.opencga.core.models.study.Study; import org.opencb.opencga.core.response.OpenCGAResult; @@ -42,7 +43,7 @@ public void ensureAuthOriginExistsTest() throws CatalogException { @Test public void ensureAuthOriginCannotBeRemovedTest() throws CatalogException { OrganizationUpdateParams updateParams = new OrganizationUpdateParams().setConfiguration(new OrganizationConfiguration( - Collections.emptyList(), null)); + Collections.emptyList(), null, new TokenConfiguration())); thrown.expect(CatalogException.class); thrown.expectMessage("OPENCGA"); catalogManager.getOrganizationManager().update(organizationId, updateParams, INCLUDE_RESULT, ownerToken); @@ -50,10 +51,10 @@ public void ensureAuthOriginCannotBeRemovedTest() throws CatalogException { @Test public void avoidDuplicatedOPENCGAAuthOriginTest() throws CatalogException { - AuthenticationOrigin authOrigin = CatalogAuthenticationManager.createRandomInternalAuthenticationOrigin(); - AuthenticationOrigin authOrigin2 = CatalogAuthenticationManager.createRandomInternalAuthenticationOrigin(); + AuthenticationOrigin authOrigin = CatalogAuthenticationManager.createOpencgaAuthenticationOrigin(); + AuthenticationOrigin authOrigin2 = CatalogAuthenticationManager.createOpencgaAuthenticationOrigin(); OrganizationUpdateParams updateParams = new OrganizationUpdateParams().setConfiguration(new OrganizationConfiguration( - Arrays.asList(authOrigin, authOrigin2), null)); + Arrays.asList(authOrigin, authOrigin2), null, new TokenConfiguration())); thrown.expect(CatalogException.class); thrown.expectMessage("OPENCGA"); @@ -62,11 +63,11 @@ public void avoidDuplicatedOPENCGAAuthOriginTest() throws CatalogException { @Test public void avoidDuplicatedAuthOriginIdTest() throws CatalogException { - AuthenticationOrigin authOrigin = CatalogAuthenticationManager.createRandomInternalAuthenticationOrigin(); - AuthenticationOrigin authOrigin2 = CatalogAuthenticationManager.createRandomInternalAuthenticationOrigin(); + AuthenticationOrigin authOrigin = CatalogAuthenticationManager.createOpencgaAuthenticationOrigin(); + AuthenticationOrigin authOrigin2 = CatalogAuthenticationManager.createOpencgaAuthenticationOrigin(); authOrigin2.setType(AuthenticationOrigin.AuthenticationType.LDAP); OrganizationUpdateParams updateParams = new OrganizationUpdateParams().setConfiguration(new OrganizationConfiguration( - Arrays.asList(authOrigin, authOrigin2), null)); + Arrays.asList(authOrigin, authOrigin2), null, new TokenConfiguration())); thrown.expect(CatalogException.class); thrown.expectMessage("origin id"); @@ -75,16 +76,13 @@ public void avoidDuplicatedAuthOriginIdTest() throws CatalogException { @Test public void updateAuthOriginTest() throws CatalogException { - AuthenticationOrigin authOrigin = CatalogAuthenticationManager.createRandomInternalAuthenticationOrigin(); + AuthenticationOrigin authOrigin = CatalogAuthenticationManager.createOpencgaAuthenticationOrigin(); OrganizationUpdateParams updateParams = new OrganizationUpdateParams().setConfiguration(new OrganizationConfiguration( - Collections.singletonList(authOrigin), null)); + Collections.singletonList(authOrigin), null, new TokenConfiguration())); Organization organization = catalogManager.getOrganizationManager().update(organizationId, updateParams, INCLUDE_RESULT, ownerToken).first(); assertEquals(authOrigin.getId(), organization.getConfiguration().getAuthenticationOrigins().get(0).getId()); assertEquals(authOrigin.getType(), organization.getConfiguration().getAuthenticationOrigins().get(0).getType()); - assertEquals(authOrigin.getExpiration(), organization.getConfiguration().getAuthenticationOrigins().get(0).getExpiration()); - assertEquals(authOrigin.getSecretKey(), organization.getConfiguration().getAuthenticationOrigins().get(0).getSecretKey()); - assertEquals(authOrigin.getAlgorithm(), organization.getConfiguration().getAuthenticationOrigins().get(0).getAlgorithm()); } @Test @@ -200,4 +198,24 @@ public void updateOrganizationTest() throws CatalogException { } } + @Test + public void secretKeyIsAlwaysHiddenTest() throws CatalogException { + Organization organization = catalogManager.getOrganizationManager().get(organizationId, null, ownerToken).first(); + assertNotNull(organization.getName()); + assertNull(organization.getConfiguration().getToken()); + assertNull(organization.getConfiguration().getAuthenticationOrigins().get(0).getOptions()); + + QueryOptions options = new QueryOptions(QueryOptions.INCLUDE, OrganizationDBAdaptor.QueryParams.CONFIGURATION.key()); + organization = catalogManager.getOrganizationManager().get(organizationId, options, ownerToken).first(); + assertNull(organization.getName()); + assertNull(organization.getConfiguration().getToken()); + assertNull(organization.getConfiguration().getAuthenticationOrigins().get(0).getOptions()); + + options = new QueryOptions(QueryOptions.EXCLUDE, OrganizationDBAdaptor.QueryParams.NAME.key()); + organization = catalogManager.getOrganizationManager().get(organizationId, options, ownerToken).first(); + assertNull(organization.getName()); + assertNull(organization.getConfiguration().getToken()); + assertNull(organization.getConfiguration().getAuthenticationOrigins().get(0).getOptions()); + } + } diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/config/AuthenticationOrigin.java b/opencga-core/src/main/java/org/opencb/opencga/core/config/AuthenticationOrigin.java index 95c66a5cec7..2b8bfab8624 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/config/AuthenticationOrigin.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/config/AuthenticationOrigin.java @@ -16,9 +16,6 @@ package org.opencb.opencga.core.config; -import org.opencb.opencga.core.common.PasswordUtils; - -import java.util.Collections; import java.util.Map; /** @@ -29,9 +26,6 @@ public class AuthenticationOrigin { private String id; private AuthenticationType type; private String host; - private String algorithm; - private String secretKey; - private long expiration; // Expiration time in seconds private Map options; public enum AuthenticationType { @@ -56,22 +50,12 @@ public enum AuthenticationType { public static final String CONNECTION_TIMEOUT = "connectionTimeout"; public AuthenticationOrigin() { - this("internal", AuthenticationType.OPENCGA.name(), "localhost", "HS256", PasswordUtils.getStrongRandomPassword(32), 3600L, - Collections.emptyMap()); } public AuthenticationOrigin(String id, AuthenticationType type, String host, Map options) { - this(id, type.name(), host, "HS256", PasswordUtils.getStrongRandomPassword(32), 3600L, options); - } - - public AuthenticationOrigin(String id, String type, String host, String algorithm, String secretKey, long expiration, - Map options) { this.id = id; - this.type = AuthenticationType.valueOf(type);; + this.type = type; this.host = host; - this.algorithm = algorithm; - this.secretKey = secretKey; - this.expiration = expiration; this.options = options; } @@ -81,9 +65,6 @@ public String toString() { sb.append("id='").append(id).append('\''); sb.append(", type=").append(type); sb.append(", host='").append(host).append('\''); - sb.append(", algorithm='").append(algorithm).append('\''); - sb.append(", secretKey='").append(secretKey).append('\''); - sb.append(", expiration=").append(expiration); sb.append(", options=").append(options); sb.append('}'); return sb.toString(); @@ -116,30 +97,18 @@ public AuthenticationOrigin setHost(String host) { return this; } - public String getAlgorithm() { - return algorithm; - } - + @Deprecated public AuthenticationOrigin setAlgorithm(String algorithm) { - this.algorithm = algorithm; return this; } - public String getSecretKey() { - return secretKey; - } - + @Deprecated public AuthenticationOrigin setSecretKey(String secretKey) { - this.secretKey = secretKey; return this; } - public long getExpiration() { - return expiration; - } - + @Deprecated public AuthenticationOrigin setExpiration(long expiration) { - this.expiration = expiration; return this; } diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/organizations/OrganizationConfiguration.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/organizations/OrganizationConfiguration.java index 8a5687fe221..c8f3e849c89 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/models/organizations/OrganizationConfiguration.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/organizations/OrganizationConfiguration.java @@ -3,22 +3,22 @@ import org.opencb.opencga.core.config.AuthenticationOrigin; import org.opencb.opencga.core.config.Optimizations; -import java.util.LinkedList; import java.util.List; public class OrganizationConfiguration { private List authenticationOrigins; private Optimizations optimizations; + private TokenConfiguration token; public OrganizationConfiguration() { - this.authenticationOrigins = new LinkedList<>(); - this.optimizations = new Optimizations(); } - public OrganizationConfiguration(List authenticationOrigins, Optimizations optimizations) { + public OrganizationConfiguration(List authenticationOrigins, Optimizations optimizations, + TokenConfiguration token) { this.authenticationOrigins = authenticationOrigins; this.optimizations = optimizations; + this.token = token; } @Override @@ -26,6 +26,7 @@ public String toString() { final StringBuilder sb = new StringBuilder("OrganizationConfiguration{"); sb.append("authenticationOrigins=").append(authenticationOrigins); sb.append(", optimizations=").append(optimizations); + sb.append(", token=").append(token); sb.append('}'); return sb.toString(); } @@ -47,4 +48,13 @@ public OrganizationConfiguration setOptimizations(Optimizations optimizations) { this.optimizations = optimizations; return this; } + + public TokenConfiguration getToken() { + return token; + } + + public OrganizationConfiguration setToken(TokenConfiguration token) { + this.token = token; + return this; + } } diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/organizations/TokenConfiguration.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/organizations/TokenConfiguration.java new file mode 100644 index 00000000000..8ca89f2f285 --- /dev/null +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/organizations/TokenConfiguration.java @@ -0,0 +1,61 @@ +package org.opencb.opencga.core.models.organizations; + +import io.jsonwebtoken.SignatureAlgorithm; +import org.opencb.opencga.core.common.PasswordUtils; + +public class TokenConfiguration { + + private String algorithm; + private String secretKey; + private long expiration; + + public TokenConfiguration() { + } + + public TokenConfiguration(String algorithm, String secretKey, long expiration) { + this.algorithm = algorithm; + this.secretKey = secretKey; + this.expiration = expiration; + } + + public static TokenConfiguration init() { + return new TokenConfiguration(SignatureAlgorithm.HS256.getValue(), PasswordUtils.getStrongRandomPassword(32), 3600L); + } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("TokenConfiguration{"); + sb.append("algorithm='").append(algorithm).append('\''); + sb.append(", secretKey='").append(secretKey).append('\''); + sb.append(", expiration=").append(expiration); + sb.append('}'); + return sb.toString(); + } + + public String getAlgorithm() { + return algorithm; + } + + public TokenConfiguration setAlgorithm(String algorithm) { + this.algorithm = algorithm; + return this; + } + + public String getSecretKey() { + return secretKey; + } + + public TokenConfiguration setSecretKey(String secretKey) { + this.secretKey = secretKey; + return this; + } + + public long getExpiration() { + return expiration; + } + + public TokenConfiguration setExpiration(long expiration) { + this.expiration = expiration; + return this; + } +} diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/user/UserUpdateParams.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/user/UserUpdateParams.java index 7b069623e44..d9c44a665c8 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/models/user/UserUpdateParams.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/user/UserUpdateParams.java @@ -22,16 +22,14 @@ public class UserUpdateParams { private String name; private String email; - private String organization; private Map attributes; public UserUpdateParams() { } - public UserUpdateParams(String name, String email, String organization, Map attributes) { + public UserUpdateParams(String name, String email, Map attributes) { this.name = name; this.email = email; - this.organization = organization; this.attributes = attributes; } @@ -40,7 +38,6 @@ public String toString() { final StringBuilder sb = new StringBuilder("UserUpdateParams{"); sb.append("name='").append(name).append('\''); sb.append(", email='").append(email).append('\''); - sb.append(", organization='").append(organization).append('\''); sb.append(", attributes=").append(attributes); sb.append('}'); return sb.toString(); @@ -64,15 +61,6 @@ public UserUpdateParams setEmail(String email) { return this; } - public String getOrganization() { - return organization; - } - - public UserUpdateParams setOrganization(String organization) { - this.organization = organization; - return this; - } - public Map getAttributes() { return attributes; } From 95cb7436bae6f1cedf56e34683060805ebece941 Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 10 Apr 2024 12:17:59 +0200 Subject: [PATCH 05/59] app: fix migration script, #TASK-5923 --- ...s.java => AuthOriginSimplificationMigration.java} | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) rename opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/{AuthOriginSimplificationMigrations.java => AuthOriginSimplificationMigration.java} (83%) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigrations.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigration.java similarity index 83% rename from opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigrations.java rename to opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigration.java index de0cba37442..e913941bafd 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigrations.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_1_0/AuthOriginSimplificationMigration.java @@ -16,9 +16,9 @@ import java.util.List; -@Migration(id = "add_organizations", description = "Add new Organization layer #TASK-4389", version = "3.0.0", - language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20231212) -public class AuthOriginSimplificationMigrations extends MigrationTool { +@Migration(id = "hide_secret_key", description = "Hide secret key #TASK-5923", version = "3.1.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20240410) +public class AuthOriginSimplificationMigration extends MigrationTool { @Override protected void run() throws Exception { @@ -53,6 +53,12 @@ protected void run() throws Exception { Updates.set("configuration", configuration))); } }); + + // Change authOrigin id from all "internal" users + getMongoCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION) + .updateMany( + new Document("account.authentication.id", "internal"), + Updates.set("account.authentication.id", "OPENCGA")); } } From dd6baf9fc041b32e16118a7956a4426033ed381f Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 15 Apr 2024 12:11:02 +0200 Subject: [PATCH 06/59] catalog: propagate exception, #TASK-5922 --- .../OrganizationCatalogMongoDBIterator.java | 10 ++++-- .../exceptions/CatalogRuntimeException.java | 34 +++++++++++++++++++ 2 files changed, 41 insertions(+), 3 deletions(-) create mode 100644 opencga-catalog/src/main/java/org/opencb/opencga/catalog/exceptions/CatalogRuntimeException.java diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java index 505cf26392a..8d277a9295d 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java @@ -15,6 +15,7 @@ import org.opencb.opencga.catalog.db.mongodb.ProjectMongoDBAdaptor; import org.opencb.opencga.catalog.exceptions.CatalogAuthorizationException; import org.opencb.opencga.catalog.exceptions.CatalogDBException; +import org.opencb.opencga.catalog.exceptions.CatalogRuntimeException; import org.opencb.opencga.core.models.notes.Note; import org.opencb.opencga.core.response.OpenCGAResult; import org.slf4j.Logger; @@ -83,6 +84,7 @@ public E next() { private void fetchNextBatch() { if (mongoCursor.hasNext()) { Document organizationDocument = mongoCursor.next(); + String orgId = organizationDocument.getString(OrganizationDBAdaptor.QueryParams.ID.key()); if (!options.getBoolean(NATIVE_QUERY)) { List migrationFields = Arrays.asList(OrganizationDBAdaptor.QueryParams.INTERNAL.key(), @@ -111,7 +113,7 @@ private void fetchNextBatch() { OpenCGAResult result = noteMongoDBAdaptor.nativeGet(clientSession, query, noteOptions); organizationDocument.put(OrganizationDBAdaptor.QueryParams.NOTES.key(), result.getResults()); } catch (CatalogDBException e) { - logger.warn("Could not obtain the organization notes", e); + throw CatalogRuntimeException.internalException(e, "Could not fetch notes for organization '" + orgId + "'."); } } @@ -124,10 +126,12 @@ private void fetchNextBatch() { } else { openCGAResult = projectMongoDBAdaptor.nativeGet(clientSession, new Query(), projectOptions); } - } catch (CatalogDBException | CatalogAuthorizationException e) { + organizationDocument.put(OrganizationDBAdaptor.QueryParams.PROJECTS.key(), openCGAResult.getResults()); + } catch (CatalogAuthorizationException e) { logger.warn("Could not fetch projects for organization.", e); + } catch (CatalogDBException | RuntimeException e) { + throw CatalogRuntimeException.internalException(e, "Could not fetch projects for organization '" + orgId + "'."); } - organizationDocument.put(OrganizationDBAdaptor.QueryParams.PROJECTS.key(), openCGAResult.getResults()); } } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/exceptions/CatalogRuntimeException.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/exceptions/CatalogRuntimeException.java new file mode 100644 index 00000000000..81dc17b16af --- /dev/null +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/exceptions/CatalogRuntimeException.java @@ -0,0 +1,34 @@ +package org.opencb.opencga.catalog.exceptions; + +import org.apache.commons.lang3.StringUtils; + +public class CatalogRuntimeException extends IllegalArgumentException { + + public CatalogRuntimeException(String message) { + super(message); + } + + public CatalogRuntimeException(String message, Throwable cause) { + super(message, cause); + } + + public static CatalogRuntimeException internalException(Exception e, String message) { + if (e instanceof CatalogRuntimeException) { + return ((CatalogRuntimeException) e); + } else { + if (StringUtils.isEmpty(message)) { + message = e.getMessage(); + if (StringUtils.isEmpty(message)) { + message = e.toString(); + } + } + return new CatalogRuntimeException("Internal exception: " + message, e); + } + } + + public static CatalogRuntimeException internalException(Exception e) { + return internalException(e, ""); + } + + +} From f5cb4d6185818e6c2f7c8e5edcc7d08cee8e09c5 Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 15 Apr 2024 12:13:27 +0200 Subject: [PATCH 07/59] catalog: add orgId to logger, #TASK-5922 --- .../mongodb/iterators/OrganizationCatalogMongoDBIterator.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java index 8d277a9295d..4dee071b079 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java @@ -128,7 +128,7 @@ private void fetchNextBatch() { } organizationDocument.put(OrganizationDBAdaptor.QueryParams.PROJECTS.key(), openCGAResult.getResults()); } catch (CatalogAuthorizationException e) { - logger.warn("Could not fetch projects for organization.", e); + logger.warn("Could not fetch projects for organization '{}'.", orgId, e); } catch (CatalogDBException | RuntimeException e) { throw CatalogRuntimeException.internalException(e, "Could not fetch projects for organization '" + orgId + "'."); } From 50c07cc95cd4f5b7fc6c3009f767f268281a6d6e Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 15 Apr 2024 15:23:52 +0200 Subject: [PATCH 08/59] catalog: remove user=organizationId exclusion, #TASK-6032 --- .../db/mongodb/UserMongoDBAdaptor.java | 15 ++--- .../opencga/catalog/managers/UserManager.java | 4 +- .../catalog/managers/CatalogManagerTest.java | 60 +++++++++++++++++++ 3 files changed, 67 insertions(+), 12 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java index a8db293e258..d2c0f14cd5f 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/UserMongoDBAdaptor.java @@ -353,21 +353,16 @@ private void extractSharedProjects(DataResult userDataResult, QueryOptions studyMap.put(study.getFqn(), study); studyProjectMap.put(study.getFqn(), project.getFqn()); - String owner = study.getFqn().split("@")[0]; - if (study.getGroups() != null) { for (Group group : study.getGroups()) { if (StudyManager.MEMBERS.equals(group.getId())) { // Add all the users that should be able to see the study to the map for (String userId : group.getUserIds()) { - // Exclude owner of the project - if (!owner.equals(userId)) { - if (users.contains(userId)) { - if (!userStudyMap.containsKey(userId)) { - userStudyMap.put(userId, new ArrayList<>()); - } - userStudyMap.get(userId).add(study.getFqn()); + if (users.contains(userId)) { + if (!userStudyMap.containsKey(userId)) { + userStudyMap.put(userId, new ArrayList<>()); } + userStudyMap.get(userId).add(study.getFqn()); } } break; @@ -378,7 +373,7 @@ private void extractSharedProjects(DataResult userDataResult, QueryOptions } } - // Add sharedProject information + // Add project information for (User user : userDataResult.getResults()) { if (userStudyMap.containsKey(user.getId())) { Map> projectStudyMap = new HashMap<>(); diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java index 96098fedcff..f6a50e63890 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java @@ -519,7 +519,7 @@ public OpenCGAResult get(String organizationId, String userId, QueryOption * @return The requested users * @throws CatalogException CatalogException */ - public OpenCGAResult get(String organizationId, List userIdList, QueryOptions options, String token) + public OpenCGAResult get(@Nullable String organizationId, List userIdList, QueryOptions options, String token) throws CatalogException { ParamUtils.checkNotEmptyArray(userIdList, "userId"); ParamUtils.checkParameter(token, "token"); @@ -532,7 +532,7 @@ public OpenCGAResult get(String organizationId, List userIdList, Q .append("token", token); JwtPayload jwtPayload = validateToken(token); - if (userIdList.size() == 1 && jwtPayload.getUserId().equals(userIdList.get(0)) && StringUtils.isEmpty(organizationId)) { + if (StringUtils.isEmpty(organizationId)) { organizationId = jwtPayload.getOrganization(); } String userId = jwtPayload.getUserId(organizationId); diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java index 07edb4610b7..4854b1bb8da 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java @@ -17,6 +17,7 @@ package org.opencb.opencga.catalog.managers; import com.mongodb.BasicDBObject; +import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.RandomStringUtils; import org.apache.commons.lang3.StringUtils; import org.junit.Ignore; @@ -256,6 +257,65 @@ public void testGetUserInfo() throws CatalogException { studyAdminToken1); } + @Test + public void testGetProjectsFromUserInfo() throws CatalogException { + String userId = organizationId; + catalogManager.getUserManager().create(userId, "test", "mail@mail.com", TestParamConstants.PASSWORD, organizationId, null, + opencgaToken); + catalogManager.getStudyManager().updateGroup(studyFqn, ParamConstants.MEMBERS_GROUP, ParamUtils.BasicUpdateAction.ADD, + new GroupUpdateParams(Collections.singletonList("test")), ownerToken); + String token = catalogManager.getUserManager().login(organizationId, userId, TestParamConstants.PASSWORD).getToken(); + + DataResult user = catalogManager.getUserManager().get(organizationId, userId, new QueryOptions(), token); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(organizationId, normalUserId3, new QueryOptions(), normalToken3); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(organizationId, orgOwnerUserId, new QueryOptions(), ownerToken); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(organizationId, orgAdminUserId1, new QueryOptions(), orgAdminToken1); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(organizationId, studyAdminUserId1, new QueryOptions(), studyAdminToken1); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(organizationId, normalUserId1, new QueryOptions(), orgAdminToken1); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + + user = catalogManager.getUserManager().get(null, normalUserId1, new QueryOptions(), normalToken1); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(null, normalUserId3, new QueryOptions(), normalToken3); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(null, orgOwnerUserId, new QueryOptions(), ownerToken); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(null, orgAdminUserId1, new QueryOptions(), orgAdminToken1); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(null, studyAdminUserId1, new QueryOptions(), studyAdminToken1); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + + user = catalogManager.getUserManager().get(null, normalUserId1, new QueryOptions(), orgAdminToken1); + assertTrue(CollectionUtils.isNotEmpty(user.first().getProjects())); + System.out.println(user.first().getProjects().size()); + } + @Test public void testModifyUser() throws CatalogException, InterruptedException, IOException { ObjectMap params = new ObjectMap(); From 220cb885e2b0b7b4b86d0190c4e4dc7907cf362c Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 17 Apr 2024 12:48:31 +0200 Subject: [PATCH 09/59] catalog: Fix NPE when creating a new organization, #TASK-5923 --- .../catalog/managers/OrganizationManager.java | 4 ++-- .../catalog/managers/OrganizationManagerTest.java | 13 +++++++++---- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java index 247bd5d26d7..f89d0595c30 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/OrganizationManager.java @@ -182,10 +182,10 @@ public OpenCGAResult create(OrganizationCreateParams organizationC // Fetch created organization queryResult.setResults(result.getResults()); } - privatizeResults(queryResult); - // Add required authentication manager for the new organization authenticationFactory.configureOrganizationAuthenticationManager(organization); + + privatizeResults(queryResult); } catch (CatalogException e) { if (!ParamConstants.ADMIN_ORGANIZATION.equals(organizationCreateParams.getId())) { auditManager.auditCreate(ParamConstants.ADMIN_ORGANIZATION, userId, Enums.Resource.ORGANIZATION, diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java index abd6aa90ccb..b408fec74c1 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/OrganizationManagerTest.java @@ -14,10 +14,7 @@ import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.core.api.ParamConstants; import org.opencb.opencga.core.config.AuthenticationOrigin; -import org.opencb.opencga.core.models.organizations.Organization; -import org.opencb.opencga.core.models.organizations.OrganizationConfiguration; -import org.opencb.opencga.core.models.organizations.OrganizationUpdateParams; -import org.opencb.opencga.core.models.organizations.TokenConfiguration; +import org.opencb.opencga.core.models.organizations.*; import org.opencb.opencga.core.models.project.Project; import org.opencb.opencga.core.models.study.Group; import org.opencb.opencga.core.models.study.Study; @@ -86,6 +83,14 @@ public void updateAuthOriginTest() throws CatalogException { assertEquals(authOrigin.getType(), organization.getConfiguration().getAuthenticationOrigins().get(0).getType()); } + @Test + public void createNewOrganizationTest() throws CatalogException { + OpenCGAResult result = catalogManager.getOrganizationManager().create(new OrganizationCreateParams().setId("org2"), INCLUDE_RESULT, opencgaToken); + assertEquals(1, result.getNumInserted()); + assertEquals(1, result.getNumMatches()); + assertEquals("org2", result.first().getId()); + } + @Test public void organizationInfoIncludeProjectsTest() throws CatalogException { Organization organization = catalogManager.getOrganizationManager().get(organizationId, QueryOptions.empty(), ownerToken).first(); From f55ec332c670bbe45757878fd2b53545e6c4fd2d Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 29 Apr 2024 16:25:09 +0200 Subject: [PATCH 10/59] catalog: implement user search for org admins, #TASK-5980 --- .../catalog/managers/AdminManager.java | 34 ++++++--------- .../opencga/catalog/managers/UserManager.java | 41 +++++++++++++++++++ .../catalog/managers/CatalogManagerTest.java | 29 +++++++++++++ .../opencga/core/api/ParamConstants.java | 7 ++-- .../opencga/server/rest/UserWSServer.java | 26 ++++++++++++ .../server/rest/admin/AdminWSServer.java | 1 - 6 files changed, 111 insertions(+), 27 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java index e02defb1fc2..09bc57aabf1 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java @@ -47,9 +47,6 @@ public class AdminManager extends AbstractManager { public OpenCGAResult userSearch(String organizationId, Query query, QueryOptions options, String token) throws CatalogException { - query = ParamUtils.defaultObject(query, Query::new); - options = ParamUtils.defaultObject(options, QueryOptions::new); - ObjectMap auditParams = new ObjectMap() .append("organizationId", organizationId) .append("query", query) @@ -58,30 +55,23 @@ public OpenCGAResult userSearch(String organizationId, Query query, QueryO JwtPayload jwtPayload = catalogManager.getUserManager().validateToken(token); try { authorizationManager.checkIsOpencgaAdministrator(jwtPayload); - - // Fix query object - if (query.containsKey(ParamConstants.USER)) { - query.put(UserDBAdaptor.QueryParams.ID.key(), query.get(ParamConstants.USER)); - query.remove(ParamConstants.USER); - } - if (query.containsKey(ParamConstants.USER_AUTHENTICATION_ORIGIN)) { - query.put(UserDBAdaptor.QueryParams.ACCOUNT_AUTHENTICATION_ID.key(), query.get(ParamConstants.USER_AUTHENTICATION_ORIGIN)); - query.remove(ParamConstants.USER_AUTHENTICATION_ORIGIN); - } - if (query.containsKey(ParamConstants.USER_CREATION_DATE)) { - query.put(UserDBAdaptor.QueryParams.ACCOUNT_CREATION_DATE.key(), query.get(ParamConstants.USER_CREATION_DATE)); - query.remove(ParamConstants.USER_CREATION_DATE); - } - - OpenCGAResult userDataResult = getUserDBAdaptor(organizationId).get(query, options); - auditManager.auditSearch(organizationId, jwtPayload.getUserId(organizationId), Enums.Resource.USER, "", "", auditParams, - new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS)); - return userDataResult; } catch (CatalogException e) { auditManager.auditSearch(organizationId, jwtPayload.getUserId(organizationId), Enums.Resource.USER, "", "", auditParams, new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError())); throw e; } + + // Fix query object + if (query.containsKey(ParamConstants.USER)) { + query.put(UserDBAdaptor.QueryParams.ID.key(), query.get(ParamConstants.USER)); + query.remove(ParamConstants.USER); + } + if (query.containsKey(ParamConstants.USER_CREATION_DATE)) { + query.put(UserDBAdaptor.QueryParams.ACCOUNT_CREATION_DATE.key(), query.get(ParamConstants.USER_CREATION_DATE)); + query.remove(ParamConstants.USER_CREATION_DATE); + } + + return catalogManager.getUserManager().search(organizationId, query, options, token); } public OpenCGAResult updateGroups(String organizationId, String userId, List studyIds, List groupIds, diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java index 3708e64c9ed..15f4fb24d02 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java @@ -203,6 +203,47 @@ public OpenCGAResult create(String id, String name, String email, String p return create(user, password, token); } + /** + * Search users from Organization. Token must belong to at least an Organization administrator. + * + * @param organizationId Organization id. + * @param query Query object. + * @param options QueryOptions object. + * @param token JWT token. + * @return OpenCGAResult with the list of users. + * @throws CatalogException if the token does not belong to an Organization administrator or there are any parameters wrong. + */ + public OpenCGAResult search(@Nullable String organizationId, Query query, QueryOptions options, String token) + throws CatalogException { + JwtPayload tokenPayload = catalogManager.getUserManager().validateToken(token); + ObjectMap auditParams = new ObjectMap() + .append("organizationId", organizationId) + .append("query", query) + .append("options", options) + .append("token", token); + + options = ParamUtils.defaultObject(options, QueryOptions::new); + String myOrganizationId = StringUtils.isNotEmpty(organizationId) ? organizationId : tokenPayload.getOrganization(); + try { + authorizationManager.checkIsAtLeastOrganizationOwnerOrAdmin(myOrganizationId, tokenPayload.getUserId(myOrganizationId)); + + // Fix query params + if (query.containsKey(ParamConstants.USER_AUTHENTICATION_ORIGIN)) { + query.put(UserDBAdaptor.QueryParams.ACCOUNT_AUTHENTICATION_ID.key(), query.get(ParamConstants.USER_AUTHENTICATION_ORIGIN)); + query.remove(ParamConstants.USER_AUTHENTICATION_ORIGIN); + } + + OpenCGAResult result = getUserDBAdaptor(myOrganizationId).get(query, options); + auditManager.auditSearch(myOrganizationId, tokenPayload.getUserId(myOrganizationId), Enums.Resource.USER, "", "", auditParams, + new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS)); + return result; + } catch (CatalogException e) { + auditManager.auditSearch(myOrganizationId, tokenPayload.getUserId(myOrganizationId), Enums.Resource.USER, "", "", auditParams, + new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError())); + throw e; + } + } + public JwtPayload validateToken(String token) throws CatalogException { JwtPayload jwtPayload = new JwtPayload(token); ParamUtils.checkParameter(jwtPayload.getUserId(), "jwt user"); diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java index e605ba0796b..21d0322207b 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/CatalogManagerTest.java @@ -104,6 +104,35 @@ public void testAdminUserExists() throws Exception { assertEquals(ParamConstants.ADMIN_ORGANIZATION, payload.getOrganization()); } + @Test + public void searchUsersTest() throws CatalogException { + OpenCGAResult search = catalogManager.getUserManager().search(organizationId, new Query(), QueryOptions.empty(), opencgaToken); + assertEquals(8, search.getNumResults()); + for (User user : search.getResults()) { + if (noAccessUserId1.equals(user.getId())) { + assertEquals(0, user.getProjects().size()); + } else if (user.getId().startsWith("normalUser")) { + assertEquals(1, user.getProjects().size()); + } else { + assertEquals(2, user.getProjects().size()); + } + } + + search = catalogManager.getUserManager().search(null, new Query(), QueryOptions.empty(), ownerToken); + assertEquals(8, search.getNumResults()); + + search = catalogManager.getUserManager().search(null, new Query(), QueryOptions.empty(), orgAdminToken2); + assertEquals(8, search.getNumResults()); + + search = catalogManager.getUserManager().search(null, new Query(), QueryOptions.empty(), orgAdminToken1); + assertEquals(8, search.getNumResults()); + + assertThrows(CatalogAuthorizationException.class, () -> catalogManager.getUserManager().search(null, new Query(), + QueryOptions.empty(), studyAdminToken1)); + assertThrows(CatalogAuthorizationException.class, () -> catalogManager.getUserManager().search(null, new Query(), + QueryOptions.empty(), normalToken1)); + } + @Test public void testGetToken() throws Exception { String token = catalogManager.getUserManager().loginAsAdmin(TestParamConstants.ADMIN_PASSWORD).getToken(); diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index 41c17e5a787..6bf964e760f 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -77,7 +77,7 @@ public class ParamConstants { public static final String DISORDERS_DESCRIPTION = "Comma separated list of disorder ids or names" + REGEX_SUPPORT; public static final String BODY_PARAM = "body"; public static final String OVERWRITE = "overwrite"; - + private static final String UP_TO_100 = " up to a maximum of 100"; public static final String CELLBASE_URL = "https://ws.zettagenomics.com/cellbase"; public static final String CELLBASE_VERSION = "v5.2"; @@ -155,10 +155,10 @@ public class ParamConstants { public static final String ORGANIZATION_DESCRIPTION = "Organization id"; public static final String ORGANIZATION = "organization"; // --------------------------------------------- + public static final String USER_ID_DESCRIPTION = "Comma separated list user IDs" + UP_TO_100 + REGEX_SUPPORT; + public static final String USER_ID_PARAM = "id"; public static final String USER_DESCRIPTION = "User ID"; public static final String USERS_DESCRIPTION = "Comma separated list of user IDs"; - public static final String USER_ACCOUNT_TYPE = "account"; - public static final String USER_ACCOUNT_TYPE_DESCRIPTION = "Account type [GUEST, FULL, ADMINISTRATOR]"; public static final String USER_AUTHENTICATION_ORIGIN = "authenticationId"; public static final String USER_AUTHENTICATION_ORIGIN_DESCRIPTION = "Authentication origin ID"; public static final String USER_CREATION_DATE = "creationDate"; @@ -1487,7 +1487,6 @@ public class ParamConstants { public static final String ADMIN_CATALOG_INSTALL_EMAIL = "The body web service email parameter"; public static final String ADMIN_CATALOG_INSTALL_ORGANIZATION = "The body web service organization parameter"; public static final String ADMIN_CATALOG_JWT_SECRETKEY = "The body web service secretKey parameter"; - private static final String UP_TO_100 = " up to a maximum of 100"; public static final String FILES_DESCRIPTION = "Comma separated list of file IDs or names" + UP_TO_100; public static final String FILES_ID_DESCRIPTION = "Comma separated list of file IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String FILES_UUID_DESCRIPTION = "Comma separated list file UUIDs" + UP_TO_100; diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/UserWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/UserWSServer.java index b354adaf8d8..d76db93c398 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/UserWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/UserWSServer.java @@ -69,6 +69,32 @@ public Response create( } } + @GET + @Path("/search") + @ApiOperation(value = "User search method", response = User.class) + @ApiImplicitParams({ + @ApiImplicitParam(name = QueryOptions.INCLUDE, value = ParamConstants.INCLUDE_DESCRIPTION, example = "name,attributes", + dataType = "string", paramType = "query"), + @ApiImplicitParam(name = QueryOptions.EXCLUDE, value = ParamConstants.EXCLUDE_DESCRIPTION, example = "id,status", dataType = + "string", paramType = "query"), + @ApiImplicitParam(name = QueryOptions.LIMIT, value = ParamConstants.LIMIT_DESCRIPTION, dataType = "integer", paramType = + "query"), + @ApiImplicitParam(name = QueryOptions.SKIP, value = ParamConstants.SKIP_DESCRIPTION, dataType = "integer", paramType = "query"), + @ApiImplicitParam(name = QueryOptions.COUNT, value = ParamConstants.COUNT_DESCRIPTION, defaultValue = "false", dataType = + "boolean", paramType = "query") + }) + public Response search( + @ApiParam(value = ParamConstants.ORGANIZATION_DESCRIPTION) @QueryParam(ParamConstants.ORGANIZATION) String organizationId, + @ApiParam(value = ParamConstants.USER_ID_DESCRIPTION) @QueryParam(ParamConstants.USER_ID_PARAM) String userId, + @ApiParam(value = ParamConstants.USER_AUTHENTICATION_ORIGIN_DESCRIPTION) @QueryParam(ParamConstants.USER_AUTHENTICATION_ORIGIN) String authentication) { + try { + query.remove(ParamConstants.ORGANIZATION); + return createOkResponse(catalogManager.getUserManager().search(organizationId, query, queryOptions, token)); + } catch (Exception e) { + return createErrorResponse(e); + } + } + @GET @Path("/{users}/info") @ApiOperation(value = "Return the user information including its projects and studies", response = User.class) diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/admin/AdminWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/admin/AdminWSServer.java index b1a7c1b80ff..c0345d421f5 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/admin/AdminWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/admin/AdminWSServer.java @@ -71,7 +71,6 @@ public AdminWSServer(@Context UriInfo uriInfo, @Context HttpServletRequest httpS public Response userSearch( @ApiParam(value = ParamConstants.ORGANIZATION_DESCRIPTION) @QueryParam(ParamConstants.ORGANIZATION) String organizationId, @ApiParam(value = ParamConstants.USER_DESCRIPTION) @QueryParam(ParamConstants.USER) String user, - @ApiParam(value = ParamConstants.USER_ACCOUNT_TYPE_DESCRIPTION) @QueryParam(ParamConstants.USER_ACCOUNT_TYPE) String account, @ApiParam(value = ParamConstants.USER_AUTHENTICATION_ORIGIN_DESCRIPTION) @QueryParam(ParamConstants.USER_AUTHENTICATION_ORIGIN) String authentication) { try { return createOkResponse(catalogManager.getAdminManager().userSearch(organizationId, query, queryOptions, token)); From 9dcca291e9e3af4ef93f1841ee88f445d448f91e Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 29 Apr 2024 16:27:25 +0200 Subject: [PATCH 11/59] client: automatically generate cli, #TASK-5980 --- .../app/cli/main/OpenCgaCompleter.java | 4 +- .../app/cli/main/OpencgaCliOptionsParser.java | 3 +- .../main/executors/AdminCommandExecutor.java | 1 - .../OrganizationsCommandExecutor.java | 1 + .../main/executors/UsersCommandExecutor.java | 22 ++++++++++- .../cli/main/options/AdminCommandOptions.java | 3 -- .../cli/main/options/UsersCommandOptions.java | 37 +++++++++++++++++-- opencga-client/src/main/R/R/Admin-methods.R | 5 +-- .../src/main/R/R/Alignment-methods.R | 2 +- opencga-client/src/main/R/R/AllGenerics.R | 20 +++++----- .../src/main/R/R/Clinical-methods.R | 4 +- opencga-client/src/main/R/R/Cohort-methods.R | 4 +- opencga-client/src/main/R/R/Family-methods.R | 4 +- opencga-client/src/main/R/R/File-methods.R | 4 +- opencga-client/src/main/R/R/GA4GH-methods.R | 2 +- .../src/main/R/R/Individual-methods.R | 4 +- opencga-client/src/main/R/R/Job-methods.R | 4 +- opencga-client/src/main/R/R/Meta-methods.R | 2 +- .../src/main/R/R/Operation-methods.R | 2 +- .../src/main/R/R/Organization-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 4 +- opencga-client/src/main/R/R/Project-methods.R | 2 +- opencga-client/src/main/R/R/Sample-methods.R | 4 +- opencga-client/src/main/R/R/Study-methods.R | 4 +- opencga-client/src/main/R/R/User-methods.R | 18 ++++++++- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../client/rest/clients/AdminClient.java | 3 +- .../client/rest/clients/AlignmentClient.java | 2 +- .../rest/clients/ClinicalAnalysisClient.java | 2 +- .../client/rest/clients/CohortClient.java | 2 +- .../rest/clients/DiseasePanelClient.java | 2 +- .../client/rest/clients/FamilyClient.java | 2 +- .../client/rest/clients/FileClient.java | 2 +- .../client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 2 +- .../client/rest/clients/JobClient.java | 2 +- .../client/rest/clients/MetaClient.java | 2 +- .../rest/clients/OrganizationClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 2 +- .../client/rest/clients/StudyClient.java | 2 +- .../client/rest/clients/UserClient.java | 22 ++++++++++- .../client/rest/clients/VariantClient.java | 2 +- .../rest/clients/VariantOperationClient.java | 2 +- opencga-client/src/main/javascript/Admin.js | 3 +- .../src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- .../src/main/javascript/Organization.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- opencga-client/src/main/javascript/Study.js | 2 +- opencga-client/src/main/javascript/User.js | 20 +++++++++- opencga-client/src/main/javascript/Variant.js | 2 +- .../src/main/javascript/VariantOperation.js | 2 +- .../pyopencga/rest_clients/admin_client.py | 3 +- .../rest_clients/alignment_client.py | 2 +- .../rest_clients/clinical_analysis_client.py | 2 +- .../pyopencga/rest_clients/cohort_client.py | 2 +- .../rest_clients/disease_panel_client.py | 2 +- .../pyopencga/rest_clients/family_client.py | 2 +- .../pyopencga/rest_clients/file_client.py | 2 +- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../rest_clients/individual_client.py | 2 +- .../pyopencga/rest_clients/job_client.py | 2 +- .../pyopencga/rest_clients/meta_client.py | 2 +- .../rest_clients/organization_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 2 +- .../pyopencga/rest_clients/study_client.py | 2 +- .../pyopencga/rest_clients/user_client.py | 25 ++++++++++++- .../pyopencga/rest_clients/variant_client.py | 2 +- .../rest_clients/variant_operation_client.py | 2 +- 80 files changed, 228 insertions(+), 108 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 623e23db9fb..1ff476d5003 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2024-04-10 OpenCB +* Copyright 2015-2024-04-29 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -85,7 +85,7 @@ public abstract class OpenCgaCompleter implements Completer { .map(Candidate::new) .collect(toList()); - private List usersList = asList( "anonymous","create","login","password","info","configs","configs-update","filters","password-reset","update") + private List usersList = asList( "anonymous","create","login","password","search","info","configs","configs-update","filters","password-reset","update") .stream() .map(Candidate::new) .collect(toList()); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index 5b96a113110..f2bcf34a63c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2024-04-10 OpenCB +* Copyright 2015-2024-04-29 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -229,6 +229,7 @@ public OpencgaCliOptionsParser() { usersSubCommands.addCommand("create", usersCommandOptions.createCommandOptions); usersSubCommands.addCommand("login", usersCommandOptions.loginCommandOptions); usersSubCommands.addCommand("password", usersCommandOptions.passwordCommandOptions); + usersSubCommands.addCommand("search", usersCommandOptions.searchCommandOptions); usersSubCommands.addCommand("info", usersCommandOptions.infoCommandOptions); usersSubCommands.addCommand("configs", usersCommandOptions.configsCommandOptions); usersSubCommands.addCommand("configs-update", usersCommandOptions.updateConfigsCommandOptions); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java index 4c8467fc108..e78430b3f96 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java @@ -262,7 +262,6 @@ private RestResponse searchUsers() throws Exception { queryParams.putIfNotNull("count", commandOptions.count); queryParams.putIfNotEmpty("organization", commandOptions.organization); queryParams.putIfNotEmpty("user", commandOptions.user); - queryParams.putIfNotEmpty("account", commandOptions.account); queryParams.putIfNotEmpty("authenticationId", commandOptions.authenticationId); return openCGAClient.getAdminClient().searchUsers(queryParams); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java index e18895e85b2..991f44fd9d8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OrganizationsCommandExecutor.java @@ -22,6 +22,7 @@ import org.opencb.opencga.core.models.organizations.OrganizationConfiguration; import org.opencb.opencga.core.models.organizations.OrganizationCreateParams; import org.opencb.opencga.core.models.organizations.OrganizationUpdateParams; +import org.opencb.opencga.core.models.organizations.TokenConfiguration; import org.opencb.opencga.core.response.QueryType; import org.opencb.opencga.core.response.RestResponse; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java index f8bd7213886..6eeeae17408 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java @@ -77,6 +77,9 @@ public void execute() throws Exception { case "password": queryResponse = password(); break; + case "search": + queryResponse = search(); + break; case "info": queryResponse = info(); break; @@ -188,6 +191,24 @@ private RestResponse password() throws Exception { return openCGAClient.getUserClient().password(passwordChangeParams); } + private RestResponse search() throws Exception { + logger.debug("Executing search in Users command line"); + + UsersCommandOptions.SearchCommandOptions commandOptions = usersCommandOptions.searchCommandOptions; + + ObjectMap queryParams = new ObjectMap(); + queryParams.putIfNotEmpty("include", commandOptions.include); + queryParams.putIfNotEmpty("exclude", commandOptions.exclude); + queryParams.putIfNotNull("limit", commandOptions.limit); + queryParams.putIfNotNull("skip", commandOptions.skip); + queryParams.putIfNotNull("count", commandOptions.count); + queryParams.putIfNotEmpty("organization", commandOptions.organization); + queryParams.putIfNotEmpty("id", commandOptions.id); + queryParams.putIfNotEmpty("authenticationId", commandOptions.authenticationId); + + return openCGAClient.getUserClient().search(queryParams); + } + private RestResponse info() throws Exception { logger.debug("Executing info in Users command line"); @@ -284,7 +305,6 @@ private RestResponse update() throws Exception { ObjectMap beanParams = new ObjectMap(); putNestedIfNotEmpty(beanParams, "name",commandOptions.name, true); putNestedIfNotEmpty(beanParams, "email",commandOptions.email, true); - putNestedIfNotEmpty(beanParams, "organization",commandOptions.organization, true); putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true); userUpdateParams = JacksonUtils.getDefaultObjectMapper().copy() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AdminCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AdminCommandOptions.java index 50b075e7688..60684639ca0 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AdminCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AdminCommandOptions.java @@ -243,9 +243,6 @@ public class SearchUsersCommandOptions { @Parameter(names = {"--user", "-u"}, description = "User ID", required = false, arity = 1) public String user; - @Parameter(names = {"--account"}, description = "Account type [GUEST, FULL, ADMINISTRATOR]", required = false, arity = 1) - public String account; - @Parameter(names = {"--authentication-id"}, description = "Authentication origin ID", required = false, arity = 1) public String authenticationId; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/UsersCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/UsersCommandOptions.java index e17ed6588e4..885a2ffaa70 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/UsersCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/UsersCommandOptions.java @@ -37,6 +37,7 @@ public class UsersCommandOptions extends CustomUsersCommandOptions { public CreateCommandOptions createCommandOptions; public LoginCommandOptions loginCommandOptions; public PasswordCommandOptions passwordCommandOptions; + public SearchCommandOptions searchCommandOptions; public InfoCommandOptions infoCommandOptions; public ConfigsCommandOptions configsCommandOptions; public UpdateConfigsCommandOptions updateConfigsCommandOptions; @@ -52,6 +53,7 @@ public UsersCommandOptions(CommonCommandOptions commonCommandOptions, JCommander this.createCommandOptions = new CreateCommandOptions(); this.loginCommandOptions = new LoginCommandOptions(); this.passwordCommandOptions = new PasswordCommandOptions(); + this.searchCommandOptions = new SearchCommandOptions(); this.infoCommandOptions = new InfoCommandOptions(); this.configsCommandOptions = new ConfigsCommandOptions(); this.updateConfigsCommandOptions = new UpdateConfigsCommandOptions(); @@ -136,6 +138,38 @@ public class PasswordCommandOptions { } + @Parameters(commandNames = {"search"}, commandDescription ="User search method") + public class SearchCommandOptions { + + @ParametersDelegate + public CommonCommandOptions commonOptions = commonCommandOptions; + + @Parameter(names = {"--include", "-I"}, description = "Fields included in the response, whole JSON path must be provided", required = false, arity = 1) + public String include; + + @Parameter(names = {"--exclude", "-E"}, description = "Fields excluded in the response, whole JSON path must be provided", required = false, arity = 1) + public String exclude; + + @Parameter(names = {"--limit"}, description = "Number of results to be returned", required = false, arity = 1) + public Integer limit; + + @Parameter(names = {"--skip"}, description = "Number of results to skip", required = false, arity = 1) + public Integer skip; + + @Parameter(names = {"--count"}, description = "Get the total number of results matching the query. Deactivated by default.", required = false, help = true, arity = 0) + public boolean count = false; + + @Parameter(names = {"--organization"}, description = "Organization id", required = false, arity = 1) + public String organization; + + @Parameter(names = {"--id"}, description = "Comma separated list user IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) + public String id; + + @Parameter(names = {"--authentication-id"}, description = "Authentication origin ID", required = false, arity = 1) + public String authenticationId; + + } + @Parameters(commandNames = {"info"}, commandDescription ="Return the user information including its projects and studies") public class InfoCommandOptions { @@ -251,9 +285,6 @@ public class UpdateCommandOptions { @Parameter(names = {"--email"}, description = "The body web service email parameter", required = false, arity = 1) public String email; - @Parameter(names = {"--organization"}, description = "The body web service organization parameter", required = false, arity = 1) - public String organization; - @DynamicParameter(names = {"--attributes"}, description = "The body web service attributes parameter. Use: --attributes key=value", required = false) public java.util.Map attributes = new HashMap<>(); //Dynamic parameters must be initialized; diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 8f5d4877e7f..21ccff3b4da 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -26,7 +26,7 @@ #' | createUsers | /{apiVersion}/admin/users/create | body[*] | #' | importUsers | /{apiVersion}/admin/users/import | organization, body[*] | #' | permissionsUsers | /{apiVersion}/admin/users/permissions | study, entryIds, permissions, category | -#' | searchUsers | /{apiVersion}/admin/users/search | include, exclude, limit, skip, count, organization, user, account, authenticationId | +#' | searchUsers | /{apiVersion}/admin/users/search | include, exclude, limit, skip, count, organization, user, authenticationId | #' | syncUsers | /{apiVersion}/admin/users/sync | organization, body[*] | #' | usersUpdateGroups | /{apiVersion}/admin/users/{user}/groups/update | organization, user[*], action, body[*] | #' @@ -97,7 +97,6 @@ setMethod("adminClient", "OpencgaR", function(OpencgaR, user, endpointName, para #' @param count Get the total number of results matching the query. Deactivated by default. #' @param organization Organization id. #' @param user User ID. - #' @param account Account type [GUEST, FULL, ADMINISTRATOR]. #' @param authenticationId Authentication origin ID. searchUsers=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="users", subcategoryId=NULL, action="search", params=params, httpMethod="GET", as.queryParam=NULL, ...), diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index e9b2195c871..363efca3f8f 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index fe127eafb19..3d6e69ee4cb 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -5,7 +5,7 @@ setGeneric("organizationClient", function(OpencgaR, organization, id, endpointNa # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, users, user, filterId, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, users, filterId, user, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -15,42 +15,42 @@ setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, study, studies, variableSet, group, templateId, members, id, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, members, group, id, variableSet, templateId, study, studies, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, file, folder, annotationSet, members, files, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, members, folder, files, annotationSet, file, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, samples, annotationSet, members, sample, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, members, samples, annotationSet, sample, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, individual, annotationSet, members, individuals, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, members, individuals, individual, annotationSet, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, families, members, family, annotationSet, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, members, families, annotationSet, family, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, cohort, members, cohorts, annotationSet, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## ## PanelClient -setGeneric("panelClient", function(OpencgaR, panels, members, endpointName, params=NULL, ...) +setGeneric("panelClient", function(OpencgaR, members, panels, endpointName, params=NULL, ...) standardGeneric("panelClient")) # ############################################################################## @@ -65,7 +65,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretations, interpretation, annotationSet, members, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, members, interpretation, clinicalAnalysis, clinicalAnalyses, interpretations, annotationSet, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index 32983a2b6bc..675d8f0c9bb 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -62,7 +62,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretations, interpretation, annotationSet, members, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, interpretation, clinicalAnalysis, clinicalAnalyses, interpretations, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 6f37317a6fb..771d7d16480 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, members, cohorts, annotationSet, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index 18950845d09..dc1ad726ed4 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -37,7 +37,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, families, members, family, annotationSet, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, members, families, annotationSet, family, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 2a108bf3c3c..52d5b80e3f6 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, file, folder, annotationSet, members, files, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, files, annotationSet, file, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 6962ac02c5d..b134810eeb3 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 6db8609a2e0..ab204922c49 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, annotationSet, members, individuals, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individuals, individual, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index a08f7f1cff9..c48e3ae9691 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index e07d2af2b26..8fd2202e69f 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 466172bd59c..868d718b61c 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Organization-methods.R b/opencga-client/src/main/R/R/Organization-methods.R index 178042aea75..fd5681c5378 100644 --- a/opencga-client/src/main/R/R/Organization-methods.R +++ b/opencga-client/src/main/R/R/Organization-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index a5302a2260d..6f9d0bebb47 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -36,7 +36,7 @@ #' [*]: Required parameter #' @export -setMethod("panelClient", "OpencgaR", function(OpencgaR, panels, members, endpointName, params=NULL, ...) { +setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/panels/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 2b1e2a13c3e..41235ecea72 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index 14252d367ec..b61ca7558ca 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, annotationSet, members, sample, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, samples, annotationSet, sample, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 55a5cc88b4c..81f0e582a7c 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -49,7 +49,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, study, studies, variableSet, group, templateId, members, id, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, members, group, id, variableSet, templateId, study, studies, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index f074c546a88..4b6e2d76c67 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -24,6 +24,7 @@ #' | create | /{apiVersion}/users/create | body[*] | #' | login | /{apiVersion}/users/login | body | #' | password | /{apiVersion}/users/password | body[*] | +#' | search | /{apiVersion}/users/search | include, exclude, limit, skip, count, organization, id, authenticationId | #' | info | /{apiVersion}/users/{users}/info | include, exclude, organization, users[*] | #' | configs | /{apiVersion}/users/{user}/configs | user[*], name | #' | updateConfigs | /{apiVersion}/users/{user}/configs/update | user[*], action, body[*] | @@ -39,7 +40,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, users, user, filterId, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, users, filterId, user, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/anonymous: @@ -67,6 +68,19 @@ setMethod("userClient", "OpencgaR", function(OpencgaR, users, user, filterId, en password=fetchOpenCGA(object=OpencgaR, category="users", categoryId=NULL, subcategory=NULL, subcategoryId=NULL, action="password", params=params, httpMethod="POST", as.queryParam=NULL, ...), + #' @section Endpoint /{apiVersion}/users/search: + #' User search method. + #' @param include Fields included in the response, whole JSON path must be provided. + #' @param exclude Fields excluded in the response, whole JSON path must be provided. + #' @param limit Number of results to be returned. + #' @param skip Number of results to skip. + #' @param count Get the total number of results matching the query. Deactivated by default. + #' @param organization Organization id. + #' @param id Comma separated list user IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param authenticationId Authentication origin ID. + search=fetchOpenCGA(object=OpencgaR, category="users", categoryId=NULL, subcategory=NULL, subcategoryId=NULL, + action="search", params=params, httpMethod="GET", as.queryParam=NULL, ...), + #' @section Endpoint /{apiVersion}/users/{users}/info: #' Return the user information including its projects and studies. #' @param include Fields included in the response, whole JSON path must be provided. diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 2b18e5f5063..8bc5c25558b 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-10 +# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index 77e825b9edb..a74cbd784c4 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -153,7 +153,6 @@ public RestResponse permissionsUsers(ObjectMap params) throws ClientExcepti * count: Get the total number of results matching the query. Deactivated by default. * organization: Organization id. * user: User ID. - * account: Account type [GUEST, FULL, ADMINISTRATOR]. * authenticationId: Authentication origin ID. * @return a RestResponse object. * @throws ClientException ClientException if there is any server error. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index 916156065b5..5d3cef8c796 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index 4ad23e20b19..f12aa75b765 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -55,7 +55,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index db3160eeb6c..127e40de626 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index 83d0ffa1175..d55854b6127 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 8f8bd680ffc..663903149db 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 02e3d914f6d..0fe1fba1940 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index b687c3d0e47..0e14eba34d8 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index 09e91a32ff7..5598bf2ec81 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index f6d27510706..02037990104 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index 3e77702534c..8826ff88f90 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java index 1415aeb5605..e1ec2b30ebf 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java @@ -33,7 +33,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 4f241541143..23b5a0f0afd 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -31,7 +31,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index 5feb046554a..5f69fa0997a 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index a5187a4c7d8..02383dedf92 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -47,7 +47,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index 71b158bca58..bdadc50c29b 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -103,6 +103,26 @@ public RestResponse password(PasswordChangeParams data) throws ClientExcep return execute("users", null, null, null, "password", params, POST, User.class); } + /** + * User search method. + * @param params Map containing any of the following optional parameters. + * include: Fields included in the response, whole JSON path must be provided. + * exclude: Fields excluded in the response, whole JSON path must be provided. + * limit: Number of results to be returned. + * skip: Number of results to skip. + * count: Get the total number of results matching the query. Deactivated by default. + * organization: Organization id. + * id: Comma separated list user IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * authenticationId: Authentication origin ID. + * @return a RestResponse object. + * @throws ClientException ClientException if there is any server error. + */ + public RestResponse search(ObjectMap params) throws ClientException { + params = params != null ? params : new ObjectMap(); + return execute("users", null, null, null, "search", params, GET, User.class); + } + /** * Return the user information including its projects and studies. * @param users Comma separated list of user IDs. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index bf91b0a72df..58f15654b8d 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index b208b0332f5..31b832fd1bd 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-10 +* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index a17bf1209e7..7fcab038434 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -107,7 +107,6 @@ export default class Admin extends OpenCGAParentClass { * value is false. * @param {String} [params.organization] - Organization id. * @param {String} [params.user] - User ID. - * @param {String} [params.account] - Account type [GUEST, FULL, ADMINISTRATOR]. * @param {String} [params.authenticationId] - Authentication origin ID. * @returns {Promise} Promise object in the form of RestResponse instance. */ diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 3b0cf840b5a..1ec703a5d46 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 3a2d4044b61..e445a613946 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index e8c016fe834..6f9ac1e3c22 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index f9401a6090f..4343bc420dc 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index 1568ca19ad2..245c24abe04 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index 3aaf33d45a4..0a085be817c 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index 50c5f456909..1bef974d359 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index 81bc55cc81d..ce94d506024 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index a7faefab056..1d2aa95b0cc 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 5f46d66682f..6d9869452f1 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Organization.js b/opencga-client/src/main/javascript/Organization.js index 6e96cfe293a..a429ccf6868 100644 --- a/opencga-client/src/main/javascript/Organization.js +++ b/opencga-client/src/main/javascript/Organization.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index 8728cf80482..e58af550ded 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index 5687de66b71..f4ae4e29625 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index 1d8a7d97876..d13f1d427c3 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index 1b72aa833c4..e478e03db6f 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -64,6 +64,24 @@ export default class User extends OpenCGAParentClass { return this._post("users", null, null, null, "password", data); } + /** User search method + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. + * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. + * @param {Number} [params.limit] - Number of results to be returned. + * @param {Number} [params.skip] - Number of results to skip. + * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default + * value is false. + * @param {String} [params.organization] - Organization id. + * @param {String} [params.id] - Comma separated list user IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.authenticationId] - Authentication origin ID. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + search(params) { + return this._get("users", null, null, null, "search", params); + } + /** Return the user information including its projects and studies * @param {String} users - Comma separated list of user IDs. * @param {Object} [params] - The Object containing the following optional parameters: diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index 60baa0f5a0d..c341d110c64 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index bfd6f99aa40..a178fbbddcf 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-10 + * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index 1f344f41988..ead2235886b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -117,7 +117,6 @@ def search_users(self, **options): Deactivated by default. :param str organization: Organization id. :param str user: User ID. - :param str account: Account type [GUEST, FULL, ADMINISTRATOR]. :param str authentication_id: Authentication origin ID. """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index 08ba05a5b76..313d3223ade 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index c8cf1a2e23b..d43bfa65210 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 1d37bffadd2..5772cf02ee5 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 61d984ad048..0688b1f4c07 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index 9df67f56a94..e13a27bddf0 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 881832c2eef..0d9c9655f4b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index 4b66f11cf5f..c7e9bb9efeb 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index 5bef563d519..a3c184edacd 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 94b4b8d27e5..22d31ddfacd 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index a89eb56e683..130fa0aa824 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py index 2ba35452d48..681e988c54d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index 46bc074062d..28bf4f3e914 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index 74636b383fb..8f6753319e5 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 42433932e42..b6f496bf061 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index d1ebc104bd8..6bc479ff5f0 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -63,6 +63,29 @@ def password(self, data=None, **options): return self._post(category='users', resource='password', data=data, **options) + def search(self, **options): + """ + User search method. + PATH: /{apiVersion}/users/search + + :param str include: Fields included in the response, whole JSON path + must be provided. + :param str exclude: Fields excluded in the response, whole JSON path + must be provided. + :param int limit: Number of results to be returned. + :param int skip: Number of results to skip. + :param bool count: Get the total number of results matching the query. + Deactivated by default. + :param str organization: Organization id. + :param str id: Comma separated list user IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str authentication_id: Authentication origin ID. + """ + + return self._get(category='users', resource='search', **options) + def info(self, users, **options): """ Return the user information including its projects and studies. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index ecc28f50daa..db47d5553a7 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index 688badda837..ffaa0dbb2e4 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-10 + Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. From c0df2216831a6767b1ab11291ecdc28afdd1f711 Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 6 May 2024 16:05:31 +0200 Subject: [PATCH 12/59] server: handle runtime exceptions, #TASK-5980 --- .../org/opencb/opencga/catalog/managers/UserManager.java | 4 ++-- .../java/org/opencb/opencga/server/rest/UserWSServer.java | 8 +++----- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java index 15f4fb24d02..d882015eae5 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/UserManager.java @@ -237,9 +237,9 @@ public OpenCGAResult search(@Nullable String organizationId, Query query, auditManager.auditSearch(myOrganizationId, tokenPayload.getUserId(myOrganizationId), Enums.Resource.USER, "", "", auditParams, new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS)); return result; - } catch (CatalogException e) { + } catch (Exception e) { auditManager.auditSearch(myOrganizationId, tokenPayload.getUserId(myOrganizationId), Enums.Resource.USER, "", "", auditParams, - new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError())); + new AuditRecord.Status(AuditRecord.Status.Result.ERROR, new Error(0, "User search", e.getMessage()))); throw e; } } diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/UserWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/UserWSServer.java index d76db93c398..31fcd3a9720 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/UserWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/UserWSServer.java @@ -87,12 +87,10 @@ public Response search( @ApiParam(value = ParamConstants.ORGANIZATION_DESCRIPTION) @QueryParam(ParamConstants.ORGANIZATION) String organizationId, @ApiParam(value = ParamConstants.USER_ID_DESCRIPTION) @QueryParam(ParamConstants.USER_ID_PARAM) String userId, @ApiParam(value = ParamConstants.USER_AUTHENTICATION_ORIGIN_DESCRIPTION) @QueryParam(ParamConstants.USER_AUTHENTICATION_ORIGIN) String authentication) { - try { + return run(() -> { query.remove(ParamConstants.ORGANIZATION); - return createOkResponse(catalogManager.getUserManager().search(organizationId, query, queryOptions, token)); - } catch (Exception e) { - return createErrorResponse(e); - } + return catalogManager.getUserManager().search(organizationId, query, queryOptions, token); + }); } @GET From c527577b4398d7d5a3b3432df940c6422a15f616 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 8 May 2024 17:24:30 +0200 Subject: [PATCH 13/59] cicd: flavor hadoop as choice in manual deploy docker #TASK-6186 --- .github/workflows/manual-deploy-docker.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/manual-deploy-docker.yml b/.github/workflows/manual-deploy-docker.yml index 06cf9d51dcd..64976c25fa3 100644 --- a/.github/workflows/manual-deploy-docker.yml +++ b/.github/workflows/manual-deploy-docker.yml @@ -11,10 +11,15 @@ on: type: string required: true hadoop: - type: string + type: choice description: 'Hadoop flavour. Any of: [hdp3.1, hdi5.1, emr6.1, emr6.13]' required: false - default: "hdp3.1" + default: hdp3.1 + options: + - hdp3.1 + - hdi5.1 + - emr6.1 + - emr6.13 jobs: build: From 15ae9a6c0005383f248d5115ea14aec50280675f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 9 May 2024 12:44:51 +0200 Subject: [PATCH 14/59] cicd: Delete RClient profile --- .github/workflows/manual-deploy-docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/manual-deploy-docker.yml b/.github/workflows/manual-deploy-docker.yml index 7f940c5800d..731d96e5b42 100644 --- a/.github/workflows/manual-deploy-docker.yml +++ b/.github/workflows/manual-deploy-docker.yml @@ -40,7 +40,7 @@ jobs: ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} ${{ inputs.hadoop }} fi - name: Maven Build (skip tests) - run: mvn -T 2 clean install -DskipTests -P${{ inputs.hadoop }},RClient -Dopencga.war.name=opencga -Dcheckstyle.skip + run: mvn -T 2 clean install -DskipTests -P${{ inputs.hadoop }} -Dopencga.war.name=opencga -Dcheckstyle.skip - uses: actions/upload-artifact@v4 with: name: build-folder From 868f5e27fdacc2dfedecc0eb4f6a555eb65e640b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 9 May 2024 17:43:26 +0100 Subject: [PATCH 15/59] storage: Exclude jetty.http2 from jar-with-dependencies. #TASK-6209 --- .../opencga-storage-hadoop-lib/src/main/assembly/src.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/src/main/assembly/src.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/src/main/assembly/src.xml index 6c5519fe13b..497d6819cf0 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/src/main/assembly/src.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/src/main/assembly/src.xml @@ -16,6 +16,7 @@ com.sun.jersey:* org.eclipse.jetty:* + org.eclipse.jetty.http2:* org.eclipse.jetty.websocket:* org.apache.logging.log4j:log4j-slf4j-impl org.apache.commons:commons-lang3 From 334fe852ebefd35720b7991dddd3221f6cdd2a39 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 14 May 2024 10:52:15 +0200 Subject: [PATCH 16/59] cicd: Added new jobs and needs to release step #TASK-6204 #TASK-6185 --- .github/workflows/release.yml | 66 ++++++++++++++++++++++++++++------- 1 file changed, 54 insertions(+), 12 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 86bcb471976..28e0bfcfbaf 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -7,39 +7,81 @@ on: workflow_dispatch: jobs: - build: + # Add the build-hdp and deploy-docker-hdp jobs + build-hdp: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P hdp3.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip - deploy-maven: - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop - needs: build + deploy-docker-hdp: + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop + needs: build-hdp with: - maven_opts: -P hdp3.1 -Dopencga.war.name=opencga + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-hdp.outputs.version }} + secrets: inherit + + # Add the build-hdi and deploy-docker-hdi jobs + build-hdi: + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop + with: + maven_opts: -P hdi5.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip + + deploy-docker-hdi: + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop + needs: build-hdi + with: + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-hdi.outputs.version }} secrets: inherit - deploy-docker: + # Add the build-emr and deploy-docker-emr jobs + build-emr: + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop + with: + maven_opts: -P emr6.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip + + deploy-docker-emr: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop - needs: build + needs: build-emr with: - cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build.outputs.version }} + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-emr.outputs.version }} + secrets: inherit + + # Add the build-emr613 and deploy-docker-emr613 jobs + build-emr613: + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop + with: + maven_opts: -P emr6.13,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip + + deploy-docker-emr613: + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop + needs: build-emr613 + with: + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-emr613.outputs.version }} + secrets: inherit + + # Add the deploy-maven and deploy-python jobs they depend on the build-hdp job + deploy-maven: + uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop + needs: build-hdp + with: + maven_opts: -P hdp3.1 -Dopencga.war.name=opencga secrets: inherit deploy-python: uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop - needs: build + needs: build-hdp with: cli: ./clients/python/python-build.sh push artifact: build-folder secrets: inherit + # Add the release job that depends on all the previous jobs release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build, deploy-maven, deploy-docker, deploy-python ] + needs: [ build-hdp, deploy-docker-hdp, build-hdi, deploy-docker-hdi, build-emr, deploy-docker-emr, build-emr613, deploy-docker-emr613, deploy-maven, deploy-docker, deploy-python ] with: artifact: build-folder file: | - opencga-client-${{ needs.build.outputs.version }}.tar.gz - clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz + opencga-client-${{ needs.build-hdp.outputs.version }}.tar.gz + clients/R/opencgaR_${{ needs.build-hdp.outputs.version }}.tar.gz From 77fbcf14de9b20c98e9b7e374aeae53968371248 Mon Sep 17 00:00:00 2001 From: pfurio Date: Fri, 17 May 2024 09:41:09 +0200 Subject: [PATCH 17/59] app: add default authOrigin in the Organizations, #TASK-6245 --- .../opencga/app/migrations/v3_0_0/OrganizationMigration.java | 1 + 1 file changed, 1 insertion(+) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java index c2f9efa57f8..aedc4d6c633 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java @@ -393,6 +393,7 @@ protected void run() throws Exception { authOriginDoc.put("algorithm", algorithm); authOriginDoc.put("secretKey", secretKey); authOriginDoc.put("expiration", 3600L); + authOrigins.add(authOriginDoc); // Set organization counter, owner and authOrigins orgCol.updateOne(Filters.eq("id", organizationId), Updates.combine( From bd89cc735321c73b961503f32fb3604faf6a2991 Mon Sep 17 00:00:00 2001 From: pfurio Date: Fri, 17 May 2024 11:11:39 +0200 Subject: [PATCH 18/59] app: disable main migration for this v3.1.0 release, #TASK-6245 --- .../v3_0_0/OrganizationMigration.java | 402 +----------------- .../catalog/migration/MigrationException.java | 5 + 2 files changed, 8 insertions(+), 399 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java index aedc4d6c633..0b9982c6f71 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java @@ -1,416 +1,20 @@ package org.opencb.opencga.app.migrations.v3_0_0; -import com.mongodb.client.*; -import com.mongodb.client.model.Filters; -import com.mongodb.client.model.InsertOneModel; -import com.mongodb.client.model.Projections; -import com.mongodb.client.model.Updates; -import com.mongodb.client.result.DeleteResult; -import org.apache.commons.collections4.CollectionUtils; -import org.apache.commons.lang3.StringUtils; -import org.bson.Document; -import org.bson.conversions.Bson; -import org.opencb.commons.datastore.mongodb.MongoDataStore; -import org.opencb.commons.utils.CryptoUtils; -import org.opencb.opencga.catalog.auth.authentication.CatalogAuthenticationManager; -import org.opencb.opencga.catalog.db.api.StudyDBAdaptor; -import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptorFactory; -import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory; -import org.opencb.opencga.catalog.exceptions.CatalogAuthorizationException; -import org.opencb.opencga.catalog.exceptions.CatalogException; -import org.opencb.opencga.catalog.exceptions.CatalogIOException; -import org.opencb.opencga.catalog.io.CatalogIOManager; -import org.opencb.opencga.catalog.io.IOManagerFactory; -import org.opencb.opencga.catalog.managers.CatalogManager; import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; import org.opencb.opencga.catalog.migration.MigrationTool; -import org.opencb.opencga.core.api.ParamConstants; -import org.opencb.opencga.core.config.AuthenticationOrigin; import org.opencb.opencga.core.config.Configuration; -import org.opencb.opencga.core.models.migration.MigrationRun; -import org.opencb.opencga.core.models.organizations.OrganizationCreateParams; - -import java.nio.file.Files; -import java.nio.file.Paths; -import java.security.NoSuchAlgorithmException; -import java.util.*; -import java.util.stream.Collectors; @Migration(id = "add_organizations", description = "Add new Organization layer #TASK-4389", version = "3.0.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20231212) public class OrganizationMigration extends MigrationTool { - private final Configuration configuration; - private final String adminPassword; - private String userId; - - private MongoDBAdaptorFactory mongoDBAdaptorFactory; - private String oldDatabase; - private MongoDataStore oldDatastore; - private Set userIdsToDiscardData; - - private MigrationStatus status; - - private enum MigrationStatus { - MIGRATED, - PENDING_MIGRATION, - ERROR - } - - public OrganizationMigration(Configuration configuration, String adminPassword, String userId) throws CatalogException { - this.configuration = configuration; - this.adminPassword = adminPassword; - this.userId = userId; - - this.status = checkAndInit(); - } - - private MigrationStatus checkAndInit() throws CatalogException { - this.oldDatabase = configuration.getDatabasePrefix() + "_catalog"; - this.mongoDBAdaptorFactory = new MongoDBAdaptorFactory(configuration, new IOManagerFactory()); - this.oldDatastore = mongoDBAdaptorFactory.getMongoManager().get(oldDatabase, mongoDBAdaptorFactory.getMongoDbConfiguration()); - - MongoCollection userCol = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION); - FindIterable iterable = userCol.find(Filters.eq("id", ParamConstants.OPENCGA_USER_ID)); - try (MongoCursor cursor = iterable.cursor()) { - if (!cursor.hasNext()) { - MongoIterable collectionNames = oldDatastore.getDb().listCollectionNames(); - try (MongoCursor tmpCursor = collectionNames.cursor()) { - if (!tmpCursor.hasNext()) { - logger.info("Database '{}' not found. Database already migrated.", this.oldDatabase); - return MigrationStatus.MIGRATED; - } else { - List collections = new LinkedList<>(); - tmpCursor.forEachRemaining(collections::add); - logger.debug("Found '{}' collections in '{}' database", StringUtils.join(collections, ", "), this.oldDatabase); - return MigrationStatus.ERROR; - } - } - } - Document userDoc = cursor.next(); - String password = userDoc.getString("_password"); - // Check admin password - try { - if (!CryptoUtils.sha1(adminPassword).equals(password)) { - throw CatalogAuthorizationException.opencgaAdminOnlySupportedOperation(); - } - } catch (NoSuchAlgorithmException e) { - throw new RuntimeException(e); - } - } - - // Check write access to file system - if (!Files.isWritable(Paths.get(configuration.getWorkspace()))) { - throw new CatalogException("Please grant write access to path '" + configuration.getWorkspace() + "'"); - } - // TODO: Check last migration is 2.2.?? - MongoCollection migrationCol = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION); - long count = migrationCol.countDocuments(Filters.in("status", MigrationRun.MigrationStatus.PENDING, - MigrationRun.MigrationStatus.ON_HOLD, MigrationRun.MigrationStatus.ERROR)); - if (count > 0) { - throw new CatalogException("Please check past migrations. Found migrations with status '" + MigrationRun.MigrationStatus.PENDING - + "', '" + MigrationRun.MigrationStatus.ON_HOLD + "', or '" + MigrationRun.MigrationStatus.ERROR + "'."); - } - - // Retrieve all users with data - DistinctIterable userIdIterable = userCol.distinct("id", - Filters.and( - Filters.ne("projects", null), - Filters.ne("projects", Collections.emptyList())), - String.class); - List userIds = new LinkedList<>(); - try (MongoCursor iterator = userIdIterable.iterator()) { - while (iterator.hasNext()) { - String tmpUserId = iterator.next(); - if (!ParamConstants.OPENCGA_USER_ID.equals(tmpUserId)) { - userIds.add(tmpUserId); - } - } - } - if (StringUtils.isNotEmpty(userId)) { - if (!userIds.contains(userId)) { - throw new CatalogException("User '" + userId + "' does not have any data. Available users to migrate are " - + userIds.stream() - .collect(Collectors.joining(", "))); - } - // Extract users that will need to remove data from - this.userIdsToDiscardData = userIds.stream() - .filter(u -> !userId.equals(u)) - .collect(Collectors.toSet()); - } else { - if (userIds.size() > 1) { - throw new CatalogException("More than 1 user containing data found. Available users to migrate are " - + StringUtils.join(userIds, ", ") + ". Please, choose which one to migrate."); - } else if (userIds.isEmpty()) { - throw new CatalogException("No users found to migrate."); - } - this.userId = userIds.get(0); - this.userIdsToDiscardData = new HashSet<>(); - } - - this.organizationId = this.userId; - this.catalogManager = new CatalogManager(configuration); - return MigrationStatus.PENDING_MIGRATION; + public OrganizationMigration(Configuration configuration, String adminPassword, String userId) { } @Override protected void run() throws Exception { - if (this.status == MigrationStatus.ERROR) { - throw new CatalogException("Corrupted database '" + this.oldDatabase + "' found. Could not migrate."); - } else if (this.status == MigrationStatus.MIGRATED) { - return; - } - - MongoCollection metadataCol = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.METADATA_COLLECTION); - FindIterable iterable = metadataCol.find(new Document()); - Document metaDoc; - long counter; - String secretKey; - String algorithm; - try (MongoCursor cursor = iterable.cursor()) { - metaDoc = cursor.next(); - counter = metaDoc.get("idCounter", Number.class).longValue(); - Document admin = metaDoc.get("admin", Document.class); - secretKey = admin.getString("secretKey"); - algorithm = admin.getString("algorithm"); - } - - if (!userIdsToDiscardData.isEmpty()) { - MongoCollection studyCol = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION); - // First, remove unnecessary data - queryMongo(studyCol, Filters.in("_ownerId", userIdsToDiscardData), Projections.include("uid"), studyDoc -> { - long studyUid = studyDoc.get("uid", Number.class).longValue(); - Bson query = Filters.eq("studyUid", studyUid); - - // Delete data associated to the study - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.FILE_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.JOB_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.INDIVIDUAL_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.COHORT_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.FAMILY_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.PANEL_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.CLINICAL_ANALYSIS_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_ARCHIVE_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.INDIVIDUAL_ARCHIVE_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.FAMILY_ARCHIVE_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.PANEL_ARCHIVE_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.INTERPRETATION_ARCHIVE_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.DELETED_FILE_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.DELETED_JOB_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.DELETED_SAMPLE_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.DELETED_INDIVIDUAL_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.DELETED_COHORT_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.DELETED_FAMILY_COLLECTION).deleteMany(query); - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.DELETED_PANEL_COLLECTION).deleteMany(query); - }); - - // Delete studies - DeleteResult result = studyCol.deleteMany(Filters.in("_ownerId", userIdsToDiscardData)); - if (result.getDeletedCount() > 0) { - logger.info("Deleted {} unnecessary studies", result.getDeletedCount()); - } - - // Remove projects from users - oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION).updateMany( - Filters.in("id", userIdsToDiscardData), - Updates.set("projects", Collections.emptyList()) - ); - } - - // Create admin organization - catalogManager.installCatalogDB(algorithm, secretKey, "MyStr0NgT!mP0r4lP4sWSoRd", "tempmail@tempmail.com", false); - - // Create admin organization - MongoCollection oldUserCollection = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION); - queryMongo(oldUserCollection, Filters.eq("id", ParamConstants.OPENCGA_USER_ID), Projections.exclude("_id"), document -> { - String organizationId = ParamConstants.ADMIN_ORGANIZATION; - try { - MongoCollection userCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION); - MongoCollection projectCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION); - MongoCollection studyCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION); - MongoCollection fileCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.FILE_COLLECTION); - // Empty data from collections with default data - userCollection.deleteMany(new Document()); - projectCollection.deleteMany(new Document()); - studyCollection.deleteMany(new Document()); - fileCollection.deleteMany(new Document()); - - // Replace user in organization - userCollection.insertOne(document); - - MongoDatabase orgDatabase = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb(); - - // Extract projects - List projects = document.getList("projects", Document.class); - for (Document project : projects) { - long projectUid = project.get("uid", Number.class).longValue(); - - // Look for studies - MongoCollection oldStudyCol = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION); - MongoCollection orgStudyCol = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION); - - queryMongo(oldStudyCol, Filters.eq("_project.uid", projectUid), Projections.exclude("_id"), studyDoc -> { - // Insert study in new organization collection - orgStudyCol.insertOne(studyDoc); - - long studyUid = studyDoc.get("uid", Number.class).longValue(); - - // Move data belonging to the study - replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_COLLECTION), - orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.SAMPLE_COLLECTION)); - replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.INDIVIDUAL_COLLECTION), - orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.INDIVIDUAL_COLLECTION)); - replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.COHORT_COLLECTION), - orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.COHORT_COLLECTION)); - replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.FILE_COLLECTION), - orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.FILE_COLLECTION)); - replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.FAMILY_COLLECTION), - orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.FAMILY_COLLECTION)); - replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.PANEL_COLLECTION), - orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.PANEL_COLLECTION)); - replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.JOB_COLLECTION), - orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.JOB_COLLECTION)); - replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.CLINICAL_ANALYSIS_COLLECTION), - orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.CLINICAL_ANALYSIS_COLLECTION)); - replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION), - orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION)); - - - oldStudyCol.deleteOne(Filters.eq("uid", studyUid)); - }); - - } - - // Remove user from the source database - oldUserCollection.deleteOne(Filters.eq("id", ParamConstants.OPENCGA_USER_ID)); - } catch (CatalogException e) { - throw new RuntimeException(e); - } - }); - - // Create new organization - String opencgaToken = catalogManager.getUserManager().login(ParamConstants.ADMIN_ORGANIZATION, ParamConstants.OPENCGA_USER_ID, adminPassword).getToken(); - catalogManager.getOrganizationManager().create(new OrganizationCreateParams().setId(organizationId), null, opencgaToken); - OrganizationMongoDBAdaptorFactory orgFactory = mongoDBAdaptorFactory.getOrganizationMongoDBAdaptorFactory(organizationId); - String newDatabase = orgFactory.getMongoDataStore().getDatabaseName(); - - // Rename database to main organization database - MongoDataStore adminDatastore = mongoDBAdaptorFactory.getMongoManager().get("admin", mongoDBAdaptorFactory.getMongoDbConfiguration()); - for (String collectionName : oldDatastore.getCollectionNames()) { - if (!OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION.equals(collectionName)) { - logger.info("Renaming collection {} to {}", oldDatabase + "." + collectionName, newDatabase + "." + collectionName); - adminDatastore.getDb().runCommand(new Document() - .append("renameCollection", oldDatabase + "." + collectionName) - .append("to", newDatabase + "." + collectionName) - .append("dropTarget", true) - ); - } else { - // Remove collections - oldDatastore.getDb().getCollection(collectionName).drop(); - } - } - - CatalogIOManager ioManager = new CatalogIOManager(configuration); - - // Loop over all organizations to perform additional data model changes - for (String organizationId : mongoDBAdaptorFactory.getOrganizationIds()) { - ioManager.createOrganization(organizationId); - - MongoDatabase database = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb(); - MongoCollection userCollection = database.getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION); - - // Extract projects from users - queryMongo(userCollection, new Document(), Projections.exclude("_id"), document -> { - List projects = document.getList("projects", Document.class); - if (CollectionUtils.isNotEmpty(projects)) { - // Create project directory - for (Document project : projects) { - Long projectUid = project.get("uid", Long.class); - try { - ioManager.createProject(organizationId, Long.toString(projectUid)); - } catch (CatalogIOException e) { - throw new RuntimeException("Couldn't create project folder for project '" + project.getString("fqn") + "'.", e); - } - } - - MongoCollection projectCol = database.getCollection(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION); - projectCol.insertMany(projects); - } - }); - - // Remove account type, projects and sharedProjects from User - for (String collection : Arrays.asList(OrganizationMongoDBAdaptorFactory.USER_COLLECTION, OrganizationMongoDBAdaptorFactory.DELETED_USER_COLLECTION)) { - MongoCollection mongoCollection = database.getCollection(collection); - mongoCollection.updateMany(new Document(), - Updates.combine( - Updates.set("projects", Collections.emptyList()), - Updates.set("organization", organizationId), - Updates.unset("sharedProjects"), - Updates.unset("account.type") - ) - ); - } - - // Add owner as admin of every study and remove _ownerId field - for (String collection : Arrays.asList(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION, OrganizationMongoDBAdaptorFactory.DELETED_STUDY_COLLECTION)) { - MongoCollection mongoCollection = database.getCollection(collection); - mongoCollection.updateMany( - Filters.eq(StudyDBAdaptor.QueryParams.GROUP_ID.key(), ParamConstants.ADMINS_GROUP), - Updates.combine( - Updates.unset("_ownerId"), - Updates.push("groups.$.userIds", organizationId) - )); - } - - // Set organization counter - MongoCollection orgCol = database.getCollection(OrganizationMongoDBAdaptorFactory.ORGANIZATION_COLLECTION); - - List authOrigins = new ArrayList<>(); - // Super admins organization will only have one authentication origin - internal - if (!ParamConstants.ADMIN_ORGANIZATION.equals(organizationId)) { - if (configuration.getAuthentication() != null && CollectionUtils.isNotEmpty(configuration.getAuthentication().getAuthenticationOrigins())) { - for (AuthenticationOrigin authenticationOrigin : configuration.getAuthentication().getAuthenticationOrigins()) { - if (authenticationOrigin.getType().equals(AuthenticationOrigin.AuthenticationType.OPENCGA) - && "internal".equals(authenticationOrigin.getId())) { - continue; - } - Document authOriginDoc = convertToDocument(authenticationOrigin); - authOriginDoc.put("algorithm", algorithm); - authOriginDoc.put("secretKey", secretKey); - authOriginDoc.put("expiration", 3600L); - authOrigins.add(authOriginDoc); - } - } - } - Document authOriginDoc = convertToDocument(CatalogAuthenticationManager.createOpencgaAuthenticationOrigin()); - authOriginDoc.put("id", "internal"); - authOriginDoc.put("algorithm", algorithm); - authOriginDoc.put("secretKey", secretKey); - authOriginDoc.put("expiration", 3600L); - authOrigins.add(authOriginDoc); - - // Set organization counter, owner and authOrigins - orgCol.updateOne(Filters.eq("id", organizationId), Updates.combine( - Updates.set("_idCounter", counter), - Updates.set("owner", organizationId), - Updates.set("configuration.authenticationOrigins", authOrigins) - )); - } - } - - private void replicateData(long studyUid, MongoCollection sourceCol, MongoCollection targetCol) { - // Move data to the new collection - logger.info("Moving data from {} to {}", sourceCol.getNamespace(), targetCol.getNamespace()); - migrateCollection(sourceCol, targetCol, Filters.eq("studyUid", studyUid), Projections.exclude("_id"), - (document, bulk) -> bulk.add(new InsertOneModel<>(document))); - // Remove data from the source collection - sourceCol.deleteMany(Filters.eq("studyUid", studyUid)); + throw MigrationException.outdatedMigration(getAnnotation(), "3.1.0"); } } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java index 63f666eac14..e59e1e659e3 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java @@ -20,4 +20,9 @@ public static MigrationException offlineMigrationException(Migration migration) return new MigrationException("Migration '" + migration.id() + "' requires database to be offline. Please, ensure the database " + "cannot be accessed and run try again with '--offline' flag."); } + + public static MigrationException outdatedMigration(Migration migration, String version) { + return new MigrationException("Migration '" + migration.id() + "' is outdated since version " + version + ". Please, update the " + + "migration from the previous latest version."); + } } From 595b8f5612f4b03dbbc3b2ae4b61cf5bb9f58a61 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 12:08:41 +0200 Subject: [PATCH 19/59] Prepare development branch 3.0.0.x #TASK-6256 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 27 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index b207d265360..8e87f263f06 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 955c526ad6e..bfbd58793b9 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 9ec39cb0aa7..16647aebdec 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index d267e075341..832dde11be9 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f996aa69c44..e18104a17bc 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 5b93869e400..eb2c6d0f786 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index c689e382215..7e3925bb9fe 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index dc20e3dcf3a..be27dc552d0 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6b1f0a28fb5..6eb6c110bd5 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index fb71790dc5e..80c167215df 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 3688c101f6b..2e2ee67cc27 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 44fd8cf29d7..2d5dbebf91b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 327725fd2e4..9708846e4f8 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 4f094c0a282..797c371a6a7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index be88884b590..2d1922b3655 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index d6758ba7e39..803fee44a25 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 508b1b2468b..0a7cea85134 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 177e7d79267..452570b992b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 2152ce3ec3e..7c6cbacda94 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index a0fae207eff..0cca28f1721 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index f273977d555..7e8d9e80136 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 94139ce36d5..10d9d270831 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 46501dba0bf..ac1e8071fb5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index dc9acd1a6b1..69f063a9a44 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 164e769ee99..0347eca3180 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 1076e3ad276..da8d02db513 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index ea34c50ade0..181affb30a7 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT pom OpenCGA From e187d6b244e10b5ce3189de18f0cb59451eec528 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 16:39:04 +0200 Subject: [PATCH 20/59] Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index a82fde15ccc..78e82fd250e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 6dcf364e559..2aa894fb7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index ff10c269d7f..00ac1b15fb7 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index ce253ddc6ae..74ce4002f32 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 215d392ce1c..f5c2e89e04b 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 432db00c834..64616005a87 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index eda14c31ea1..3353ba8dcd8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 7632ed6d65f..f39d9d674a6 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index cc692c6fcea..6ac3574fe95 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index bae503e0e91..9dea4c86c74 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 0dffe6806ff..7edb5708703 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index deac888af82..7b22e17d9b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 661d9416a8f..386dba5ab41 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 358590f69f6..d4376a789f5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index 394e6c90e16..ba01b370a09 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 58aac8414c5..1e8f6fa681a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8c00149ba90..1adc2854e5a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 45370142854..47a11d3fbf0 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 82a3d1f0fdc..b61a7f4591c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index c4839e1c646..783fb051572 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 8d09832b15a..72796b835d4 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 0326f2479f3..a40d5eb78bb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7d97161a5e3..91e477e70bb 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 054ab3bc9de..16d83021da1 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index c3f5166b7fd..fa537ec1586 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 12981fefe10..f6897603638 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 24e41953d60..8c725c30198 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0_dev - 3.1.0_dev - 6.1.0-SNAPSHOT - 3.1.0-SNAPSHOT - 5.1.0-SNAPSHOT - 3.1.0-SNAPSHOT + 3.1.0 + 3.1.0 + 6.0.0 + 3.1.0 + 5.1.0 + 3.1.0 0.2.0 2.14.3 From 108e15e9b9efb65264f6a0a7216b36065f45e3b4 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 16:43:15 +0200 Subject: [PATCH 21/59] Prepare new development branch release-3.1.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 78e82fd250e..3b96f1b246e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 2aa894fb7f7..1c77750c7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 00ac1b15fb7..d15b4768e59 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 74ce4002f32..2582a5f2003 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f5c2e89e04b..16aff526b3e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 64616005a87..73047a516e9 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3353ba8dcd8..2348ef6f6f7 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f39d9d674a6..d222153c1c3 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6ac3574fe95..1834d5c7e64 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9dea4c86c74..02953389c2d 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 7edb5708703..a7a2c8adbbb 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 7b22e17d9b9..ea3dbc32689 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 386dba5ab41..927d616c88c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index d4376a789f5..a84279ad4de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ba01b370a09..ea5b63a7b6f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 1e8f6fa681a..705f7b4104c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 1adc2854e5a..066630724a2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 47a11d3fbf0..3675d760a35 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index b61a7f4591c..ee08e659ae7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 783fb051572..ffd41bdf7ca 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 72796b835d4..435818c24cf 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index a40d5eb78bb..495de2ebf89 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 91e477e70bb..7de2add12c5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 16d83021da1..d6d92f43dda 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index fa537ec1586..316589d12ff 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index f6897603638..76a6360d5e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 8c725c30198..0e1de519a9b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0 - 3.1.0 - 6.0.0 - 3.1.0 - 5.1.0 - 3.1.0 + 3.2.0_dev + 3.2.0_dev + 6.1.0-SNAPSHOT + 3.2.0-SNAPSHOT + 5.2.0-SNAPSHOT + 3.2.0-SNAPSHOT 0.2.0 2.14.3 From f1083ec6da3b7819e0aa641dc9f4c237d03f1bfe Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 16:43:44 +0200 Subject: [PATCH 22/59] Prepare new development branch release-3.1.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 3b96f1b246e..d43f173b4ff 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 1c77750c7f7..67bd1fa34e0 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index d15b4768e59..11535022d1b 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 2582a5f2003..c9461e9c4de 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 16aff526b3e..adb57573b45 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 73047a516e9..0153566efea 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 2348ef6f6f7..3cbbbb2fa89 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index d222153c1c3..804b83e792b 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 1834d5c7e64..a31567cb3bc 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 02953389c2d..ff97332afff 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index a7a2c8adbbb..12c0f24a27b 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index ea3dbc32689..e63a1dfcc78 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 927d616c88c..85caa7da48e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index a84279ad4de..719b5cf072a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ea5b63a7b6f..a8a16269d93 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 705f7b4104c..a2d228c120d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 066630724a2..eab3b7f565e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 3675d760a35..1292ba96965 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index ee08e659ae7..4b4ab70de2b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index ffd41bdf7ca..b9f0fcc7696 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 435818c24cf..d48ef593c4d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 495de2ebf89..cddf51ec925 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7de2add12c5..943b2ff3eb8 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index d6d92f43dda..891225e9311 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 316589d12ff..f89a8783b7f 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 76a6360d5e2..70f7e126a02 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 0e1de519a9b..1b5cc6907e7 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.1-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.2.0_dev - 3.2.0_dev - 6.1.0-SNAPSHOT - 3.2.0-SNAPSHOT - 5.2.0-SNAPSHOT - 3.2.0-SNAPSHOT + 3.1.1_dev + 3.1.1_dev + 6.0.1-SNAPSHOT + 3.1.1-SNAPSHOT + 5.1.1-SNAPSHOT + 3.1.1-SNAPSHOT 0.2.0 2.14.3 From 77876a24f4a93b4cbbde53610572f87253f59816 Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 20 May 2024 16:46:57 +0200 Subject: [PATCH 23/59] app: keep track of old migrations, #TASK-6256 - recover old v2.x migrations and marked them as deprecated - check all previous migrations were successfully run before moving to v3.0.0 - keep track of previous migrations --- .../executors/MigrationCommandExecutor.java | 2 +- .../v2/v2_0_3/catalog/java/Migration1.java | 14 ++ .../v2_0_5/catalog/java/initialiseGroups.java | 15 ++ ...removeDeletedFileReferencesFromSample.java | 16 ++ ...tationSetsInClinicalAnalysisMigration.java | 20 +++ ...pleteClinicalReportDataModelMigration.java | 19 +++ .../catalog/java/AddMissingIndexes.java | 18 +++ .../java/AddPanelsToInterpretations.java | 17 ++ .../catalog/java/CreateAuditIndexes.java | 19 +++ .../v2/v2_1_0/catalog/java/PanelLock.java | 18 +++ .../RemoveRCVersionsFromMigrationRuns.java | 18 +++ ...RenameDatastoreConfigurationToOptions.java | 18 +++ .../StudyClinicalConfigurationRelocation.java | 19 +++ .../java/VariantFileStatsRelocation.java | 18 +++ .../v2_1_0/catalog/javascript/Migration1.java | 14 ++ .../v2_1_0/catalog/javascript/Migration2.java | 14 ++ .../v2_1_0/catalog/javascript/Migration3.java | 14 ++ .../v2_1_0/catalog/javascript/Migration4.java | 14 ++ .../AddCellbaseConfigurationToProject.java | 18 +++ .../DefaultSampleIndexConfiguration.java | 18 +++ .../NewClinicalSignificanceFields.java | 18 +++ .../catalog/AddMissingClinicalAudit.java | 17 ++ .../v2_2_0/catalog/AddNameFieldInCohort.java | 16 ++ .../v2_2_0/catalog/AddNewAllowedBiotype.java | 17 ++ .../catalog/AddNewFileInternalIndex_1850.java | 17 ++ .../AddSampleInternalVariant_1851.java | 17 ++ .../catalog/ChangeInterpretationMethods.java | 16 ++ .../ClinicalVariantEvidenceMigration.java | 16 ++ .../catalog/DeleteUnusedVariableSets.java | 18 +++ .../v2_2_0/catalog/FixFamilyReferences.java | 17 ++ .../catalog/FixNonExistingMoIFromPanels.java | 18 +++ ...ImproveClinicalAnalysisQualityControl.java | 17 ++ .../catalog/ImproveFileQualityControl.java | 17 ++ .../ImproveIndividualQualityControl.java | 16 ++ ...mproveVariableSetNamesAndDescriptions.java | 16 ++ .../v2_2_0/catalog/RemoveFileDocsFromCA.java | 16 ++ .../v2_2_0/catalog/RemoveParallelIndexes.java | 16 ++ .../RenameFamilyQualityControlFields.java | 16 ++ .../RenameFileQualityControlFields.java | 16 ++ .../RenameIndividualQualityControlFields.java | 16 ++ .../RenameInterpretationFindingStats.java | 17 ++ .../RenameSampleQualityControlFields.java | 18 +++ ...allerInterpretationStudyConfiguration.java | 16 ++ .../AddInternalLastModified.java | 10 ++ ...AddModificationDateToClinicalInternal.java | 13 ++ .../AddModificationDateToCohortInternal.java | 13 ++ .../AddModificationDateToFamilyInternal.java | 13 ++ .../AddModificationDateToFileInternal.java | 13 ++ ...dModificationDateToIndividualInternal.java | 13 ++ ...ificationDateToInterpretationInternal.java | 13 ++ .../AddModificationDateToJobInternal.java | 13 ++ .../AddModificationDateToProjectInternal.java | 14 ++ .../AddModificationDateToSampleInternal.java | 13 ++ .../AddModificationDateToStudyInternal.java | 13 ++ .../catalog/addInterpretationStats.java | 17 ++ .../AddRegistrationDate.java | 10 ++ ...AddRegistrationDateToClinicalInternal.java | 13 ++ .../AddRegistrationDateToCohortInternal.java | 13 ++ .../AddRegistrationDateToFamilyInternal.java | 13 ++ .../AddRegistrationDateToFileInternal.java | 13 ++ ...dRegistrationDateToIndividualInternal.java | 13 ++ ...istrationDateToInterpretationInternal.java | 13 ++ .../AddRegistrationDateToJobInternal.java | 13 ++ .../AddRegistrationDateToProjectInternal.java | 14 ++ .../AddRegistrationDateToSampleInternal.java | 13 ++ .../AddRegistrationDateToStudyInternal.java | 13 ++ .../catalog/addRgaIndexToStudyInternal.java | 17 ++ .../issue_1795/AddFamilyIdsInIndividual.java | 15 ++ .../issue_1796/AddCohortIdsInSample.java | 15 ++ .../CompleteClinicalStatusDataModel.java | 17 ++ .../CompleteCohortStatusDataModel.java | 16 ++ .../CompleteFamilyStatusDataModel.java | 16 ++ .../CompleteFileStatusDataModel.java | 16 ++ .../CompleteIndividualStatusDataModel.java | 16 ++ ...CompleteInterpretationStatusDataModel.java | 16 ++ .../CompleteJobStatusDataModel.java | 16 ++ .../CompletePanelStatusDataModel.java | 16 ++ .../CompleteProjectStatusDataModel.java | 16 ++ .../CompleteSampleStatusDataModel.java | 16 ++ .../CompleteStudyStatusDataModel.java | 16 ++ .../CompleteUserStatusDataModel.java | 16 ++ .../IndividualOntologyTermMigration.java | 17 ++ .../NewStudyDataModelFields.java | 17 ++ .../SampleProcessingAndCollectionChanges.java | 16 ++ .../renameVariableSetFieldFromVariable.java | 18 +++ .../storage/SynchronizeCatalogStorage.java | 17 ++ .../storage/UpdateSampleIndexStatus.java | 17 ++ .../v2/v2_2_1/catalog/AddMissingBiotypes.java | 16 ++ .../v2_2_1/catalog/AddPanelGeneNameIndex.java | 17 ++ .../catalog/InitSharedProjectField.java | 16 ++ ...pleIndexConfigurationAddMissingStatus.java | 15 ++ .../catalog/AddLockedToInterpretation.java | 17 ++ .../v2_3_0/catalog/AddPanelInternalField.java | 17 ++ .../v2_3_0/catalog/AutoIncrementVersion.java | 19 +++ .../catalog/InitSampleIndexConfiguration.java | 18 +++ ...eCellbaseFromProjectInternalToProject.java | 19 +++ .../catalog/RenameDeletedCollections.java | 17 ++ .../RenameDeprecatedVariantStorageToolId.java | 18 +++ .../v2/v2_3_0/catalog/UpdateJWTSecretKey.java | 18 +++ .../storage/AddMissingColumnsToPhoenix.java | 14 ++ ...aseFromProjectInternalToProjectBugFix.java | 19 +++ .../catalog/AddClinicalStatusType_607.java | 18 +++ .../v2_4_0/catalog/AddPrivateDueDate_803.java | 18 +++ .../v2/v2_4_0/catalog/IndexPanelSource.java | 18 +++ .../AddMissingEndDateOnFinishedJobs.java | 20 +++ .../SynchronizeCatalogStorageStatuses.java | 18 +++ .../catalog/SignatureFittingsMigration.java | 18 +++ .../v2_4_2/catalog/AddClinicalDiscussion.java | 17 ++ .../catalog/RecoverProbandSamplesInCases.java | 19 +++ .../v2_4_3/catalog/MigrateToClinicalAcmg.java | 18 +++ .../catalog/ShortenIndexedFieldVariables.java | 17 ++ .../AvoidCaseStatusIdNullMigration.java | 18 +++ .../RemoveBiotypeAllowedKeysMigration.java | 17 ++ .../InvalidateVariantArchivesMigration.java | 16 ++ .../storage/AddCellbaseDataRelease.java | 20 +++ ...ncerRoleAndModeOfInheritanceMigration.java | 20 +++ .../CalculatePedigreeGraphMigration.java | 19 +++ .../MarkUnknownLargestVariantLength.java | 20 +++ .../catalog/RenameCellBaseToken2ApiKey.java | 20 +++ .../v3_0_0/OrganizationMigration.java | 152 ++++++++++++++---- .../opencga/catalog/migration/Migration.java | 5 + .../catalog/migration/MigrationManager.java | 5 + 122 files changed, 2051 insertions(+), 30 deletions(-) create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java rename opencga-app/src/main/java/org/opencb/opencga/app/migrations/{ => v3}/v3_0_0/OrganizationMigration.java (76%) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java index eb6f7ae747c..3f5f7cee80f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java @@ -6,7 +6,7 @@ import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.opencga.app.cli.admin.options.MigrationCommandOptions; import org.opencb.opencga.app.cli.main.io.Table; -import org.opencb.opencga.app.migrations.v3_0_0.OrganizationMigration; +import org.opencb.opencga.app.migrations.v3.v3_0_0.OrganizationMigration; import org.opencb.opencga.catalog.exceptions.CatalogException; import org.opencb.opencga.catalog.managers.CatalogManager; import org.opencb.opencga.catalog.migration.Migration; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java new file mode 100644 index 00000000000..ded1293c0d9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_0_3.catalog.java; + +import org.opencb.opencga.catalog.exceptions.CatalogException; +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "recalculate_roles", description = "Recalculate roles from Family #1763", version = "2.0.3", date = 20210528, + deprecatedSince = "v3.0.0") +public class Migration1 extends MigrationTool { + + @Override + protected void run() throws CatalogException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java new file mode 100644 index 00000000000..a5b971d44fa --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_0_5.catalog.java; + + +import org.opencb.opencga.catalog.exceptions.CatalogException; +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "initialise_groups", description = "Initialise userIds list from groups #1791", version = "2.0.5", date = 20210621, + deprecatedSince = "v3.0.0") +public class initialiseGroups extends MigrationTool { + + @Override + protected void run() throws CatalogException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java new file mode 100644 index 00000000000..b2ffea9be48 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_0_6.catalog; + + +import org.opencb.opencga.catalog.exceptions.CatalogException; +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_file_references_from_sample", description = "Remove deleted file references from samples #1815", version = "2.0.6", + date = 20210901, deprecatedSince = "v3.0.0") +public class removeDeletedFileReferencesFromSample extends MigrationTool { + + @Override + protected void run() throws CatalogException { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java new file mode 100644 index 00000000000..79d15bbfe2d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_12_0.catalog; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_annotation_sets_to_clinical_analysis" , + description = "Add private annotation fields to ClinicalAnalysis documents #TASK-5198", + version = "2.12.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20231116, + deprecatedSince = "v3.0.0" +) +public class AddAnnotationSetsInClinicalAnalysisMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java new file mode 100644 index 00000000000..10effae5a66 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_12_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_clinical_report_data_model" , + description = "Complete Clinical Report data model #TASK-5198", + version = "2.12.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20231128, + deprecatedSince = "v3.0.0" +) +public class CompleteClinicalReportDataModelMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java new file mode 100644 index 00000000000..ecd911181d0 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_indexes", + description = "Add missing indexes", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210928, + deprecatedSince = "v3.0.0") +public class AddMissingIndexes extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java new file mode 100644 index 00000000000..984e214aed5 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panels_to_interpretations", + description = "Add panels to Interpretations #1802", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20210713, + deprecatedSince = "v3.0.0") +public class AddPanelsToInterpretations extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java new file mode 100644 index 00000000000..da1220d2595 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "create_audit_indexes", description = "Create Audit indexes", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210622, + deprecatedSince = "v3.0.0") +public class CreateAuditIndexes extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} + diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java new file mode 100644 index 00000000000..763e3568ae3 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panel_lock", + description = "Add new panelLock to ClinicalAnalysis #1802", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210713, + deprecatedSince = "v3.0.0") +public class PanelLock extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java new file mode 100644 index 00000000000..2f6c73e610a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_rc_version_from_migration_runs", + description = "Remove RC versions from migration runs stored in catalog", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210723, + deprecatedSince = "v3.0.0") +public class RemoveRCVersionsFromMigrationRuns extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java new file mode 100644 index 00000000000..09f6facd0ae --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_datastore_configuration_to_options", description = "Rename project.internal.datastores.variant.configuration to options", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210617, + deprecatedSince = "v3.0.0") +public class RenameDatastoreConfigurationToOptions extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java new file mode 100644 index 00000000000..3a0c9fe1224 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "move_study_clinical_config_to_internal", + description = "Move Study ClinicalConfiguration to internal.configuration", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210708, + deprecatedSince = "v3.0.0") +public class StudyClinicalConfigurationRelocation extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java new file mode 100644 index 00000000000..5a61db123b9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "move_variant_file_stats_to_qc", description = "Move opencga_file_variant_stats annotation set from variable sets to " + + "FileQualityControl", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + patch = 1, + date = 20210614, + deprecatedSince = "v3.0.0") +public class VariantFileStatsRelocation extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java new file mode 100644 index 00000000000..c531bfcbb4f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "build_rga_indexes", description = "Create index for sample RGA status #1693", version = "2.1.0", + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") +public class Migration1 extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java new file mode 100644 index 00000000000..f6fff9fbd50 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "init_userId_group_arrays", description = "Initialise all userIds arrays from groups #1735", version = "2.1.0", + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") +public class Migration2 extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java new file mode 100644 index 00000000000..d449cc8fe86 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "init_ca_panel_arrays", description = "Initialise panels array in Clinical Analysis #1759", version = "2.1.0", + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") +public class Migration3 extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} \ No newline at end of file diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java new file mode 100644 index 00000000000..0093d746f08 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "update_qc_file_sample_fields", description = "Update QC fields from Sample and File #1730", version = "2.1.0", + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210531, patch = 4, deprecatedSince = "v3.0.0") +public class Migration4 extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java new file mode 100644 index 00000000000..a85a315e52a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.storage; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_cellbase_configuration_to_project", description = "Add cellbase configuration from storage-configuration.yml to project.internal.cellbase", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + patch = 3, + date = 20210616, + deprecatedSince = "v3.0.0") +public class AddCellbaseConfigurationToProject extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java new file mode 100644 index 00000000000..3ef78abd74f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.storage; + + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "default_sample_index_configuration", description = "Add a default backward compatible sample index configuration", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + patch = 7, + date = 20210721, + deprecatedSince = "v3.0.0") // Needs to run after StudyClinicalConfigurationRelocation +public class DefaultSampleIndexConfiguration extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java new file mode 100644 index 00000000000..fd70c48eb00 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + + +@Migration(id = "new_clinical_significance_fields", description = "Add new clinical significance fields and combinations for variant storage and solr", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + patch = 1, + date = 20210708, + deprecatedSince = "v3.0.0") +public class NewClinicalSignificanceFields extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java new file mode 100644 index 00000000000..33a03883d93 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_create_interpretation_in_clinical_audit", + description = "Add missing CREATE_INTERPRETATION audits in ClinicalAnalysis", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211227, deprecatedSince = "v3.0.0") +public class AddMissingClinicalAudit extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java new file mode 100644 index 00000000000..2860f82cd1b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_name_field_in_cohort_1902", + description = "Add new name field to Cohort #1902", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220228, deprecatedSince = "v3.0.0") +public class AddNameFieldInCohort extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java new file mode 100644 index 00000000000..32324263f93 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_new_allowed_biotype", + description = "Add new allowed biotype 'guide_RNA', #1856", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20211209, deprecatedSince = "v3.0.0") +public class AddNewAllowedBiotype extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java new file mode 100644 index 00000000000..5e944869f84 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "new_file_internal_index_1850", + description = "Add new FileInternalVariant and FileInternalAlignment index #1850", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211127, deprecatedSince = "v3.0.0") +public class AddNewFileInternalIndex_1850 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java new file mode 100644 index 00000000000..0bf80272613 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_sample_internal_variant_1851", + description = "Add new SampleInternalVariant #1851", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211129, deprecatedSince = "v3.0.0") +public class AddSampleInternalVariant_1851 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java new file mode 100644 index 00000000000..f7acbb2afe1 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "change_interpretation_method", + description = "Remove list of methods from Interpretations #1841", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211112, deprecatedSince = "v3.0.0") +public class ChangeInterpretationMethods extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java new file mode 100644 index 00000000000..ac2d8053f40 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_clinical_variant_evidence_review", + description = "Add new ClinicalVariantEvidenceReview object, #1874", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220112, deprecatedSince = "v3.0.0") +public class ClinicalVariantEvidenceMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java new file mode 100644 index 00000000000..8dce7c69ff9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "delete_unused_variablesets", + description = "Delete unused VariableSets, #1859", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20211210, deprecatedSince = "v3.0.0") +public class DeleteUnusedVariableSets extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java new file mode 100644 index 00000000000..b1884d5db2f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "fix_family_references_in_individual", + description = "Fix Family references, #TASK-489", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220324, deprecatedSince = "v3.0.0") +public class FixFamilyReferences extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java new file mode 100644 index 00000000000..a4e46dde580 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "fix_non_existing_mois_from_panels", + description = "Remove non-existing MOIs from Panels", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20220111, deprecatedSince = "v3.0.0") +public class FixNonExistingMoIFromPanels extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java new file mode 100644 index 00000000000..29c9b704e4b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "improve_ca_quality_control", + description = "Quality control normalize comments and fields #1826", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211001, deprecatedSince = "v3.0.0") +public class ImproveClinicalAnalysisQualityControl extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java new file mode 100644 index 00000000000..e334fc6e892 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "improve_file_quality_control", + description = "Quality control normalize comments and fields #1826", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211001, deprecatedSince = "v3.0.0") +public class ImproveFileQualityControl extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java new file mode 100644 index 00000000000..aa365610323 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "improve_individual_quality_control", + description = "Quality control normalize comments and fields #1826", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211001, deprecatedSince = "v3.0.0") +public class ImproveIndividualQualityControl extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java new file mode 100644 index 00000000000..39b2df0d2a2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "improveVariableSetNamesAndDescriptions", + description = "Improve VariableSet names and descriptions", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211210) +public class ImproveVariableSetNamesAndDescriptions extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java new file mode 100644 index 00000000000..b39fca366f7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_file_docs_from_clinical_analyses", + description = "Store references of File in Clinical Analysis and not full File documents #1837", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211102, deprecatedSince = "v3.0.0") +public class RemoveFileDocsFromCA extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java new file mode 100644 index 00000000000..18d3359497e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_parallel_indexes", + description = "Remove parallel array indexes #CU-20jc4tx", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220310, deprecatedSince = "v3.0.0") +public class RemoveParallelIndexes extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java new file mode 100644 index 00000000000..e51a0b7a664 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_family_quality_control_fields", + description = "Rename FamilyQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211119, deprecatedSince = "v3.0.0") +public class RenameFamilyQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java new file mode 100644 index 00000000000..268d98b7ca2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_file_quality_control_fields", + description = "Rename FileQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211119, deprecatedSince = "v3.0.0") +public class RenameFileQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java new file mode 100644 index 00000000000..59d341e14fb --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_individual_quality_control_fields", + description = "Rename IndividualQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211119, deprecatedSince = "v3.0.0") +public class RenameIndividualQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java new file mode 100644 index 00000000000..c54d782361b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_interpretation_stats_field", + description = "Rename interpretation stats field #1819", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211115, deprecatedSince = "v3.0.0") +public class RenameInterpretationFindingStats extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java new file mode 100644 index 00000000000..48304e52905 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_sample_quality_control_fields", + description = "Rename SampleQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20211119, deprecatedSince = "v3.0.0") +public class RenameSampleQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java new file mode 100644 index 00000000000..b461bda8aa2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_variant_caller_interpretation_configuration", + description = "Add default variant caller Interpretation Study configuration #1822", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20210916, deprecatedSince = "v3.0.0") +public class addDefaultVariantCallerInterpretationStudyConfiguration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java new file mode 100644 index 00000000000..28e32235bb0 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java @@ -0,0 +1,10 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.MigrationTool; + +public abstract class AddInternalLastModified extends MigrationTool { + + protected void addInternalModificationDate(String collection) { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java new file mode 100644 index 00000000000..e206f4ea633 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_clinical.internal", description = "Add internal modificationDate to Clinical #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToClinicalInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java new file mode 100644 index 00000000000..051db7caee2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_cohort.internal", description = "Add internal modificationDate to Cohort #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToCohortInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java new file mode 100644 index 00000000000..dde58535dac --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_family.internal", description = "Add internal modificationDate to Family #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToFamilyInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java new file mode 100644 index 00000000000..169e97a6450 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_file.internal", description = "Add internal modificationDate to File #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToFileInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java new file mode 100644 index 00000000000..b4dac080bc4 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_individual.internal", description = "Add internal modificationDate to Individual #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToIndividualInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java new file mode 100644 index 00000000000..c86eef70177 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_interpretation.internal", description = "Add internal modificationDate to Interpretation #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToInterpretationInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java new file mode 100644 index 00000000000..3afebad7f42 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_job.internal", description = "Add internal modificationDate to Job #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToJobInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java new file mode 100644 index 00000000000..06c7aa94aa4 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_modificationDate_to_project.internal", description = "Add internal modificationDate to Project #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToProjectInternal extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java new file mode 100644 index 00000000000..2d343956073 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_sample.internal", description = "Add internal modificationDate to Sample #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToSampleInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java new file mode 100644 index 00000000000..0f217355e4b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_study.internal", description = "Add internal modificationDate to Study #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToStudyInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java new file mode 100644 index 00000000000..3eee2d60222 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_interpretation_stats", + description = "Add interpretation stats #1819", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20210908, deprecatedSince = "v3.0.0") +public class addInterpretationStats extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java new file mode 100644 index 00000000000..efd1107ba7b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java @@ -0,0 +1,10 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.MigrationTool; + +public abstract class AddRegistrationDate extends MigrationTool { + + protected void addRegistrationDate(String collection) { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java new file mode 100644 index 00000000000..4881ae2a3f7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_clinical.internal", description = "Add registrationDate to Clinical #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToClinicalInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java new file mode 100644 index 00000000000..900d7fa7392 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_cohort.internal", description = "Add registrationDate to Cohort #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToCohortInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java new file mode 100644 index 00000000000..eca622902ff --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_family.internal", description = "Add registrationDate to Family #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToFamilyInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java new file mode 100644 index 00000000000..d8c408a9412 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_file.internal", description = "Add registrationDate to File #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToFileInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java new file mode 100644 index 00000000000..9a52e5c510f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_individual.internal", description = "Add registrationDate to Individual #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToIndividualInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java new file mode 100644 index 00000000000..403e5ab6ca7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_interpretation.internal", description = "Add registrationDate to Interpretation #1804", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToInterpretationInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java new file mode 100644 index 00000000000..fffe8e9d092 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_job.internal", description = "Add registrationDate to Job #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToJobInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java new file mode 100644 index 00000000000..2648228bbdb --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_registrationDate_to_project.internal", description = "Add registrationDate to Project #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToProjectInternal extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java new file mode 100644 index 00000000000..094728d97c2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_sample.internal", description = "Add registrationDate to Sample #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToSampleInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java new file mode 100644 index 00000000000..90201d3d80d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_study.internal", description = "Add registrationDate to Study #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToStudyInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java new file mode 100644 index 00000000000..69939498085 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_rga_index_summary_to_study_internal", + description = "Add RGA Index information to Study Internal #", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210719, deprecatedSince = "v3.0.0") +public class addRgaIndexToStudyInternal extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java new file mode 100644 index 00000000000..343d8f4a578 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1795; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_familyIds_in_individual", description = "Add new list of familyIds in Individual #1795", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, date = 20210630, deprecatedSince = "v3.0.0") +public class AddFamilyIdsInIndividual extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} + diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java new file mode 100644 index 00000000000..60a08ba5c24 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1796; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_cohortIds_in_sample", description = "Add new list of cohortIds in Sample #1796", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, date = 20210706, deprecatedSince = "v3.0.0") +public class AddCohortIdsInSample extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} + diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java new file mode 100644 index 00000000000..868bf9289d9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_clinical_status_models", + description = "Complete Clinical Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, + deprecatedSince = "v3.0.0") +public class CompleteClinicalStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java new file mode 100644 index 00000000000..e5e76661b9c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_cohort_status_models", + description = "Complete Cohort Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteCohortStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java new file mode 100644 index 00000000000..7c91e83876e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_family_status_models", + description = "Complete Family Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteFamilyStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java new file mode 100644 index 00000000000..e1855bdaf34 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_file_status_models", + description = "Complete File Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteFileStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java new file mode 100644 index 00000000000..4111517a8db --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_individual_status_models", + description = "Complete Individual Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteIndividualStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java new file mode 100644 index 00000000000..4d4406e0ffe --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_interpretation_status_models", + description = "Complete Interpretation Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteInterpretationStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java new file mode 100644 index 00000000000..37ca338a57b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_job_status_models", + description = "Complete Job Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteJobStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java new file mode 100644 index 00000000000..6827d44467a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_panel_status_models", + description = "Complete Panel Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompletePanelStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java new file mode 100644 index 00000000000..a703e408fe3 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_project_status_models", + description = "Complete Project Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteProjectStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java new file mode 100644 index 00000000000..c42d6ac6a16 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_sample_status_models", + description = "Complete Sample Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteSampleStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java new file mode 100644 index 00000000000..401e823dc38 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_study_status_models", + description = "Complete Study Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteStudyStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java new file mode 100644 index 00000000000..7fd2e6bb798 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_user_status_models", + description = "Complete User Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteUserStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java new file mode 100644 index 00000000000..14d9bf980be --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issues_1853_1855; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "individual_ontology_term_migration_#1853", + description = "Change sex and ethnicity types for OntologyTermAnnotation #1855", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211203, deprecatedSince = "v3.0.0") +public class IndividualOntologyTermMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java new file mode 100644 index 00000000000..5d8beb45356 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issues_1853_1855; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "new_study_data_model_fields_#1853", + description = "New Study 'sources', 'type' and 'additionalInfo' fields #1853", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211202, deprecatedSince = "v3.0.0") +public class NewStudyDataModelFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java new file mode 100644 index 00000000000..e5fdc1bd5d7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issues_1853_1855; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "sample_source_treatments_#1854", + description = "Sample source, treatments, processing and collection changes #1854", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211201, patch = 2, deprecatedSince = "v3.0.0") +public class SampleProcessingAndCollectionChanges extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java new file mode 100644 index 00000000000..8a7b5d55aa2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_variableset_field", + description = "Rename Variable variableSet field to variables #1823", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20210920, deprecatedSince = "v3.0.0") +public class renameVariableSetFieldFromVariable extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java new file mode 100644 index 00000000000..d7fdc3493fb --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "synchronize_catalog_storage_1850_1851", + description = "Synchronize catalog storage #1850 #1851", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220118, deprecatedSince = "v3.0.0") +public class SynchronizeCatalogStorage extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java new file mode 100644 index 00000000000..c5b1d88f3e7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "update_sample_index_status_1901", + description = " Improve sample-index multi-schema management. #1901", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220302, deprecatedSince = "v3.0.0") +public class UpdateSampleIndexStatus extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java new file mode 100644 index 00000000000..79cda07260b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_biotypes", + description = "Add missing biotypes, #TASK-625", version = "2.2.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220412, deprecatedSince = "v3.0.0") +public class AddMissingBiotypes extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java new file mode 100644 index 00000000000..ef6f593863a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panel_gene_name_index", + description = "Add Panel gene.name index #TASK-602", version = "2.2.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220406, deprecatedSince = "v3.0.0") +public class AddPanelGeneNameIndex extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java new file mode 100644 index 00000000000..a87e7a0344e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "init_shared_project", + description = "Initialise sharedProjects #TASK-702", version = "2.2.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220502, deprecatedSince = "v3.0.0") +public class InitSharedProjectField extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java new file mode 100644 index 00000000000..ceb9b7ec53c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "sample_index_configuration_add_missing_status", + description = "Sample index configuration add missing status #TASK-512", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220328, deprecatedSince = "v3.0.0") +public class SampleIndexConfigurationAddMissingStatus extends StorageMigrationTool { + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java new file mode 100644 index 00000000000..9d012bf9756 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_locked_to_interpretation_TASK-552", + description = "Add new 'locked' field to Interpretation #TASK-552", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220401, + deprecatedSince = "v3.0.0") +public class AddLockedToInterpretation extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java new file mode 100644 index 00000000000..acc9ad7f4b8 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panel_internal_field-TASK_734", + description = "Add 'internal' to Panel data model #TASK-734", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220509, + deprecatedSince = "v3.0.0") +public class AddPanelInternalField extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java new file mode 100644 index 00000000000..1ab7ae34186 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "autoincrement_version_TASK-323", + description = "Reorganise data in new collections (autoincrement version) #TASK-323", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + offline = true, + date = 20220512, + deprecatedSince = "v3.0.0") +public class AutoIncrementVersion extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java new file mode 100644 index 00000000000..58aaee84f5c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "init_sampleIndexConfiguration-TASK550", + description = "Initialise SampleIndexConfiguration in Study internal #TASK-550", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220502, + deprecatedSince = "v3.0.0") +public class InitSampleIndexConfiguration extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java new file mode 100644 index 00000000000..17ef927ac00 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "move_cellbase_from_project_internal_to_project_TASK-354", + description = "Move cellbase from project.internal to project #TASK-354", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220422, + deprecatedSince = "v3.0.0") + +public class MoveCellbaseFromProjectInternalToProject extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java new file mode 100644 index 00000000000..907f44a7542 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_deleted_collections_TASK-359", + description = "Rename deleted collections #TASK-359", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220502, + deprecatedSince = "v3.0.0") +public class RenameDeletedCollections extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java new file mode 100644 index 00000000000..cd9daa6c5b6 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_variant_storage_tool_ids_TASK-705", + description = "Rename variant storage tool ids #TASK-705", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220506, + deprecatedSince = "v3.0.0") +public class RenameDeprecatedVariantStorageToolId extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java new file mode 100644 index 00000000000..5533165c027 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "update_jwt_secret_key_TASK-807", + description = "Update JWT secret key #TASK-807", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220513, + deprecatedSince = "v3.0.0") +public class UpdateJWTSecretKey extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java new file mode 100644 index 00000000000..23b999d338d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id="add_missing_columns_to_phoenix_TASK-789", description = "Add missing 1000G columns to phoenix #TASK-789", + version = "2.3.0", domain = Migration.MigrationDomain.STORAGE, date = 20220614, deprecatedSince = "v3.0.0" +) +public class AddMissingColumnsToPhoenix extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java new file mode 100644 index 00000000000..58342c39b41 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "bugfix_move_cellbase_from_project_internal_to_project_TASK-1100", + description = "Bugfix: Move cellbase from project.internal to project #TASK-1100", version = "2.3.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220620, + deprecatedSince = "v3.0.0") + +public class MoveCellbaseFromProjectInternalToProjectBugFix extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java new file mode 100644 index 00000000000..69a95f79bc6 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_clinical_status_type_TASK-607", + description = "Automatically close cases depending on the new clinical status type #TASK-607", version = "2.4.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220610, + deprecatedSince = "v3.0.0") +public class AddClinicalStatusType_607 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java new file mode 100644 index 00000000000..157ad23070d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_private_dueDate_TASK-803", + description = "Add private _dueDate to ClinicalAnalysis #TASK-803", version = "2.4.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220530, + deprecatedSince = "v3.0.0") +public class AddPrivateDueDate_803 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java new file mode 100644 index 00000000000..4b4839eba62 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "index_panel_source_TASK-473", + description = "Index panel source #TASK-473", version = "2.4.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220530, + deprecatedSince = "v3.0.0") +public class IndexPanelSource extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java new file mode 100644 index 00000000000..55b102ce06e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_10.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_endDate_on_finished_jobs" , + description = "Add missing end date on finished jobs", + version = "2.4.10", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20221026, + deprecatedSince = "v3.0.0" +) +public class AddMissingEndDateOnFinishedJobs extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java new file mode 100644 index 00000000000..c4428b3204c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_11; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "synchronize_catalog_storage_statuses", + description = "Synchronize catalog internal statuses from storage, #TASK-1304", version = "2.4.11", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20221117, + deprecatedSince = "v3.0.0") +public class SynchronizeCatalogStorageStatuses extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java new file mode 100644 index 00000000000..0300dd60eae --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_11.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "signature_fittings" , + description = "Replace fitting for fittings in Signature", + version = "2.4.11", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20221109, + deprecatedSince = "v3.0.0" +) +public class SignatureFittingsMigration extends MigrationTool { + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java new file mode 100644 index 00000000000..a20caa8ac9c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_2.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_clinical_discussion_TASK-1472", + description = "Add ClinicalDiscussion #TASK-1472", version = "2.4.2", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220727, + deprecatedSince = "v3.0.0") +public class AddClinicalDiscussion extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java new file mode 100644 index 00000000000..5fb3e88f9d5 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_2.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "recover_proband_samples_in_cases_TASK-1470", + description = "Recover lost samples in clinical collection #TASK-1470", version = "2.4.2", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220725, + patch = 2, + deprecatedSince = "v3.0.0") +public class RecoverProbandSamplesInCases extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java new file mode 100644 index 00000000000..c92a6789215 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_3.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "migrate_to_clinical_acmg_TASK-1194", + description = "Migrate to ClinicalAcmg #TASK-1194", version = "2.4.3", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220809, + deprecatedSince = "v3.0.0") +public class MigrateToClinicalAcmg extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java new file mode 100644 index 00000000000..2dde0ff7165 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_3.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "shorten_indexed_field_variables-1386", + description = "Shorten indexed field variables #TASK-1386", version = "2.4.3", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220809, + deprecatedSince = "v3.0.0") +public class ShortenIndexedFieldVariables extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java new file mode 100644 index 00000000000..bd1f1a496e0 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_4.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "avoidCaseStatusIdNull-1938", + description = "Avoid nullable status id in Clinical Analysis #TASK-1938", version = "2.4.4", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220914, + deprecatedSince = "v3.0.0") +public class AvoidCaseStatusIdNullMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java new file mode 100644 index 00000000000..05d6967de74 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_4.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_biotype_allowed_keys_TASK-1849", + description = "Remove biotype and consequence type allowed keys from variable sets #TASK-1849", version = "2.4.4", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220905, + deprecatedSince = "v3.0.0") +public class RemoveBiotypeAllowedKeysMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java new file mode 100644 index 00000000000..4283c433ede --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_4.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "invalidate_variant_archives_migration-633", + description = "Invalidate variant archives from variant storage hadoop #TASK-633", version = "2.4.4", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220825, + deprecatedSince = "v3.0.0") +public class InvalidateVariantArchivesMigration extends StorageMigrationTool { + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java new file mode 100644 index 00000000000..4dc66aabcea --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_6_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_cellbase_data_release" , + description = "Add default cellbase data release if missing", + version = "2.6.0", + domain = Migration.MigrationDomain.STORAGE, + language = Migration.MigrationLanguage.JAVA, + patch = 2, + date = 20230104, + deprecatedSince = "v3.0.0" +) +public class AddCellbaseDataRelease extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java new file mode 100644 index 00000000000..f7fcaa12a55 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_7_0.catalog; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "panel_roles_and_modesOfInheritance" , + description = "Change panel cancer.role and modeOfInheritance for cancer.roles[] and modesOfInheritance[]", + version = "2.7.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230117, + deprecatedSince = "v3.0.0" +) +public class CancerRoleAndModeOfInheritanceMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java new file mode 100644 index 00000000000..d3f44141067 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_8_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "calculate_pedigree_graph" , + description = "Calculate Pedigree Graph for all the families", + version = "2.8.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230313, + deprecatedSince = "v3.0.0" +) +public class CalculatePedigreeGraphMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java new file mode 100644 index 00000000000..fdb1a44da12 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_8_6.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "mark_unknown_largest_variant_length" , + description = "Mark as unknown largest variant length", + version = "2.8.6", + domain = Migration.MigrationDomain.STORAGE, + language = Migration.MigrationLanguage.JAVA, + patch = 1, + date = 20230927, + deprecatedSince = "v3.0.0" +) +public class MarkUnknownLargestVariantLength extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java new file mode 100644 index 00000000000..79dd1aab762 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_9_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_cellbase_token_2_api_key" , + description = "Rename CellBase Token to ApiKey", + version = "2.9.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230829, + deprecatedSince = "v3.0.0" +) +public class RenameCellBaseToken2ApiKey extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java similarity index 76% rename from opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java rename to opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index 04c976812c4..d1f749bafe0 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.app.migrations.v3_0_0; +package org.opencb.opencga.app.migrations.v3.v3_0_0; import com.mongodb.client.*; import com.mongodb.client.model.Filters; @@ -28,7 +28,14 @@ import org.opencb.opencga.core.config.Configuration; import org.opencb.opencga.core.models.migration.MigrationRun; import org.opencb.opencga.core.models.organizations.OrganizationCreateParams; - +import org.reflections.Reflections; +import org.reflections.scanners.SubTypesScanner; +import org.reflections.scanners.TypeAnnotationsScanner; +import org.reflections.util.ClasspathHelper; +import org.reflections.util.ConfigurationBuilder; + +import java.lang.reflect.Modifier; +import java.net.URL; import java.nio.file.Files; import java.nio.file.Paths; import java.security.NoSuchAlgorithmException; @@ -102,13 +109,52 @@ private MigrationStatus checkAndInit() throws CatalogException { throw new CatalogException("Please grant write access to path '" + configuration.getWorkspace() + "'"); } - // TODO: Check last migration is 2.2.?? + Set> availableMigrations = getAvailableMigrations(); + + // Check all previous v2.x migrations have been run successfully MongoCollection migrationCol = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION); - long count = migrationCol.countDocuments(Filters.in("status", MigrationRun.MigrationStatus.PENDING, + long count = migrationCol.countDocuments(); + // We take out 1 to the availableMigrations.size() because it will consider the present migration, which is not part of the check + logger.debug("Found '{}' Java migrations", availableMigrations.size() - 1); + logger.debug("Found '{}' migrations registered in the database", count); + if (count < availableMigrations.size() - 1) { + Set migrations = new HashSet<>(); + for (Class availableMigration : availableMigrations) { + Migration annotation = availableMigration.getAnnotation(Migration.class); + // Only consider previous migrations, not the present one + if (!annotation.version().equals("3.0.0")) { + migrations.add(annotation.id() + ":v" + annotation.version()); + } + } + + Set processedMigrations = new HashSet<>(); + Set onlyInJava = new HashSet<>(); + Set onlyInDB = new HashSet<>(); + migrationCol.find().forEach((document) -> { + String migrationId = document.getString("id") + ":v" + document.getString("version"); + processedMigrations.add(migrationId); + if (!migrations.contains(migrationId)) { + onlyInDB.add(migrationId); + } + }); + for (String migration : migrations) { + if (!processedMigrations.contains(migration)) { + onlyInJava.add(migration); + } + } + logger.debug("Migrations not registered in the database: {}", String.join(", ", onlyInJava)); + logger.debug("Migrations only found in the DB: {}", String.join(", ", onlyInDB)); + + throw new CatalogException("Please check past migrations before moving to v3.0.0. Found " + + (availableMigrations.size() -1 - count) + " missing migrations available."); + } + + count = migrationCol.countDocuments(Filters.in("status", MigrationRun.MigrationStatus.PENDING, MigrationRun.MigrationStatus.ON_HOLD, MigrationRun.MigrationStatus.ERROR)); if (count > 0) { - throw new CatalogException("Please check past migrations. Found migrations with status '" + MigrationRun.MigrationStatus.PENDING - + "', '" + MigrationRun.MigrationStatus.ON_HOLD + "', or '" + MigrationRun.MigrationStatus.ERROR + "'."); + throw new CatalogException("Please check past migrations. Found " + count + " migrations with status '" + + MigrationRun.MigrationStatus.PENDING + "', '" + MigrationRun.MigrationStatus.ON_HOLD + "', or '" + + MigrationRun.MigrationStatus.ERROR + "'."); } // Retrieve all users with data @@ -226,25 +272,23 @@ protected void run() throws Exception { queryMongo(oldUserCollection, Filters.eq("id", ParamConstants.OPENCGA_USER_ID), Projections.exclude("_id"), document -> { String organizationId = ParamConstants.ADMIN_ORGANIZATION; try { - MongoCollection userCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION); - MongoCollection projectCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION); - MongoCollection studyCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION); - MongoCollection fileCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.FILE_COLLECTION); + MongoDatabase orgDatabase = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb(); + + MongoCollection userCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION); + MongoCollection projectCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION); + MongoCollection studyCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION); + MongoCollection fileCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.FILE_COLLECTION); + MongoCollection migrationCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION); // Empty data from collections with default data userCollection.deleteMany(new Document()); projectCollection.deleteMany(new Document()); studyCollection.deleteMany(new Document()); fileCollection.deleteMany(new Document()); + migrationCollection.deleteMany(new Document()); // Replace user in organization userCollection.insertOne(document); - MongoDatabase orgDatabase = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb(); - // Extract projects List projects = document.getList("projects", Document.class); for (Document project : projects) { @@ -280,12 +324,16 @@ protected void run() throws Exception { replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION), orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION)); - oldStudyCol.deleteOne(Filters.eq("uid", studyUid)); }); - } + // Copy migration history + MongoCollection oldMigrationCollection = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION); + logger.info("Copying Migration data from {} to {}", oldMigrationCollection.getNamespace(), migrationCollection.getNamespace()); + migrateCollection(oldMigrationCollection, migrationCollection, new Document(), Projections.exclude("_id"), + (tmpDocument, bulk) -> bulk.add(new InsertOneModel<>(tmpDocument))); + // Remove user from the source database oldUserCollection.deleteOne(Filters.eq("id", ParamConstants.OPENCGA_USER_ID)); } catch (CatalogException e) { @@ -302,17 +350,12 @@ protected void run() throws Exception { // Rename database to main organization database MongoDataStore adminDatastore = mongoDBAdaptorFactory.getMongoManager().get("admin", mongoDBAdaptorFactory.getMongoDbConfiguration()); for (String collectionName : oldDatastore.getCollectionNames()) { - if (!OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION.equals(collectionName)) { - logger.info("Renaming collection {} to {}", oldDatabase + "." + collectionName, newDatabase + "." + collectionName); - adminDatastore.getDb().runCommand(new Document() - .append("renameCollection", oldDatabase + "." + collectionName) - .append("to", newDatabase + "." + collectionName) - .append("dropTarget", true) - ); - } else { - // Remove collections - oldDatastore.getDb().getCollection(collectionName).drop(); - } + logger.info("Renaming collection {} to {}", oldDatabase + "." + collectionName, newDatabase + "." + collectionName); + adminDatastore.getDb().runCommand(new Document() + .append("renameCollection", oldDatabase + "." + collectionName) + .append("to", newDatabase + "." + collectionName) + .append("dropTarget", true) + ); } CatalogIOManager ioManager = new CatalogIOManager(configuration); @@ -395,6 +438,57 @@ protected void run() throws Exception { Updates.set("configuration.authenticationOrigins", authOrigins) )); } + + // Skip current migration for both organizations + catalogManager.getMigrationManager().skipPendingMigrations(ParamConstants.ADMIN_ORGANIZATION, opencgaToken); + catalogManager.getMigrationManager().skipPendingMigrations(organizationId, opencgaToken); + } + + Set> getAvailableMigrations() { + Reflections reflections = new Reflections(new ConfigurationBuilder() + .setScanners( + new SubTypesScanner(), + new TypeAnnotationsScanner().filterResultsBy(s -> StringUtils.equals(s, Migration.class.getName())) + ) + .addUrls(getUrls()) + .filterInputsBy(input -> input != null && input.endsWith(".class")) + ); + + Set> migrations = reflections.getSubTypesOf(MigrationTool.class); + migrations.removeIf(c -> Modifier.isAbstract(c.getModifiers())); + + // Validate unique ids and rank + Map> versionIdMap = new HashMap<>(); + + for (Class migration : migrations) { + Migration annotation = migration.getAnnotation(Migration.class); + + if (!versionIdMap.containsKey(annotation.version())) { + versionIdMap.put(annotation.version(), new HashSet<>()); + } + if (versionIdMap.get(annotation.version()).contains(annotation.id())) { + throw new IllegalStateException("Found duplicated migration id '" + annotation.id() + "' in version " + + annotation.version()); + } + if (String.valueOf(annotation.date()).length() != 8) { + throw new IllegalStateException("Found unexpected date '" + annotation.date() + "' in migration '" + annotation.id() + + "' from version " + annotation.version() + ". Date format is YYYYMMDD."); + } + versionIdMap.get(annotation.version()).add(annotation.id()); + } + + return migrations; + } + + private Collection getUrls() { + Collection urls = new LinkedList<>(); + for (URL url : ClasspathHelper.forPackage("org.opencb.opencga")) { + String name = url.getPath().substring(url.getPath().lastIndexOf('/') + 1); + if (name.isEmpty() || (name.contains("opencga") && !name.contains("opencga-hadoop-shaded"))) { + urls.add(url); + } + } + return urls; } private void replicateData(long studyUid, MongoCollection sourceCol, MongoCollection targetCol) { diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java index 7fb3b1dabf8..3c5ddea26d3 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java @@ -54,6 +54,11 @@ */ boolean manual() default false; + /** + * @return the version when the migration was deprecated. + */ + String deprecatedSince() default ""; + enum MigrationDomain { CATALOG, STORAGE diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java index 7809f4fb0f7..543e378cba3 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java @@ -622,6 +622,11 @@ private MigrationRun run(String organizationId, Class r String token) throws MigrationException { Migration annotation = getMigrationAnnotation(runnableMigration); + if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { + throw new MigrationException("Migration '" + annotation.id() + "' can't be run since version '" + annotation.deprecatedSince() + + "'. Please, run this migration from a previous OpenCGA version."); + } + MigrationTool migrationTool; try { migrationTool = runnableMigration.newInstance(); From bc569c3c9246a18b3329b4c73782a7eb6022b264 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 16:50:32 +0200 Subject: [PATCH 24/59] release.yml; Delete old dependency for release step #TASK-6185 --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 28e0bfcfbaf..881b60add10 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -78,7 +78,7 @@ jobs: # Add the release job that depends on all the previous jobs release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build-hdp, deploy-docker-hdp, build-hdi, deploy-docker-hdi, build-emr, deploy-docker-emr, build-emr613, deploy-docker-emr613, deploy-maven, deploy-docker, deploy-python ] + needs: [ build-hdp, deploy-docker-hdp, build-hdi, deploy-docker-hdi, build-emr, deploy-docker-emr, build-emr613, deploy-docker-emr613, deploy-maven, deploy-python ] with: artifact: build-folder file: | From ec4691c21839f30b13dc97d9d639e7a88f16eaf3 Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 20 May 2024 16:57:48 +0200 Subject: [PATCH 25/59] app: remove v from deprecatedSince version field, #TASK-6256 --- .../app/migrations/v2/v2_0_3/catalog/java/Migration1.java | 2 +- .../app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java | 2 +- .../v2_0_6/catalog/removeDeletedFileReferencesFromSample.java | 2 +- .../catalog/AddAnnotationSetsInClinicalAnalysisMigration.java | 2 +- .../catalog/CompleteClinicalReportDataModelMigration.java | 2 +- .../migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java | 2 +- .../v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java | 2 +- .../migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/java/PanelLock.java | 2 +- .../v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java | 2 +- .../catalog/java/RenameDatastoreConfigurationToOptions.java | 2 +- .../catalog/java/StudyClinicalConfigurationRelocation.java | 2 +- .../v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java | 2 +- .../v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java | 2 +- .../v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java | 2 +- .../v2/v2_1_0/storage/NewClinicalSignificanceFields.java | 2 +- .../migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java | 2 +- .../v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java | 2 +- .../v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java | 2 +- .../v2/v2_2_0/catalog/ChangeInterpretationMethods.java | 2 +- .../v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java | 2 +- .../migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java | 2 +- .../v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java | 2 +- .../v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java | 2 +- .../migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java | 2 +- .../v2/v2_2_0/catalog/ImproveIndividualQualityControl.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java | 2 +- .../v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java | 2 +- .../v2/v2_2_0/catalog/RenameFileQualityControlFields.java | 2 +- .../v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java | 2 +- .../v2/v2_2_0/catalog/RenameInterpretationFindingStats.java | 2 +- .../v2/v2_2_0/catalog/RenameSampleQualityControlFields.java | 2 +- ...addDefaultVariantCallerInterpretationStudyConfiguration.java | 2 +- .../AddModificationDateToClinicalInternal.java | 2 +- .../AddModificationDateToCohortInternal.java | 2 +- .../AddModificationDateToFamilyInternal.java | 2 +- .../AddModificationDateToFileInternal.java | 2 +- .../AddModificationDateToIndividualInternal.java | 2 +- .../AddModificationDateToInterpretationInternal.java | 2 +- .../AddModificationDateToJobInternal.java | 2 +- .../AddModificationDateToProjectInternal.java | 2 +- .../AddModificationDateToSampleInternal.java | 2 +- .../AddModificationDateToStudyInternal.java | 2 +- .../migrations/v2/v2_2_0/catalog/addInterpretationStats.java | 2 +- .../AddRegistrationDateToClinicalInternal.java | 2 +- .../AddRegistrationDateToCohortInternal.java | 2 +- .../AddRegistrationDateToFamilyInternal.java | 2 +- .../addRegistrationDate/AddRegistrationDateToFileInternal.java | 2 +- .../AddRegistrationDateToIndividualInternal.java | 2 +- .../AddRegistrationDateToInterpretationInternal.java | 2 +- .../addRegistrationDate/AddRegistrationDateToJobInternal.java | 2 +- .../AddRegistrationDateToProjectInternal.java | 2 +- .../AddRegistrationDateToSampleInternal.java | 2 +- .../addRegistrationDate/AddRegistrationDateToStudyInternal.java | 2 +- .../v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java | 2 +- .../v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java | 2 +- .../v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java | 2 +- .../catalog/issue_1849/CompleteClinicalStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteCohortStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteFamilyStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteIndividualStatusDataModel.java | 2 +- .../issue_1849/CompleteInterpretationStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteProjectStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteSampleStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java | 2 +- .../issues_1853_1855/IndividualOntologyTermMigration.java | 2 +- .../catalog/issues_1853_1855/NewStudyDataModelFields.java | 2 +- .../issues_1853_1855/SampleProcessingAndCollectionChanges.java | 2 +- .../v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java | 2 +- .../migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java | 2 +- .../migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java | 2 +- .../app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java | 2 +- .../app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java | 2 +- .../migrations/v2/v2_2_1/catalog/InitSharedProjectField.java | 2 +- .../storage/SampleIndexConfigurationAddMissingStatus.java | 2 +- .../migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java | 2 +- .../app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java | 2 +- .../app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java | 2 +- .../v2/v2_3_0/catalog/InitSampleIndexConfiguration.java | 2 +- .../catalog/MoveCellbaseFromProjectInternalToProject.java | 2 +- .../migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java | 2 +- .../v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java | 2 +- .../app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java | 2 +- .../v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java | 2 +- .../catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java | 2 +- .../migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java | 2 +- .../app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java | 2 +- .../app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java | 2 +- .../v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java | 2 +- .../v2/v2_4_11/SynchronizeCatalogStorageStatuses.java | 2 +- .../v2/v2_4_11/catalog/SignatureFittingsMigration.java | 2 +- .../app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java | 2 +- .../v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java | 2 +- .../app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java | 2 +- .../v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java | 2 +- .../v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java | 2 +- .../v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java | 2 +- .../v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java | 2 +- .../migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java | 2 +- .../v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java | 2 +- .../v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java | 2 +- .../v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java | 2 +- .../v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java | 2 +- 115 files changed, 115 insertions(+), 115 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java index ded1293c0d9..425fd72353f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "recalculate_roles", description = "Recalculate roles from Family #1763", version = "2.0.3", date = 20210528, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class Migration1 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java index a5b971d44fa..0c0273e7820 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java @@ -6,7 +6,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "initialise_groups", description = "Initialise userIds list from groups #1791", version = "2.0.5", date = 20210621, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class initialiseGroups extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java index b2ffea9be48..b99e0a9f1d5 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java @@ -6,7 +6,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "remove_file_references_from_sample", description = "Remove deleted file references from samples #1815", version = "2.0.6", - date = 20210901, deprecatedSince = "v3.0.0") + date = 20210901, deprecatedSince = "3.0.0") public class removeDeletedFileReferencesFromSample extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java index 79d15bbfe2d..06a78900ab0 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java @@ -10,7 +10,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20231116, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class AddAnnotationSetsInClinicalAnalysisMigration extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java index 10effae5a66..96f702d96f4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20231128, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class CompleteClinicalReportDataModelMigration extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java index ecd911181d0..7efdea6a56a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210928, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddMissingIndexes extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java index 984e214aed5..a35f794d130 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20210713, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddPanelsToInterpretations extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java index da1220d2595..48cd8ce2f3b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java @@ -8,7 +8,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210622, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class CreateAuditIndexes extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java index 763e3568ae3..747feb3bbcb 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210713, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class PanelLock extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java index 2f6c73e610a..58625266d9b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210723, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RemoveRCVersionsFromMigrationRuns extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java index 09f6facd0ae..452e99d627f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java @@ -8,7 +8,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210617, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RenameDatastoreConfigurationToOptions extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java index 3a0c9fe1224..18e6272d7a6 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java @@ -10,7 +10,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210708, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class StudyClinicalConfigurationRelocation extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java index 5a61db123b9..f37d46cb9f2 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.STORAGE, patch = 1, date = 20210614, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class VariantFileStatsRelocation extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java index c531bfcbb4f..0530e369b04 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "build_rga_indexes", description = "Create index for sample RGA status #1693", version = "2.1.0", - language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "3.0.0") public class Migration1 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java index f6fff9fbd50..a0c0938de73 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "init_userId_group_arrays", description = "Initialise all userIds arrays from groups #1735", version = "2.1.0", - language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "3.0.0") public class Migration2 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java index d449cc8fe86..9b21dcdbc9c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "init_ca_panel_arrays", description = "Initialise panels array in Clinical Analysis #1759", version = "2.1.0", - language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "3.0.0") public class Migration3 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java index 0093d746f08..ef72a501f44 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "update_qc_file_sample_fields", description = "Update QC fields from Sample and File #1730", version = "2.1.0", - language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210531, patch = 4, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210531, patch = 4, deprecatedSince = "3.0.0") public class Migration4 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java index a85a315e52a..5dac53d4688 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.STORAGE, patch = 3, date = 20210616, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddCellbaseConfigurationToProject extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java index 3ef78abd74f..7b33bd7d709 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.STORAGE, patch = 7, date = 20210721, - deprecatedSince = "v3.0.0") // Needs to run after StudyClinicalConfigurationRelocation + deprecatedSince = "3.0.0") // Needs to run after StudyClinicalConfigurationRelocation public class DefaultSampleIndexConfiguration extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java index fd70c48eb00..b4d243ee279 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.STORAGE, patch = 1, date = 20210708, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class NewClinicalSignificanceFields extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java index 33a03883d93..7008388f42e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java @@ -7,7 +7,7 @@ description = "Add missing CREATE_INTERPRETATION audits in ClinicalAnalysis", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211227, deprecatedSince = "v3.0.0") + date = 20211227, deprecatedSince = "3.0.0") public class AddMissingClinicalAudit extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java index 2860f82cd1b..1f23c1b331c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java @@ -7,7 +7,7 @@ description = "Add new name field to Cohort #1902", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220228, deprecatedSince = "v3.0.0") + date = 20220228, deprecatedSince = "3.0.0") public class AddNameFieldInCohort extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java index 32324263f93..1aa51b53014 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20211209, deprecatedSince = "v3.0.0") + date = 20211209, deprecatedSince = "3.0.0") public class AddNewAllowedBiotype extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java index 5e944869f84..099dd960790 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java @@ -7,7 +7,7 @@ description = "Add new FileInternalVariant and FileInternalAlignment index #1850", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211127, deprecatedSince = "v3.0.0") + date = 20211127, deprecatedSince = "3.0.0") public class AddNewFileInternalIndex_1850 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java index 0bf80272613..21218e3222d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java @@ -7,7 +7,7 @@ description = "Add new SampleInternalVariant #1851", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211129, deprecatedSince = "v3.0.0") + date = 20211129, deprecatedSince = "3.0.0") public class AddSampleInternalVariant_1851 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java index f7acbb2afe1..7731a4510fe 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java @@ -7,7 +7,7 @@ description = "Remove list of methods from Interpretations #1841", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211112, deprecatedSince = "v3.0.0") + date = 20211112, deprecatedSince = "3.0.0") public class ChangeInterpretationMethods extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java index ac2d8053f40..6de2592fbaa 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java @@ -7,7 +7,7 @@ description = "Add new ClinicalVariantEvidenceReview object, #1874", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220112, deprecatedSince = "v3.0.0") + date = 20220112, deprecatedSince = "3.0.0") public class ClinicalVariantEvidenceMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java index 8dce7c69ff9..7ddea73508c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20211210, deprecatedSince = "v3.0.0") + date = 20211210, deprecatedSince = "3.0.0") public class DeleteUnusedVariableSets extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java index b1884d5db2f..fd160750475 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java @@ -7,7 +7,7 @@ description = "Fix Family references, #TASK-489", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220324, deprecatedSince = "v3.0.0") + date = 20220324, deprecatedSince = "3.0.0") public class FixFamilyReferences extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java index a4e46dde580..d642d8499af 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20220111, deprecatedSince = "v3.0.0") + date = 20220111, deprecatedSince = "3.0.0") public class FixNonExistingMoIFromPanels extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java index 29c9b704e4b..b7ff196615b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java @@ -7,7 +7,7 @@ description = "Quality control normalize comments and fields #1826", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211001, deprecatedSince = "v3.0.0") + date = 20211001, deprecatedSince = "3.0.0") public class ImproveClinicalAnalysisQualityControl extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java index e334fc6e892..16043d38b26 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java @@ -7,7 +7,7 @@ description = "Quality control normalize comments and fields #1826", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211001, deprecatedSince = "v3.0.0") + date = 20211001, deprecatedSince = "3.0.0") public class ImproveFileQualityControl extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java index aa365610323..b3350e099f3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java @@ -7,7 +7,7 @@ description = "Quality control normalize comments and fields #1826", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211001, deprecatedSince = "v3.0.0") + date = 20211001, deprecatedSince = "3.0.0") public class ImproveIndividualQualityControl extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java index b39fca366f7..af85465d69e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java @@ -7,7 +7,7 @@ description = "Store references of File in Clinical Analysis and not full File documents #1837", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211102, deprecatedSince = "v3.0.0") + date = 20211102, deprecatedSince = "3.0.0") public class RemoveFileDocsFromCA extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java index 18d3359497e..7b00543f9a5 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java @@ -7,7 +7,7 @@ description = "Remove parallel array indexes #CU-20jc4tx", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220310, deprecatedSince = "v3.0.0") + date = 20220310, deprecatedSince = "3.0.0") public class RemoveParallelIndexes extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java index e51a0b7a664..821fb020a28 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java @@ -7,7 +7,7 @@ description = "Rename FamilyQualityControl fields #1844", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211119, deprecatedSince = "v3.0.0") + date = 20211119, deprecatedSince = "3.0.0") public class RenameFamilyQualityControlFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java index 268d98b7ca2..c3c5d4ff7f8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java @@ -7,7 +7,7 @@ description = "Rename FileQualityControl fields #1844", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211119, deprecatedSince = "v3.0.0") + date = 20211119, deprecatedSince = "3.0.0") public class RenameFileQualityControlFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java index 59d341e14fb..6df5fc82131 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java @@ -7,7 +7,7 @@ description = "Rename IndividualQualityControl fields #1844", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211119, deprecatedSince = "v3.0.0") + date = 20211119, deprecatedSince = "3.0.0") public class RenameIndividualQualityControlFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java index c54d782361b..bd4ad966774 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java @@ -7,7 +7,7 @@ description = "Rename interpretation stats field #1819", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211115, deprecatedSince = "v3.0.0") + date = 20211115, deprecatedSince = "3.0.0") public class RenameInterpretationFindingStats extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java index 48304e52905..0c5b36cdf93 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20211119, deprecatedSince = "v3.0.0") + date = 20211119, deprecatedSince = "3.0.0") public class RenameSampleQualityControlFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java index b461bda8aa2..9a43d99ac53 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java @@ -7,7 +7,7 @@ description = "Add default variant caller Interpretation Study configuration #1822", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210916, deprecatedSince = "v3.0.0") + date = 20210916, deprecatedSince = "3.0.0") public class addDefaultVariantCallerInterpretationStudyConfiguration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java index e206f4ea633..c127e7b2695 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_clinical.internal", description = "Add internal modificationDate to Clinical #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToClinicalInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java index 051db7caee2..0aaccf98b74 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_cohort.internal", description = "Add internal modificationDate to Cohort #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToCohortInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java index dde58535dac..914b6351a0c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_family.internal", description = "Add internal modificationDate to Family #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToFamilyInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java index 169e97a6450..7ffc3cf7f37 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_file.internal", description = "Add internal modificationDate to File #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToFileInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java index b4dac080bc4..05ca7bc522d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_individual.internal", description = "Add internal modificationDate to Individual #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToIndividualInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java index c86eef70177..9340231dfde 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_interpretation.internal", description = "Add internal modificationDate to Interpretation #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToInterpretationInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java index 3afebad7f42..543e02f328e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_job.internal", description = "Add internal modificationDate to Job #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToJobInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java index 06c7aa94aa4..82a3142a222 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java @@ -5,7 +5,7 @@ @Migration(id = "add_modificationDate_to_project.internal", description = "Add internal modificationDate to Project #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToProjectInternal extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java index 2d343956073..875bbaa26a7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_sample.internal", description = "Add internal modificationDate to Sample #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToSampleInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java index 0f217355e4b..987a742cb5d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_study.internal", description = "Add internal modificationDate to Study #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToStudyInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java index 3eee2d60222..ac1c112d0a1 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20210908, deprecatedSince = "v3.0.0") + date = 20210908, deprecatedSince = "3.0.0") public class addInterpretationStats extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java index 4881ae2a3f7..14a48ed90be 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_clinical.internal", description = "Add registrationDate to Clinical #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToClinicalInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java index 900d7fa7392..a7dcf145b33 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_cohort.internal", description = "Add registrationDate to Cohort #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToCohortInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java index eca622902ff..66f375ce955 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_family.internal", description = "Add registrationDate to Family #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToFamilyInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java index d8c408a9412..cfa29de842a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_file.internal", description = "Add registrationDate to File #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToFileInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java index 9a52e5c510f..58d233f6d7f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_individual.internal", description = "Add registrationDate to Individual #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToIndividualInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java index 403e5ab6ca7..115b4e4fc6c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_interpretation.internal", description = "Add registrationDate to Interpretation #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToInterpretationInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java index fffe8e9d092..c56124cdda6 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_job.internal", description = "Add registrationDate to Job #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToJobInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java index 2648228bbdb..ae3f65b70d9 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java @@ -5,7 +5,7 @@ @Migration(id = "add_registrationDate_to_project.internal", description = "Add registrationDate to Project #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToProjectInternal extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java index 094728d97c2..e317c667a98 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_sample.internal", description = "Add registrationDate to Sample #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToSampleInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java index 90201d3d80d..7d036f65bc4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_study.internal", description = "Add registrationDate to Study #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToStudyInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java index 69939498085..d995f4ba97f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 1, - date = 20210719, deprecatedSince = "v3.0.0") + date = 20210719, deprecatedSince = "3.0.0") public class addRgaIndexToStudyInternal extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java index 343d8f4a578..25e93347812 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "add_familyIds_in_individual", description = "Add new list of familyIds in Individual #1795", version = "2.2.0", - language = Migration.MigrationLanguage.JAVA, date = 20210630, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVA, date = 20210630, deprecatedSince = "3.0.0") public class AddFamilyIdsInIndividual extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java index 60a08ba5c24..b6d1d3ff298 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "add_cohortIds_in_sample", description = "Add new list of cohortIds in Sample #1796", version = "2.2.0", - language = Migration.MigrationLanguage.JAVA, date = 20210706, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVA, date = 20210706, deprecatedSince = "3.0.0") public class AddCohortIdsInSample extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java index 868bf9289d9..fcb2313cb39 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20211126, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class CompleteClinicalStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java index e5e76661b9c..692e58cc397 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Cohort Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteCohortStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java index 7c91e83876e..5c1bfbfc2aa 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Family Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteFamilyStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java index e1855bdaf34..c1c84058b5c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete File Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteFileStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java index 4111517a8db..cb7fda578ca 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Individual Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteIndividualStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java index 4d4406e0ffe..dad8a984810 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Interpretation Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteInterpretationStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java index 37ca338a57b..4a08d4695e7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Job Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteJobStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java index 6827d44467a..8311dcc2153 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Panel Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompletePanelStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java index a703e408fe3..09ce8a4fc88 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Project Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteProjectStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java index c42d6ac6a16..bb9b3e54086 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Sample Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteSampleStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java index 401e823dc38..8b119d92cc4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Study Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteStudyStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java index 7fd2e6bb798..937e6d3f9fb 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete User Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteUserStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java index 14d9bf980be..9a5eb6cec84 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java @@ -7,7 +7,7 @@ description = "Change sex and ethnicity types for OntologyTermAnnotation #1855", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211203, deprecatedSince = "v3.0.0") + date = 20211203, deprecatedSince = "3.0.0") public class IndividualOntologyTermMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java index 5d8beb45356..e6659fb4ad7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java @@ -7,7 +7,7 @@ description = "New Study 'sources', 'type' and 'additionalInfo' fields #1853", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211202, deprecatedSince = "v3.0.0") + date = 20211202, deprecatedSince = "3.0.0") public class NewStudyDataModelFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java index e5fdc1bd5d7..a054a6a0566 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java @@ -7,7 +7,7 @@ description = "Sample source, treatments, processing and collection changes #1854", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211201, patch = 2, deprecatedSince = "v3.0.0") + date = 20211201, patch = 2, deprecatedSince = "3.0.0") public class SampleProcessingAndCollectionChanges extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java index 8a7b5d55aa2..bd3f00937e9 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java @@ -8,7 +8,7 @@ description = "Rename Variable variableSet field to variables #1823", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210920, deprecatedSince = "v3.0.0") + date = 20210920, deprecatedSince = "3.0.0") public class renameVariableSetFieldFromVariable extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java index d7fdc3493fb..609d50c915a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java @@ -7,7 +7,7 @@ description = "Synchronize catalog storage #1850 #1851", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, - date = 20220118, deprecatedSince = "v3.0.0") + date = 20220118, deprecatedSince = "3.0.0") public class SynchronizeCatalogStorage extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java index c5b1d88f3e7..2965c326760 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java @@ -7,7 +7,7 @@ description = " Improve sample-index multi-schema management. #1901", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, - date = 20220302, deprecatedSince = "v3.0.0") + date = 20220302, deprecatedSince = "3.0.0") public class UpdateSampleIndexStatus extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java index 79cda07260b..7173a402e96 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java @@ -7,7 +7,7 @@ description = "Add missing biotypes, #TASK-625", version = "2.2.1", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220412, deprecatedSince = "v3.0.0") + date = 20220412, deprecatedSince = "3.0.0") public class AddMissingBiotypes extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java index ef6f593863a..0cd9ba5ff1b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java @@ -7,7 +7,7 @@ description = "Add Panel gene.name index #TASK-602", version = "2.2.1", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220406, deprecatedSince = "v3.0.0") + date = 20220406, deprecatedSince = "3.0.0") public class AddPanelGeneNameIndex extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java index a87e7a0344e..49b4b252f60 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java @@ -7,7 +7,7 @@ description = "Initialise sharedProjects #TASK-702", version = "2.2.1", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220502, deprecatedSince = "v3.0.0") + date = 20220502, deprecatedSince = "3.0.0") public class InitSharedProjectField extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java index ceb9b7ec53c..cd11e50f8aa 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java @@ -7,7 +7,7 @@ description = "Sample index configuration add missing status #TASK-512", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, - date = 20220328, deprecatedSince = "v3.0.0") + date = 20220328, deprecatedSince = "3.0.0") public class SampleIndexConfigurationAddMissingStatus extends StorageMigrationTool { @Override protected void run() throws Exception { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java index 9d012bf9756..52a95ccf66e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220401, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddLockedToInterpretation extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java index acc9ad7f4b8..e2edbf68060 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220509, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddPanelInternalField extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java index 1ab7ae34186..8cbd5a59eef 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, offline = true, date = 20220512, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AutoIncrementVersion extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java index 58aaee84f5c..81d3f1e8628 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220502, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class InitSampleIndexConfiguration extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java index 17ef927ac00..9f4f30213fb 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220422, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class MoveCellbaseFromProjectInternalToProject extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java index 907f44a7542..2a1532c6da4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220502, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RenameDeletedCollections extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java index cd9daa6c5b6..b39a56cdbec 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220506, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RenameDeprecatedVariantStorageToolId extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java index 5533165c027..be328bbeb6a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220513, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class UpdateJWTSecretKey extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java index 23b999d338d..df2e308a727 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java @@ -4,7 +4,7 @@ import org.opencb.opencga.catalog.migration.Migration; @Migration(id="add_missing_columns_to_phoenix_TASK-789", description = "Add missing 1000G columns to phoenix #TASK-789", - version = "2.3.0", domain = Migration.MigrationDomain.STORAGE, date = 20220614, deprecatedSince = "v3.0.0" + version = "2.3.0", domain = Migration.MigrationDomain.STORAGE, date = 20220614, deprecatedSince = "3.0.0" ) public class AddMissingColumnsToPhoenix extends StorageMigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java index 58342c39b41..2c645980391 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220620, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class MoveCellbaseFromProjectInternalToProjectBugFix extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java index 69a95f79bc6..8f3886c50e8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220610, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddClinicalStatusType_607 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java index 157ad23070d..6dcab05694a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220530, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddPrivateDueDate_803 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java index 4b4839eba62..af93d04de7d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220530, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class IndexPanelSource extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java index 55b102ce06e..0759d4c7bf1 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20221026, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class AddMissingEndDateOnFinishedJobs extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java index c4428b3204c..e2fb99933cf 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, date = 20221117, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class SynchronizeCatalogStorageStatuses extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java index 0300dd60eae..ec0b49baae3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20221109, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class SignatureFittingsMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java index a20caa8ac9c..8e5825e3de7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220727, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddClinicalDiscussion extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java index 5fb3e88f9d5..aba0267d65b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, date = 20220725, patch = 2, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RecoverProbandSamplesInCases extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java index c92a6789215..7951810b105 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220809, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class MigrateToClinicalAcmg extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java index 2dde0ff7165..2d4e2cb14a8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220809, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class ShortenIndexedFieldVariables extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java index bd1f1a496e0..e26df11c03c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220914, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AvoidCaseStatusIdNullMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java index 05d6967de74..07a19a12fdb 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220905, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RemoveBiotypeAllowedKeysMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java index 4283c433ede..069e1a86e6e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, date = 20220825, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class InvalidateVariantArchivesMigration extends StorageMigrationTool { @Override protected void run() throws Exception { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java index 4dc66aabcea..06f1d871a80 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java @@ -10,7 +10,7 @@ language = Migration.MigrationLanguage.JAVA, patch = 2, date = 20230104, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class AddCellbaseDataRelease extends StorageMigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java index f7fcaa12a55..ce425e3434b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java @@ -10,7 +10,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20230117, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class CancerRoleAndModeOfInheritanceMigration extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java index d3f44141067..0be802202c4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20230313, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class CalculatePedigreeGraphMigration extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java index fdb1a44da12..e3b093906c4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java @@ -10,7 +10,7 @@ language = Migration.MigrationLanguage.JAVA, patch = 1, date = 20230927, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class MarkUnknownLargestVariantLength extends StorageMigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java index 79dd1aab762..7dbd590c27e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20230829, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class RenameCellBaseToken2ApiKey extends MigrationTool { From 55ec432ff9c6e6b1f2f134051b5d0585f0c30269 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 17:02:56 +0200 Subject: [PATCH 26/59] pom: Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 12 ++++++------ 27 files changed, 32 insertions(+), 32 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 3b96f1b246e..a82fde15ccc 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 1c77750c7f7..6dcf364e559 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index d15b4768e59..ff10c269d7f 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 2582a5f2003..ce253ddc6ae 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 16aff526b3e..215d392ce1c 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 73047a516e9..432db00c834 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 2348ef6f6f7..eda14c31ea1 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index d222153c1c3..7632ed6d65f 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 1834d5c7e64..cc692c6fcea 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 02953389c2d..bae503e0e91 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index a7a2c8adbbb..0dffe6806ff 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index ea3dbc32689..deac888af82 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 927d616c88c..661d9416a8f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index a84279ad4de..358590f69f6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ea5b63a7b6f..394e6c90e16 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 705f7b4104c..58aac8414c5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 066630724a2..8c00149ba90 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 3675d760a35..45370142854 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index ee08e659ae7..82a3d1f0fdc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index ffd41bdf7ca..c4839e1c646 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 435818c24cf..8d09832b15a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 495de2ebf89..0326f2479f3 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7de2add12c5..7d97161a5e3 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index d6d92f43dda..054ab3bc9de 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 316589d12ff..c3f5166b7fd 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 76a6360d5e2..12981fefe10 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 0e1de519a9b..24e41953d60 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.2.0_dev - 3.2.0_dev + 3.1.0_dev + 3.1.0_dev 6.1.0-SNAPSHOT - 3.2.0-SNAPSHOT - 5.2.0-SNAPSHOT - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT + 5.1.0-SNAPSHOT + 3.1.0-SNAPSHOT 0.2.0 2.14.3 From 56d344f63f277a0179dd7143be0f66f06fdd4b85 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 17:06:05 +0200 Subject: [PATCH 27/59] Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index a82fde15ccc..78e82fd250e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 6dcf364e559..2aa894fb7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index ff10c269d7f..00ac1b15fb7 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index ce253ddc6ae..74ce4002f32 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 215d392ce1c..f5c2e89e04b 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 432db00c834..64616005a87 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index eda14c31ea1..3353ba8dcd8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 7632ed6d65f..f39d9d674a6 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index cc692c6fcea..6ac3574fe95 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index bae503e0e91..9dea4c86c74 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 0dffe6806ff..7edb5708703 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index deac888af82..7b22e17d9b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 661d9416a8f..386dba5ab41 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 358590f69f6..d4376a789f5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index 394e6c90e16..ba01b370a09 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 58aac8414c5..1e8f6fa681a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8c00149ba90..1adc2854e5a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 45370142854..47a11d3fbf0 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 82a3d1f0fdc..b61a7f4591c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index c4839e1c646..783fb051572 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 8d09832b15a..72796b835d4 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 0326f2479f3..a40d5eb78bb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7d97161a5e3..91e477e70bb 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 054ab3bc9de..16d83021da1 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index c3f5166b7fd..fa537ec1586 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 12981fefe10..f6897603638 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 24e41953d60..8c725c30198 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0_dev - 3.1.0_dev - 6.1.0-SNAPSHOT - 3.1.0-SNAPSHOT - 5.1.0-SNAPSHOT - 3.1.0-SNAPSHOT + 3.1.0 + 3.1.0 + 6.0.0 + 3.1.0 + 5.1.0 + 3.1.0 0.2.0 2.14.3 From 65015f3a5d69e62b4ec432e255c168420aaa16af Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 20 May 2024 17:07:41 +0200 Subject: [PATCH 28/59] catalog: add deprecatedSince migration check in MigrationTool,#TASK-6256 --- .../org/opencb/opencga/catalog/migration/MigrationTool.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java index 6d2a7215035..805f43eb41d 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java @@ -4,6 +4,7 @@ import com.mongodb.client.MongoCursor; import com.mongodb.client.model.IndexOptions; import com.mongodb.client.model.WriteModel; +import org.apache.commons.lang3.StringUtils; import org.bson.Document; import org.bson.conversions.Bson; import org.opencb.commons.ProgressLogger; @@ -78,6 +79,11 @@ public final void setup(Configuration configuration, CatalogManager catalogManag public final void execute() throws MigrationException { try { + Migration annotation = getAnnotation(); + if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { + throw new MigrationException("Migration '" + annotation.id() + "' can't be run since version '" + + annotation.deprecatedSince() + "'. Please, run this migration from a previous OpenCGA version."); + } run(); } catch (MigrationException e) { throw e; From 5a43c8821b59bf6e19d46a1a8a8fdc3a33e73609 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 17:08:15 +0200 Subject: [PATCH 29/59] Prepare new development branch release-3.1.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index d43f173b4ff..3b96f1b246e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 67bd1fa34e0..1c77750c7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 11535022d1b..d15b4768e59 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index c9461e9c4de..2582a5f2003 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index adb57573b45..16aff526b3e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 0153566efea..73047a516e9 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3cbbbb2fa89..2348ef6f6f7 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 804b83e792b..d222153c1c3 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index a31567cb3bc..1834d5c7e64 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index ff97332afff..02953389c2d 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 12c0f24a27b..a7a2c8adbbb 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index e63a1dfcc78..ea3dbc32689 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 85caa7da48e..927d616c88c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 719b5cf072a..a84279ad4de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index a8a16269d93..ea5b63a7b6f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index a2d228c120d..705f7b4104c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index eab3b7f565e..066630724a2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 1292ba96965..3675d760a35 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 4b4ab70de2b..ee08e659ae7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index b9f0fcc7696..ffd41bdf7ca 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index d48ef593c4d..435818c24cf 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index cddf51ec925..495de2ebf89 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 943b2ff3eb8..7de2add12c5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 891225e9311..d6d92f43dda 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index f89a8783b7f..316589d12ff 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 70f7e126a02..76a6360d5e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 1b5cc6907e7..0e1de519a9b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.2.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.1_dev - 3.1.1_dev - 6.0.1-SNAPSHOT - 3.1.1-SNAPSHOT - 5.1.1-SNAPSHOT - 3.1.1-SNAPSHOT + 3.2.0_dev + 3.2.0_dev + 6.1.0-SNAPSHOT + 3.2.0-SNAPSHOT + 5.2.0-SNAPSHOT + 3.2.0-SNAPSHOT 0.2.0 2.14.3 From 36404297aa98759a0e9920662db50406ae6df2bf Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 19:02:51 +0200 Subject: [PATCH 30/59] pom: Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 78e82fd250e..a82fde15ccc 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 2aa894fb7f7..6dcf364e559 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 00ac1b15fb7..ff10c269d7f 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 74ce4002f32..ce253ddc6ae 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f5c2e89e04b..215d392ce1c 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 64616005a87..432db00c834 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3353ba8dcd8..eda14c31ea1 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f39d9d674a6..7632ed6d65f 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6ac3574fe95..cc692c6fcea 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9dea4c86c74..bae503e0e91 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 7edb5708703..0dffe6806ff 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 7b22e17d9b9..deac888af82 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 386dba5ab41..661d9416a8f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index d4376a789f5..358590f69f6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ba01b370a09..394e6c90e16 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 1e8f6fa681a..58aac8414c5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 1adc2854e5a..8c00149ba90 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 47a11d3fbf0..45370142854 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index b61a7f4591c..82a3d1f0fdc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 783fb051572..c4839e1c646 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 72796b835d4..8d09832b15a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index a40d5eb78bb..0326f2479f3 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 91e477e70bb..7d97161a5e3 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 16d83021da1..054ab3bc9de 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index fa537ec1586..c3f5166b7fd 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index f6897603638..12981fefe10 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 8c725c30198..24e41953d60 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.1.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0 - 3.1.0 - 6.0.0 - 3.1.0 - 5.1.0 - 3.1.0 + 3.1.0_dev + 3.1.0_dev + 6.1.0-SNAPSHOT + 3.1.0-SNAPSHOT + 5.1.0-SNAPSHOT + 3.1.0-SNAPSHOT 0.2.0 2.14.3 From a69635e0b96a324ff7949b199bc5f2b06953d17b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 19:08:52 +0200 Subject: [PATCH 31/59] Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index a82fde15ccc..78e82fd250e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 6dcf364e559..2aa894fb7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index ff10c269d7f..00ac1b15fb7 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index ce253ddc6ae..74ce4002f32 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 215d392ce1c..f5c2e89e04b 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 432db00c834..64616005a87 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index eda14c31ea1..3353ba8dcd8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 7632ed6d65f..f39d9d674a6 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index cc692c6fcea..6ac3574fe95 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index bae503e0e91..9dea4c86c74 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 0dffe6806ff..7edb5708703 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index deac888af82..7b22e17d9b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 661d9416a8f..386dba5ab41 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 358590f69f6..d4376a789f5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index 394e6c90e16..ba01b370a09 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 58aac8414c5..1e8f6fa681a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8c00149ba90..1adc2854e5a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 45370142854..47a11d3fbf0 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 82a3d1f0fdc..b61a7f4591c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index c4839e1c646..783fb051572 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 8d09832b15a..72796b835d4 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 0326f2479f3..a40d5eb78bb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7d97161a5e3..91e477e70bb 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 054ab3bc9de..16d83021da1 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index c3f5166b7fd..fa537ec1586 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 12981fefe10..f6897603638 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 24e41953d60..8c725c30198 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0_dev - 3.1.0_dev - 6.1.0-SNAPSHOT - 3.1.0-SNAPSHOT - 5.1.0-SNAPSHOT - 3.1.0-SNAPSHOT + 3.1.0 + 3.1.0 + 6.0.0 + 3.1.0 + 5.1.0 + 3.1.0 0.2.0 2.14.3 From bcfe52d63b5315e5bd3cd89ef697a39fd7311a7c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 19:10:38 +0200 Subject: [PATCH 32/59] Prepare new development branch release-3.1.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 78e82fd250e..3b96f1b246e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 2aa894fb7f7..1c77750c7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 00ac1b15fb7..d15b4768e59 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 74ce4002f32..2582a5f2003 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f5c2e89e04b..16aff526b3e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 64616005a87..73047a516e9 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3353ba8dcd8..2348ef6f6f7 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f39d9d674a6..d222153c1c3 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6ac3574fe95..1834d5c7e64 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9dea4c86c74..02953389c2d 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 7edb5708703..a7a2c8adbbb 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 7b22e17d9b9..ea3dbc32689 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 386dba5ab41..927d616c88c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index d4376a789f5..a84279ad4de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ba01b370a09..ea5b63a7b6f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 1e8f6fa681a..705f7b4104c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 1adc2854e5a..066630724a2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 47a11d3fbf0..3675d760a35 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index b61a7f4591c..ee08e659ae7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 783fb051572..ffd41bdf7ca 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 72796b835d4..435818c24cf 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index a40d5eb78bb..495de2ebf89 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 91e477e70bb..7de2add12c5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 16d83021da1..d6d92f43dda 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index fa537ec1586..316589d12ff 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index f6897603638..76a6360d5e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 8c725c30198..0e1de519a9b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0 - 3.1.0 - 6.0.0 - 3.1.0 - 5.1.0 - 3.1.0 + 3.2.0_dev + 3.2.0_dev + 6.1.0-SNAPSHOT + 3.2.0-SNAPSHOT + 5.2.0-SNAPSHOT + 3.2.0-SNAPSHOT 0.2.0 2.14.3 From 48bcefa62733ed7c23b084bfe126821d497f2b3c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 07:34:44 +0200 Subject: [PATCH 33/59] cicd: build app build folder as param #TASK-6185 --- .github/workflows/release.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 881b60add10..f9f7be22301 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -12,12 +12,14 @@ jobs: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P hdp3.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip + build_folder: build-folder-hdp deploy-docker-hdp: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build-hdp with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-hdp.outputs.version }} + build_folder: build-folder-hdp secrets: inherit # Add the build-hdi and deploy-docker-hdi jobs @@ -25,12 +27,14 @@ jobs: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P hdi5.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip + build_folder: build-folder-hdi deploy-docker-hdi: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build-hdi with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-hdi.outputs.version }} + build_folder: build-folder-hdi secrets: inherit # Add the build-emr and deploy-docker-emr jobs @@ -38,12 +42,14 @@ jobs: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P emr6.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip + build_folder: build-folder-emr deploy-docker-emr: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build-emr with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-emr.outputs.version }} + build_folder: build-folder-emr secrets: inherit # Add the build-emr613 and deploy-docker-emr613 jobs @@ -51,12 +57,14 @@ jobs: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P emr6.13,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip + build_folder: build-folder-emr613 deploy-docker-emr613: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build-emr613 with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-emr613.outputs.version }} + build_folder: build-folder-emr613 secrets: inherit # Add the deploy-maven and deploy-python jobs they depend on the build-hdp job From 5e87d4131f577a5837607182c2bb8949b1ee1a88 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 07:39:58 +0200 Subject: [PATCH 34/59] cicd: build app build folder as param #TASK-6185 --- .github/workflows/release.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index f9f7be22301..3f2873abaaf 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -75,18 +75,18 @@ jobs: maven_opts: -P hdp3.1 -Dopencga.war.name=opencga secrets: inherit - deploy-python: - uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop - needs: build-hdp - with: - cli: ./clients/python/python-build.sh push - artifact: build-folder - secrets: inherit +# deploy-python: +# uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop +# needs: build-hdp +# with: +# cli: ./clients/python/python-build.sh push +# artifact: build-folder +# secrets: inherit # Add the release job that depends on all the previous jobs release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build-hdp, deploy-docker-hdp, build-hdi, deploy-docker-hdi, build-emr, deploy-docker-emr, build-emr613, deploy-docker-emr613, deploy-maven, deploy-python ] + needs: [ build-hdp, deploy-docker-hdp, build-hdi, deploy-docker-hdi, build-emr, deploy-docker-emr, build-emr613, deploy-docker-emr613, deploy-maven ] with: artifact: build-folder file: | From 4ad13454be0c75149a61ca5866d4de60ce45eb47 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 07:41:57 +0200 Subject: [PATCH 35/59] pom: Release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 12 ++++++------ 27 files changed, 32 insertions(+), 32 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 3b96f1b246e..a82fde15ccc 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 1c77750c7f7..6dcf364e559 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index d15b4768e59..ff10c269d7f 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 2582a5f2003..ce253ddc6ae 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 16aff526b3e..215d392ce1c 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 73047a516e9..432db00c834 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 2348ef6f6f7..eda14c31ea1 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index d222153c1c3..7632ed6d65f 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 1834d5c7e64..cc692c6fcea 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 02953389c2d..bae503e0e91 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index a7a2c8adbbb..0dffe6806ff 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index ea3dbc32689..deac888af82 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 927d616c88c..661d9416a8f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index a84279ad4de..358590f69f6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ea5b63a7b6f..394e6c90e16 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 705f7b4104c..58aac8414c5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 066630724a2..8c00149ba90 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 3675d760a35..45370142854 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index ee08e659ae7..82a3d1f0fdc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index ffd41bdf7ca..c4839e1c646 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 435818c24cf..8d09832b15a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 495de2ebf89..0326f2479f3 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7de2add12c5..7d97161a5e3 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index d6d92f43dda..054ab3bc9de 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 316589d12ff..c3f5166b7fd 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 76a6360d5e2..12981fefe10 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 0e1de519a9b..24e41953d60 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.2.0_dev - 3.2.0_dev + 3.1.0_dev + 3.1.0_dev 6.1.0-SNAPSHOT - 3.2.0-SNAPSHOT - 5.2.0-SNAPSHOT - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT + 5.1.0-SNAPSHOT + 3.1.0-SNAPSHOT 0.2.0 2.14.3 From 96837461de6b38832644c9459a4137f8fa43bfcd Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 07:43:28 +0200 Subject: [PATCH 36/59] Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index a82fde15ccc..78e82fd250e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 6dcf364e559..2aa894fb7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index ff10c269d7f..00ac1b15fb7 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index ce253ddc6ae..74ce4002f32 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 215d392ce1c..f5c2e89e04b 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 432db00c834..64616005a87 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index eda14c31ea1..3353ba8dcd8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 7632ed6d65f..f39d9d674a6 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index cc692c6fcea..6ac3574fe95 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index bae503e0e91..9dea4c86c74 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 0dffe6806ff..7edb5708703 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index deac888af82..7b22e17d9b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 661d9416a8f..386dba5ab41 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 358590f69f6..d4376a789f5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index 394e6c90e16..ba01b370a09 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 58aac8414c5..1e8f6fa681a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8c00149ba90..1adc2854e5a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 45370142854..47a11d3fbf0 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 82a3d1f0fdc..b61a7f4591c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index c4839e1c646..783fb051572 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 8d09832b15a..72796b835d4 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 0326f2479f3..a40d5eb78bb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7d97161a5e3..91e477e70bb 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 054ab3bc9de..16d83021da1 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index c3f5166b7fd..fa537ec1586 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 12981fefe10..f6897603638 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 24e41953d60..8c725c30198 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0_dev - 3.1.0_dev - 6.1.0-SNAPSHOT - 3.1.0-SNAPSHOT - 5.1.0-SNAPSHOT - 3.1.0-SNAPSHOT + 3.1.0 + 3.1.0 + 6.0.0 + 3.1.0 + 5.1.0 + 3.1.0 0.2.0 2.14.3 From d5ebde2c7a662cc61cd7645de3a5d96eb96ab15b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 07:45:16 +0200 Subject: [PATCH 37/59] Prepare new development branch release-3.1.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 78e82fd250e..3b96f1b246e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 2aa894fb7f7..1c77750c7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 00ac1b15fb7..d15b4768e59 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 74ce4002f32..2582a5f2003 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f5c2e89e04b..16aff526b3e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 64616005a87..73047a516e9 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3353ba8dcd8..2348ef6f6f7 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f39d9d674a6..d222153c1c3 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6ac3574fe95..1834d5c7e64 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9dea4c86c74..02953389c2d 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 7edb5708703..a7a2c8adbbb 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 7b22e17d9b9..ea3dbc32689 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 386dba5ab41..927d616c88c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index d4376a789f5..a84279ad4de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ba01b370a09..ea5b63a7b6f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 1e8f6fa681a..705f7b4104c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 1adc2854e5a..066630724a2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 47a11d3fbf0..3675d760a35 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index b61a7f4591c..ee08e659ae7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 783fb051572..ffd41bdf7ca 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 72796b835d4..435818c24cf 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index a40d5eb78bb..495de2ebf89 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 91e477e70bb..7de2add12c5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 16d83021da1..d6d92f43dda 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index fa537ec1586..316589d12ff 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index f6897603638..76a6360d5e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 8c725c30198..0e1de519a9b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0 - 3.1.0 - 6.0.0 - 3.1.0 - 5.1.0 - 3.1.0 + 3.2.0_dev + 3.2.0_dev + 6.1.0-SNAPSHOT + 3.2.0-SNAPSHOT + 5.2.0-SNAPSHOT + 3.2.0-SNAPSHOT 0.2.0 2.14.3 From 1f4df0e4ef821d2a4828f4908ba3b3c75b9a6c58 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 08:11:29 +0200 Subject: [PATCH 38/59] pom: Release 3.1.0 --- .github/workflows/release.yml | 14 +++++++------- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 12 ++++++------ 28 files changed, 39 insertions(+), 39 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 3f2873abaaf..e0a482faf61 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -68,12 +68,12 @@ jobs: secrets: inherit # Add the deploy-maven and deploy-python jobs they depend on the build-hdp job - deploy-maven: - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop - needs: build-hdp - with: - maven_opts: -P hdp3.1 -Dopencga.war.name=opencga - secrets: inherit +# deploy-maven: +# uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop +# needs: build-hdp +# with: +# maven_opts: -P hdp3.1 -Dopencga.war.name=opencga +# secrets: inherit # deploy-python: # uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop @@ -86,7 +86,7 @@ jobs: # Add the release job that depends on all the previous jobs release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build-hdp, deploy-docker-hdp, build-hdi, deploy-docker-hdi, build-emr, deploy-docker-emr, build-emr613, deploy-docker-emr613, deploy-maven ] + needs: [ build-hdp, deploy-docker-hdp, build-hdi, deploy-docker-hdi, build-emr, deploy-docker-emr, build-emr613, deploy-docker-emr613 ] with: artifact: build-folder file: | diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 3b96f1b246e..a82fde15ccc 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 1c77750c7f7..6dcf364e559 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index d15b4768e59..ff10c269d7f 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 2582a5f2003..ce253ddc6ae 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 16aff526b3e..215d392ce1c 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 73047a516e9..432db00c834 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 2348ef6f6f7..eda14c31ea1 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index d222153c1c3..7632ed6d65f 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 1834d5c7e64..cc692c6fcea 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 02953389c2d..bae503e0e91 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index a7a2c8adbbb..0dffe6806ff 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index ea3dbc32689..deac888af82 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 927d616c88c..661d9416a8f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index a84279ad4de..358590f69f6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ea5b63a7b6f..394e6c90e16 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 705f7b4104c..58aac8414c5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 066630724a2..8c00149ba90 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 3675d760a35..45370142854 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index ee08e659ae7..82a3d1f0fdc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index ffd41bdf7ca..c4839e1c646 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 435818c24cf..8d09832b15a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 495de2ebf89..0326f2479f3 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7de2add12c5..7d97161a5e3 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index d6d92f43dda..054ab3bc9de 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 316589d12ff..c3f5166b7fd 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 76a6360d5e2..12981fefe10 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 0e1de519a9b..24e41953d60 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.2.0_dev - 3.2.0_dev + 3.1.0_dev + 3.1.0_dev 6.1.0-SNAPSHOT - 3.2.0-SNAPSHOT - 5.2.0-SNAPSHOT - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT + 5.1.0-SNAPSHOT + 3.1.0-SNAPSHOT 0.2.0 2.14.3 From c696fbf729b3a5dce0a40d6844d9d015c6cd94bf Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 08:15:56 +0200 Subject: [PATCH 39/59] Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index a82fde15ccc..78e82fd250e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 6dcf364e559..2aa894fb7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index ff10c269d7f..00ac1b15fb7 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index ce253ddc6ae..74ce4002f32 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 215d392ce1c..f5c2e89e04b 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 432db00c834..64616005a87 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index eda14c31ea1..3353ba8dcd8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 7632ed6d65f..f39d9d674a6 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index cc692c6fcea..6ac3574fe95 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index bae503e0e91..9dea4c86c74 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 0dffe6806ff..7edb5708703 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index deac888af82..7b22e17d9b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 661d9416a8f..386dba5ab41 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 358590f69f6..d4376a789f5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index 394e6c90e16..ba01b370a09 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 58aac8414c5..1e8f6fa681a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8c00149ba90..1adc2854e5a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 45370142854..47a11d3fbf0 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 82a3d1f0fdc..b61a7f4591c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index c4839e1c646..783fb051572 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 8d09832b15a..72796b835d4 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 0326f2479f3..a40d5eb78bb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7d97161a5e3..91e477e70bb 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 054ab3bc9de..16d83021da1 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index c3f5166b7fd..fa537ec1586 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 12981fefe10..f6897603638 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 24e41953d60..8c725c30198 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0_dev - 3.1.0_dev - 6.1.0-SNAPSHOT - 3.1.0-SNAPSHOT - 5.1.0-SNAPSHOT - 3.1.0-SNAPSHOT + 3.1.0 + 3.1.0 + 6.0.0 + 3.1.0 + 5.1.0 + 3.1.0 0.2.0 2.14.3 From ad39cda4ff839ded47af031bdfeb92b7abedda43 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 08:17:37 +0200 Subject: [PATCH 40/59] Prepare new development branch release-3.1.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 78e82fd250e..3b96f1b246e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 2aa894fb7f7..1c77750c7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 00ac1b15fb7..d15b4768e59 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 74ce4002f32..2582a5f2003 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f5c2e89e04b..16aff526b3e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 64616005a87..73047a516e9 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3353ba8dcd8..2348ef6f6f7 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f39d9d674a6..d222153c1c3 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6ac3574fe95..1834d5c7e64 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9dea4c86c74..02953389c2d 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 7edb5708703..a7a2c8adbbb 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 7b22e17d9b9..ea3dbc32689 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 386dba5ab41..927d616c88c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index d4376a789f5..a84279ad4de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ba01b370a09..ea5b63a7b6f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 1e8f6fa681a..705f7b4104c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 1adc2854e5a..066630724a2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 47a11d3fbf0..3675d760a35 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index b61a7f4591c..ee08e659ae7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 783fb051572..ffd41bdf7ca 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 72796b835d4..435818c24cf 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index a40d5eb78bb..495de2ebf89 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 91e477e70bb..7de2add12c5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 16d83021da1..d6d92f43dda 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index fa537ec1586..316589d12ff 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index f6897603638..76a6360d5e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 8c725c30198..0e1de519a9b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0 - 3.1.0 - 6.0.0 - 3.1.0 - 5.1.0 - 3.1.0 + 3.2.0_dev + 3.2.0_dev + 6.1.0-SNAPSHOT + 3.2.0-SNAPSHOT + 5.2.0-SNAPSHOT + 3.2.0-SNAPSHOT 0.2.0 2.14.3 From 0bea30ef00bd3c9ff80057d9c13bc3fcbd191af5 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 10:11:28 +0200 Subject: [PATCH 41/59] pom: Release 3.1.0 --- .github/workflows/release.yml | 2 +- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 12 ++++++------ 28 files changed, 33 insertions(+), 33 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index e0a482faf61..2f17378bc89 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -88,7 +88,7 @@ jobs: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop needs: [ build-hdp, deploy-docker-hdp, build-hdi, deploy-docker-hdi, build-emr, deploy-docker-emr, build-emr613, deploy-docker-emr613 ] with: - artifact: build-folder + artifact: build-folder-hdp file: | opencga-client-${{ needs.build-hdp.outputs.version }}.tar.gz clients/R/opencgaR_${{ needs.build-hdp.outputs.version }}.tar.gz diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 3b96f1b246e..a82fde15ccc 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 1c77750c7f7..6dcf364e559 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index d15b4768e59..ff10c269d7f 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 2582a5f2003..ce253ddc6ae 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 16aff526b3e..215d392ce1c 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 73047a516e9..432db00c834 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 2348ef6f6f7..eda14c31ea1 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index d222153c1c3..7632ed6d65f 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 1834d5c7e64..cc692c6fcea 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 02953389c2d..bae503e0e91 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index a7a2c8adbbb..0dffe6806ff 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index ea3dbc32689..deac888af82 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 927d616c88c..661d9416a8f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index a84279ad4de..358590f69f6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ea5b63a7b6f..394e6c90e16 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 705f7b4104c..58aac8414c5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 066630724a2..8c00149ba90 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 3675d760a35..45370142854 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index ee08e659ae7..82a3d1f0fdc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index ffd41bdf7ca..c4839e1c646 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 435818c24cf..8d09832b15a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 495de2ebf89..0326f2479f3 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7de2add12c5..7d97161a5e3 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index d6d92f43dda..054ab3bc9de 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 316589d12ff..c3f5166b7fd 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 76a6360d5e2..12981fefe10 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 0e1de519a9b..24e41953d60 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.2.0_dev - 3.2.0_dev + 3.1.0_dev + 3.1.0_dev 6.1.0-SNAPSHOT - 3.2.0-SNAPSHOT - 5.2.0-SNAPSHOT - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT + 5.1.0-SNAPSHOT + 3.1.0-SNAPSHOT 0.2.0 2.14.3 From 599b0fbf65633a87dc6097b99b64e5dcf0e2faf1 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 10:16:26 +0200 Subject: [PATCH 42/59] Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index a82fde15ccc..78e82fd250e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 6dcf364e559..2aa894fb7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index ff10c269d7f..00ac1b15fb7 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index ce253ddc6ae..74ce4002f32 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 215d392ce1c..f5c2e89e04b 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 432db00c834..64616005a87 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index eda14c31ea1..3353ba8dcd8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 7632ed6d65f..f39d9d674a6 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index cc692c6fcea..6ac3574fe95 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index bae503e0e91..9dea4c86c74 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 0dffe6806ff..7edb5708703 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index deac888af82..7b22e17d9b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 661d9416a8f..386dba5ab41 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 358590f69f6..d4376a789f5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index 394e6c90e16..ba01b370a09 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 58aac8414c5..1e8f6fa681a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8c00149ba90..1adc2854e5a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 45370142854..47a11d3fbf0 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 82a3d1f0fdc..b61a7f4591c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index c4839e1c646..783fb051572 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 8d09832b15a..72796b835d4 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 0326f2479f3..a40d5eb78bb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7d97161a5e3..91e477e70bb 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 054ab3bc9de..16d83021da1 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index c3f5166b7fd..fa537ec1586 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 12981fefe10..f6897603638 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 24e41953d60..8c725c30198 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0_dev - 3.1.0_dev - 6.1.0-SNAPSHOT - 3.1.0-SNAPSHOT - 5.1.0-SNAPSHOT - 3.1.0-SNAPSHOT + 3.1.0 + 3.1.0 + 6.0.0 + 3.1.0 + 5.1.0 + 3.1.0 0.2.0 2.14.3 From 0f9eb60aa82c56b9019cfc1a15311904a977e3e1 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 10:18:18 +0200 Subject: [PATCH 43/59] Prepare new development branch release-3.1.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 78e82fd250e..3b96f1b246e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 2aa894fb7f7..1c77750c7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 00ac1b15fb7..d15b4768e59 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 74ce4002f32..2582a5f2003 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f5c2e89e04b..16aff526b3e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 64616005a87..73047a516e9 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3353ba8dcd8..2348ef6f6f7 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f39d9d674a6..d222153c1c3 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6ac3574fe95..1834d5c7e64 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9dea4c86c74..02953389c2d 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 7edb5708703..a7a2c8adbbb 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 7b22e17d9b9..ea3dbc32689 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 386dba5ab41..927d616c88c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index d4376a789f5..a84279ad4de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ba01b370a09..ea5b63a7b6f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 1e8f6fa681a..705f7b4104c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 1adc2854e5a..066630724a2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 47a11d3fbf0..3675d760a35 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index b61a7f4591c..ee08e659ae7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 783fb051572..ffd41bdf7ca 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 72796b835d4..435818c24cf 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index a40d5eb78bb..495de2ebf89 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 91e477e70bb..7de2add12c5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 16d83021da1..d6d92f43dda 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index fa537ec1586..316589d12ff 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index f6897603638..76a6360d5e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 8c725c30198..0e1de519a9b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0 - 3.1.0 - 6.0.0 - 3.1.0 - 5.1.0 - 3.1.0 + 3.2.0_dev + 3.2.0_dev + 6.1.0-SNAPSHOT + 3.2.0-SNAPSHOT + 5.2.0-SNAPSHOT + 3.2.0-SNAPSHOT 0.2.0 2.14.3 From 19e70ad10e933a614f5c04ca8f276dc19d4bfc8c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 10:50:22 +0200 Subject: [PATCH 44/59] cicd: uncomment code commented for fix failed release #TASK-6185 --- .github/workflows/release.yml | 61 ++++++++++++++++++----------------- 1 file changed, 31 insertions(+), 30 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 2f17378bc89..5a68a6e931c 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -7,21 +7,49 @@ on: workflow_dispatch: jobs: - # Add the build-hdp and deploy-docker-hdp jobs + # Add the build-hdp job build-hdp: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P hdp3.1,RClient -Dopencga.war.name=opencga -Dcheckstyle.skip - build_folder: build-folder-hdp + build_folder: build-folder + # Add the deploy-docker-hdp job that depends on the build-hdp job deploy-docker-hdp: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build-hdp with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-hdp.outputs.version }} - build_folder: build-folder-hdp + build_folder: build-folder secrets: inherit + # Add the deploy-maven and deploy-python jobs they depend on the build-hdp job + deploy-maven: + uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop + needs: build-hdp + with: + maven_opts: -P hdp3.1 -Dopencga.war.name=opencga + secrets: inherit + + deploy-python: + uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop + needs: build-hdp + with: + cli: ./clients/python/python-build.sh push + artifact: build-folder + secrets: inherit + + # Add the release job that depends on all the previous jobs + release: + uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop + needs: [ build-hdp, deploy-docker-hdp, deploy-maven, deploy-python] + with: + artifact: build-folder + file: | + opencga-client-${{ needs.build-hdp.outputs.version }}.tar.gz + clients/R/opencgaR_${{ needs.build-hdp.outputs.version }}.tar.gz + + # Compile and deploy other hadoop flavours # Add the build-hdi and deploy-docker-hdi jobs build-hdi: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop @@ -66,30 +94,3 @@ jobs: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-emr613.outputs.version }} build_folder: build-folder-emr613 secrets: inherit - - # Add the deploy-maven and deploy-python jobs they depend on the build-hdp job -# deploy-maven: -# uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop -# needs: build-hdp -# with: -# maven_opts: -P hdp3.1 -Dopencga.war.name=opencga -# secrets: inherit - -# deploy-python: -# uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop -# needs: build-hdp -# with: -# cli: ./clients/python/python-build.sh push -# artifact: build-folder -# secrets: inherit - - # Add the release job that depends on all the previous jobs - release: - uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build-hdp, deploy-docker-hdp, build-hdi, deploy-docker-hdi, build-emr, deploy-docker-emr, build-emr613, deploy-docker-emr613 ] - with: - artifact: build-folder-hdp - file: | - opencga-client-${{ needs.build-hdp.outputs.version }}.tar.gz - clients/R/opencgaR_${{ needs.build-hdp.outputs.version }}.tar.gz - From 37f023585a1c66c4b37fe70433d953a14cf8ac31 Mon Sep 17 00:00:00 2001 From: pfurio Date: Tue, 21 May 2024 12:42:29 +0200 Subject: [PATCH 45/59] catalog: add new static MigrationException message, #TASK-6256 --- .../opencga/catalog/migration/MigrationException.java | 6 ++++++ .../opencb/opencga/catalog/migration/MigrationManager.java | 3 +-- .../org/opencb/opencga/catalog/migration/MigrationTool.java | 3 +-- 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java index 63f666eac14..000c46d57dc 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java @@ -20,4 +20,10 @@ public static MigrationException offlineMigrationException(Migration migration) return new MigrationException("Migration '" + migration.id() + "' requires database to be offline. Please, ensure the database " + "cannot be accessed and run try again with '--offline' flag."); } + + public static MigrationException deprecatedMigration(Migration migration) { + return new MigrationException("Migration '" + migration.id() + "' can't be run since version '" + + migration.deprecatedSince() + "'. Please, run this migration from a previous OpenCGA version."); + } + } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java index 543e378cba3..10b247a6d0d 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java @@ -623,8 +623,7 @@ private MigrationRun run(String organizationId, Class r Migration annotation = getMigrationAnnotation(runnableMigration); if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { - throw new MigrationException("Migration '" + annotation.id() + "' can't be run since version '" + annotation.deprecatedSince() - + "'. Please, run this migration from a previous OpenCGA version."); + throw MigrationException.deprecatedMigration(annotation); } MigrationTool migrationTool; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java index 805f43eb41d..f46e54277d2 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java @@ -81,8 +81,7 @@ public final void execute() throws MigrationException { try { Migration annotation = getAnnotation(); if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { - throw new MigrationException("Migration '" + annotation.id() + "' can't be run since version '" - + annotation.deprecatedSince() + "'. Please, run this migration from a previous OpenCGA version."); + throw MigrationException.deprecatedMigration(annotation); } run(); } catch (MigrationException e) { From b000d9c0166450d4975fc12d7012132d766fd67f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 13:04:50 +0200 Subject: [PATCH 46/59] cicd: Release script to test hadoop flavours #TASK-6185 --- .github/workflows/release.yml | 38 +++++++++++++++++------------------ 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 5a68a6e931c..84c84e5648b 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -19,30 +19,30 @@ jobs: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build-hdp with: - cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-hdp.outputs.version }} + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag "${{ needs.build-hdp.outputs.version }}-hdp3.1" build_folder: build-folder secrets: inherit # Add the deploy-maven and deploy-python jobs they depend on the build-hdp job - deploy-maven: - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop - needs: build-hdp - with: - maven_opts: -P hdp3.1 -Dopencga.war.name=opencga - secrets: inherit - - deploy-python: - uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop - needs: build-hdp - with: - cli: ./clients/python/python-build.sh push - artifact: build-folder - secrets: inherit +# deploy-maven: +# uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop +# needs: build-hdp +# with: +# maven_opts: -P hdp3.1 -Dopencga.war.name=opencga +# secrets: inherit +# +# deploy-python: +# uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop +# needs: build-hdp +# with: +# cli: ./clients/python/python-build.sh push +# artifact: build-folder +# secrets: inherit # Add the release job that depends on all the previous jobs release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build-hdp, deploy-docker-hdp, deploy-maven, deploy-python] + needs: [ build-hdp, deploy-docker-hdp] with: artifact: build-folder file: | @@ -61,7 +61,7 @@ jobs: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build-hdi with: - cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-hdi.outputs.version }} + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag "${{ needs.build-hdi.outputs.version }}-hdi5.1" build_folder: build-folder-hdi secrets: inherit @@ -76,7 +76,7 @@ jobs: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build-emr with: - cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-emr.outputs.version }} + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag "${{ needs.build-emr.outputs.version }}-emr6.1" build_folder: build-folder-emr secrets: inherit @@ -91,6 +91,6 @@ jobs: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build-emr613 with: - cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build-emr613.outputs.version }} + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag "${{ needs.build-emr613.outputs.version }}-emr6.13" build_folder: build-folder-emr613 secrets: inherit From 5f540e32039e27fe620137e84bace5f10a8ba289 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 13:07:35 +0200 Subject: [PATCH 47/59] cicd: Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 12 ++++++------ 27 files changed, 32 insertions(+), 32 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 3b96f1b246e..a82fde15ccc 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 1c77750c7f7..6dcf364e559 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index d15b4768e59..ff10c269d7f 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 2582a5f2003..ce253ddc6ae 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 16aff526b3e..215d392ce1c 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 73047a516e9..432db00c834 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 2348ef6f6f7..eda14c31ea1 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index d222153c1c3..7632ed6d65f 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 1834d5c7e64..cc692c6fcea 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 02953389c2d..bae503e0e91 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index a7a2c8adbbb..0dffe6806ff 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index ea3dbc32689..deac888af82 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 927d616c88c..661d9416a8f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index a84279ad4de..358590f69f6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ea5b63a7b6f..394e6c90e16 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 705f7b4104c..58aac8414c5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 066630724a2..8c00149ba90 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 3675d760a35..45370142854 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index ee08e659ae7..82a3d1f0fdc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index ffd41bdf7ca..c4839e1c646 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 435818c24cf..8d09832b15a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 495de2ebf89..0326f2479f3 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7de2add12c5..7d97161a5e3 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index d6d92f43dda..054ab3bc9de 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 316589d12ff..c3f5166b7fd 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 76a6360d5e2..12981fefe10 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 0e1de519a9b..24e41953d60 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.2.0_dev - 3.2.0_dev + 3.1.0_dev + 3.1.0_dev 6.1.0-SNAPSHOT - 3.2.0-SNAPSHOT - 5.2.0-SNAPSHOT - 3.2.0-SNAPSHOT + 3.1.0-SNAPSHOT + 5.1.0-SNAPSHOT + 3.1.0-SNAPSHOT 0.2.0 2.14.3 From 88adfbaf76a1141a788135c05769b4ec678fdadf Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 13:11:27 +0200 Subject: [PATCH 48/59] Prepare release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index a82fde15ccc..78e82fd250e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 6dcf364e559..2aa894fb7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index ff10c269d7f..00ac1b15fb7 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index ce253ddc6ae..74ce4002f32 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 215d392ce1c..f5c2e89e04b 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 432db00c834..64616005a87 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index eda14c31ea1..3353ba8dcd8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 7632ed6d65f..f39d9d674a6 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index cc692c6fcea..6ac3574fe95 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index bae503e0e91..9dea4c86c74 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 0dffe6806ff..7edb5708703 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index deac888af82..7b22e17d9b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 661d9416a8f..386dba5ab41 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 358590f69f6..d4376a789f5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index 394e6c90e16..ba01b370a09 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 58aac8414c5..1e8f6fa681a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8c00149ba90..1adc2854e5a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 45370142854..47a11d3fbf0 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 82a3d1f0fdc..b61a7f4591c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index c4839e1c646..783fb051572 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 8d09832b15a..72796b835d4 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 0326f2479f3..a40d5eb78bb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7d97161a5e3..91e477e70bb 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 054ab3bc9de..16d83021da1 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index c3f5166b7fd..fa537ec1586 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 12981fefe10..f6897603638 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 24e41953d60..9c4805b8e84 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0-SNAPSHOT + 3.1.0 pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0_dev - 3.1.0_dev - 6.1.0-SNAPSHOT - 3.1.0-SNAPSHOT - 5.1.0-SNAPSHOT - 3.1.0-SNAPSHOT + 3.1.0 + 3.1.0 + 6.1.0 + 3.1.0 + 5.1.0 + 3.1.0 0.2.0 2.14.3 From 463b5bf6eddce5045e9db68a8deb13467b51313b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 13:19:22 +0200 Subject: [PATCH 49/59] Prepare new development branch release-3.1.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 27 files changed, 33 insertions(+), 33 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 78e82fd250e..3b96f1b246e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 2aa894fb7f7..1c77750c7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 00ac1b15fb7..d15b4768e59 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 74ce4002f32..2582a5f2003 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f5c2e89e04b..16aff526b3e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 64616005a87..73047a516e9 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3353ba8dcd8..2348ef6f6f7 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f39d9d674a6..d222153c1c3 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6ac3574fe95..1834d5c7e64 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9dea4c86c74..02953389c2d 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 7edb5708703..a7a2c8adbbb 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 7b22e17d9b9..ea3dbc32689 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 386dba5ab41..927d616c88c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index d4376a789f5..a84279ad4de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index ba01b370a09..ea5b63a7b6f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 1e8f6fa681a..705f7b4104c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 1adc2854e5a..066630724a2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 47a11d3fbf0..3675d760a35 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index b61a7f4591c..ee08e659ae7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 783fb051572..ffd41bdf7ca 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 72796b835d4..435818c24cf 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index a40d5eb78bb..495de2ebf89 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 91e477e70bb..7de2add12c5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 16d83021da1..d6d92f43dda 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index fa537ec1586..316589d12ff 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index f6897603638..76a6360d5e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 9c4805b8e84..b187199de8b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.0 + 3.2.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 3.1.0 - 3.1.0 - 6.1.0 - 3.1.0 - 5.1.0 - 3.1.0 + 3.2.0_dev + 3.2.0_dev + 6.2.0-SNAPSHOT + 3.2.0-SNAPSHOT + 5.2.0-SNAPSHOT + 3.2.0-SNAPSHOT 0.2.0 2.14.3 From d326fa5e562d0e6e0e4e0c52f1ec7a6925e4b477 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 21 May 2024 14:38:20 +0200 Subject: [PATCH 50/59] cicd: uncomment code commented for fix failed release #TASK-6185 --- .github/workflows/release.yml | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 84c84e5648b..b59c92125e0 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -24,25 +24,25 @@ jobs: secrets: inherit # Add the deploy-maven and deploy-python jobs they depend on the build-hdp job -# deploy-maven: -# uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop -# needs: build-hdp -# with: -# maven_opts: -P hdp3.1 -Dopencga.war.name=opencga -# secrets: inherit -# -# deploy-python: -# uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop -# needs: build-hdp -# with: -# cli: ./clients/python/python-build.sh push -# artifact: build-folder -# secrets: inherit + deploy-maven: + uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop + needs: build-hdp + with: + maven_opts: -P hdp3.1 -Dopencga.war.name=opencga + secrets: inherit + + deploy-python: + uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop + needs: build-hdp + with: + cli: ./clients/python/python-build.sh push + artifact: build-folder + secrets: inherit # Add the release job that depends on all the previous jobs release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build-hdp, deploy-docker-hdp] + needs: [ build-hdp, deploy-docker-hdp, deploy-maven, deploy-python] with: artifact: build-folder file: | From 56a781994456f9c3ede9db0f5d61765c9312ef18 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 23 May 2024 17:06:33 +0100 Subject: [PATCH 51/59] client: Remove dates and random changes from client auto-generation process. #TASK-6302 --- .../app/misc/clients/r_client_generator.py | 1 + .../app/misc/clients/rest_client_generator.py | 2 -- .../writers/cli/AutoCompleteWriter.java | 19 ------------------- .../writers/cli/OptionsCliRestApiWriter.java | 2 -- .../writers/cli/ParserCliRestApiWriter.java | 19 ------------------- 5 files changed, 1 insertion(+), 42 deletions(-) diff --git a/opencga-app/app/misc/clients/r_client_generator.py b/opencga-app/app/misc/clients/r_client_generator.py index f07735c62a0..2d2a4840a97 100644 --- a/opencga-app/app/misc/clients/r_client_generator.py +++ b/opencga-app/app/misc/clients/r_client_generator.py @@ -75,6 +75,7 @@ def get_class_definition(self, category): myEndpoint['path'], ", ".join(endpoint_params))) path_params = set(class_path_params) + path_params = sorted(list(path_params)) text.append("#'\n#' @md") text.append("#' @seealso \\url{http://docs.opencb.org/display/opencga/Using+OpenCGA} and the RESTful API documentation") text.append("#' \\url{http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/}") diff --git a/opencga-app/app/misc/clients/rest_client_generator.py b/opencga-app/app/misc/clients/rest_client_generator.py index b4c5800e751..5fa98d9be8d 100644 --- a/opencga-app/app/misc/clients/rest_client_generator.py +++ b/opencga-app/app/misc/clients/rest_client_generator.py @@ -58,12 +58,10 @@ def __init__(self, rest_api_file, output_dir): @staticmethod def get_autogenerated_message(): - date_ = datetime.now().strftime("%Y-%m-%d") return [ 'WARNING: AUTOGENERATED CODE', '', 'This code was generated by a tool.', - 'Autogenerated on: ' + date_, '', 'Manual changes to this file may cause unexpected behavior in your application.', 'Manual changes to this file will be overwritten if the code is regenerated.' diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/AutoCompleteWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/AutoCompleteWriter.java index d4f85542ddf..1d58459b343 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/AutoCompleteWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/AutoCompleteWriter.java @@ -25,8 +25,6 @@ import java.io.File; import java.io.IOException; -import java.text.SimpleDateFormat; -import java.util.Date; public class AutoCompleteWriter extends ParentClientRestApiWriter { @@ -37,23 +35,6 @@ public AutoCompleteWriter(RestApi restApi, CommandLineConfiguration config) { @Override protected String getClassImports(String key) { StringBuilder sb = new StringBuilder(); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - sb.append("/*\n"); - sb.append("* Copyright 2015-").append(sdf.format(new Date())).append(" OpenCB\n"); - sb.append("*\n"); - sb.append("* Licensed under the Apache License, Version 2.0 (the \"License\");\n"); - sb.append("* you may not use this file except in compliance with the License.\n"); - sb.append("* You may obtain a copy of the License at\n"); - sb.append("*\n"); - sb.append("* http://www.apache.org/licenses/LICENSE-2.0\n"); - sb.append("*\n"); - sb.append("* Unless required by applicable law or agreed to in writing, software\n"); - sb.append("* distributed under the License is distributed on an \"AS IS\" BASIS,\n"); - sb.append("* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n"); - sb.append("* See the License for the specific language governing permissions and\n"); - sb.append("* limitations under the License.\n"); - sb.append("*/\n"); - sb.append("\n"); sb.append("package ").append(config.getOptions().getParserPackage()).append(";\n"); sb.append("\n"); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/OptionsCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/OptionsCliRestApiWriter.java index bfa784319b7..90b8977decc 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/OptionsCliRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/OptionsCliRestApiWriter.java @@ -28,7 +28,6 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import java.text.SimpleDateFormat; import java.util.HashSet; import java.util.Set; @@ -45,7 +44,6 @@ protected String getClassImports(String key) { StringBuilder sb = new StringBuilder(); RestCategory restCategory = availableCategories.get(key); CategoryConfig categoryConfig = availableCategoryConfigs.get(key); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); sb.append("package ").append(config.getOptions().getOptionsPackage()).append(";\n\n"); sb.append("import com.beust.jcommander.JCommander;\n"); sb.append("import com.beust.jcommander.Parameter;\n"); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java index 121166bd9d2..669a5151c61 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ParserCliRestApiWriter.java @@ -27,8 +27,6 @@ import java.io.File; import java.io.IOException; -import java.text.SimpleDateFormat; -import java.util.Date; public class ParserCliRestApiWriter extends ParentClientRestApiWriter { @@ -39,23 +37,6 @@ public ParserCliRestApiWriter(RestApi restApi, CommandLineConfiguration config) @Override protected String getClassImports(String key) { StringBuilder sb = new StringBuilder(); - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - sb.append("/*\n"); - sb.append("* Copyright 2015-").append(sdf.format(new Date())).append(" OpenCB\n"); - sb.append("*\n"); - sb.append("* Licensed under the Apache License, Version 2.0 (the \"License\");\n"); - sb.append("* you may not use this file except in compliance with the License.\n"); - sb.append("* You may obtain a copy of the License at\n"); - sb.append("*\n"); - sb.append("* http://www.apache.org/licenses/LICENSE-2.0\n"); - sb.append("*\n"); - sb.append("* Unless required by applicable law or agreed to in writing, software\n"); - sb.append("* distributed under the License is distributed on an \"AS IS\" BASIS,\n"); - sb.append("* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n"); - sb.append("* See the License for the specific language governing permissions and\n"); - sb.append("* limitations under the License.\n"); - sb.append("*/\n"); - sb.append("\n"); sb.append("package ").append(config.getOptions().getParserPackage()).append(";\n"); sb.append("\n"); From 9c6532981215c2cddf4adff5da5a2762404e9301 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 23 May 2024 17:08:16 +0100 Subject: [PATCH 52/59] client: Enable by default code auto-genration #TASK-6302 --- opencga-server/pom.xml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index d222153c1c3..6863e08197c 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -392,7 +392,9 @@ CodeGen - false + + !skipCodeGen + From be1578caed701c2d692b8b87c90cb254c93acae0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 23 May 2024 17:14:14 +0100 Subject: [PATCH 53/59] client: Remove opencga version from java and python clients. #TASK-6302 --- opencga-app/app/misc/clients/java_client_generator.py | 1 - opencga-app/app/misc/clients/python_client_generator.py | 1 - 2 files changed, 2 deletions(-) diff --git a/opencga-app/app/misc/clients/java_client_generator.py b/opencga-app/app/misc/clients/java_client_generator.py index 9555f4fe4b1..d932d08eec6 100755 --- a/opencga-app/app/misc/clients/java_client_generator.py +++ b/opencga-app/app/misc/clients/java_client_generator.py @@ -99,7 +99,6 @@ def get_class_definition(self, category): text.append('/**') text.append(' * This class contains methods for the {} webservices.'.format( self.categories[self.get_category_name(category)])) - text.append(' *{}Client version: {}'.format(' ' * 4, self.version)) text.append(' *{}PATH: {}'.format(' ' * 4, self.get_category_path(category))) text.append(' */') text.append('public class {}Client extends {} {{'.format(self.categories[self.get_category_name(category)], parentClientClass)) diff --git a/opencga-app/app/misc/clients/python_client_generator.py b/opencga-app/app/misc/clients/python_client_generator.py index 8a0ba4320c6..ada636dc5c1 100644 --- a/opencga-app/app/misc/clients/python_client_generator.py +++ b/opencga-app/app/misc/clients/python_client_generator.py @@ -70,7 +70,6 @@ def get_class_definition(self, category): text.append('{}"""'.format(' ' * 4)) text.append('{}This class contains methods for the \'{}\' webservices'.format(' ' * 4, self.get_category_name(category))) - text.append('{}Client version: {}'.format(' ' * 4, self.version)) text.append('{}PATH: {}'.format(' ' * 4, category['path'])) text.append('{}"""'.format(' ' * 4)) text.append('') From dc5b39aa4a6df88aee53489f45141cbb611ad6eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 23 May 2024 17:20:12 +0100 Subject: [PATCH 54/59] client: Autogenerate clients. #TASK-6302 --- .../app/cli/main/OpenCgaCompleter.java | 16 - .../app/cli/main/OpencgaCliOptionsParser.java | 16 - opencga-client/src/main/R/R/Admin-methods.R | 1 - .../src/main/R/R/Alignment-methods.R | 1 - opencga-client/src/main/R/R/AllGenerics.R | 22 +- .../src/main/R/R/Clinical-methods.R | 3 +- opencga-client/src/main/R/R/Cohort-methods.R | 3 +- opencga-client/src/main/R/R/Family-methods.R | 3 +- opencga-client/src/main/R/R/File-methods.R | 3 +- opencga-client/src/main/R/R/GA4GH-methods.R | 3 +- .../src/main/R/R/Individual-methods.R | 3 +- opencga-client/src/main/R/R/Job-methods.R | 3 +- opencga-client/src/main/R/R/Meta-methods.R | 1 - .../src/main/R/R/Operation-methods.R | 1 - .../src/main/R/R/Organization-methods.R | 3 +- opencga-client/src/main/R/R/Panel-methods.R | 1 - opencga-client/src/main/R/R/Project-methods.R | 1 - opencga-client/src/main/R/R/Sample-methods.R | 3 +- opencga-client/src/main/R/R/Study-methods.R | 3 +- opencga-client/src/main/R/R/User-methods.R | 3 +- opencga-client/src/main/R/R/Variant-methods.R | 1 - .../client/rest/clients/AdminClient.java | 2 - .../client/rest/clients/AlignmentClient.java | 2 - .../rest/clients/ClinicalAnalysisClient.java | 2 - .../client/rest/clients/ClinicalClient.java | 914 --------------- .../client/rest/clients/CohortClient.java | 2 - .../rest/clients/DiseasePanelClient.java | 2 - .../client/rest/clients/FamilyClient.java | 2 - .../client/rest/clients/FileClient.java | 2 - .../client/rest/clients/GA4GHClient.java | 2 - .../client/rest/clients/IndividualClient.java | 2 - .../client/rest/clients/JobClient.java | 2 - .../client/rest/clients/MetaClient.java | 2 - .../rest/clients/OrganizationClient.java | 2 - .../client/rest/clients/ProjectClient.java | 2 - .../client/rest/clients/SampleClient.java | 2 - .../client/rest/clients/StudyClient.java | 2 - .../client/rest/clients/UserClient.java | 2 - .../client/rest/clients/VariantClient.java | 2 - .../rest/clients/VariantOperationClient.java | 2 - opencga-client/src/main/javascript/Admin.js | 1 - .../src/main/javascript/Alignment.js | 1 - .../src/main/javascript/ClinicalAnalysis.js | 1 - opencga-client/src/main/javascript/Cohort.js | 1 - .../src/main/javascript/DiseasePanel.js | 1 - opencga-client/src/main/javascript/Family.js | 1 - opencga-client/src/main/javascript/File.js | 1 - opencga-client/src/main/javascript/GA4GH.js | 1 - .../src/main/javascript/Individual.js | 1 - opencga-client/src/main/javascript/Job.js | 1 - opencga-client/src/main/javascript/Meta.js | 1 - .../src/main/javascript/Organization.js | 1 - opencga-client/src/main/javascript/Project.js | 1 - opencga-client/src/main/javascript/Sample.js | 1 - opencga-client/src/main/javascript/Study.js | 1 - opencga-client/src/main/javascript/User.js | 1 - opencga-client/src/main/javascript/Variant.js | 1 - .../src/main/javascript/VariantOperation.js | 1 - .../pyopencga/rest_clients/admin_client.py | 2 - .../rest_clients/alignment_client.py | 2 - .../rest_clients/clinical_analysis_client.py | 2 - .../pyopencga/rest_clients/clinical_client.py | 1005 ----------------- .../pyopencga/rest_clients/cohort_client.py | 2 - .../rest_clients/disease_panel_client.py | 2 - .../pyopencga/rest_clients/family_client.py | 2 - .../pyopencga/rest_clients/file_client.py | 2 - .../pyopencga/rest_clients/ga4gh_client.py | 2 - .../rest_clients/individual_client.py | 2 - .../pyopencga/rest_clients/job_client.py | 2 - .../pyopencga/rest_clients/meta_client.py | 2 - .../rest_clients/organization_client.py | 2 - .../pyopencga/rest_clients/project_client.py | 2 - .../pyopencga/rest_clients/sample_client.py | 2 - .../pyopencga/rest_clients/study_client.py | 2 - .../pyopencga/rest_clients/user_client.py | 2 - .../pyopencga/rest_clients/variant_client.py | 2 - .../rest_clients/variant_operation_client.py | 2 - 77 files changed, 22 insertions(+), 2081 deletions(-) delete mode 100644 opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalClient.java delete mode 100644 opencga-client/src/main/python/pyopencga/rest_clients/clinical_client.py diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 1ff476d5003..d6bd902fff1 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,19 +1,3 @@ -/* -* Copyright 2015-2024-04-29 OpenCB -* -* Licensed under the Apache License, Version 2.0 (the "License"); -* you may not use this file except in compliance with the License. -* You may obtain a copy of the License at -* -* http://www.apache.org/licenses/LICENSE-2.0 -* -* Unless required by applicable law or agreed to in writing, software -* distributed under the License is distributed on an "AS IS" BASIS, -* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -* See the License for the specific language governing permissions and -* limitations under the License. -*/ - package org.opencb.opencga.app.cli.main; import org.jline.reader.Candidate; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index f2bcf34a63c..33d53de3bf8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,19 +1,3 @@ -/* -* Copyright 2015-2024-04-29 OpenCB -* -* Licensed under the Apache License, Version 2.0 (the "License"); -* you may not use this file except in compliance with the License. -* You may obtain a copy of the License at -* -* http://www.apache.org/licenses/LICENSE-2.0 -* -* Unless required by applicable law or agreed to in writing, software -* distributed under the License is distributed on an "AS IS" BASIS, -* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -* See the License for the specific language governing permissions and -* limitations under the License. -*/ - package org.opencb.opencga.app.cli.main; import com.beust.jcommander.JCommander; diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 21ccff3b4da..d63a1ad3478 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 363efca3f8f..398851faed5 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 3d6e69ee4cb..195b5ad36f3 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,11 +1,11 @@ # ############################################################################## ## OrganizationClient -setGeneric("organizationClient", function(OpencgaR, organization, id, endpointName, params=NULL, ...) +setGeneric("organizationClient", function(OpencgaR, id, organization, endpointName, params=NULL, ...) standardGeneric("organizationClient")) # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, users, filterId, user, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -15,37 +15,37 @@ setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, members, group, id, variableSet, templateId, study, studies, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, group, id, members, studies, study, templateId, variableSet, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, members, folder, files, annotationSet, file, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, annotationSet, file, files, folder, members, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, members, samples, annotationSet, sample, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, annotationSet, members, sample, samples, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, members, individuals, individual, annotationSet, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, annotationSet, individual, individuals, members, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, members, families, annotationSet, family, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, annotationSet, families, family, members, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, annotationSet, cohort, cohorts, members, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -65,7 +65,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, members, interpretation, clinicalAnalysis, clinicalAnalyses, interpretations, annotationSet, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, annotationSet, clinicalAnalyses, clinicalAnalysis, interpretation, interpretations, members, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## @@ -80,7 +80,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## GA4GHClient -setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...) +setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=NULL, ...) standardGeneric("ga4ghClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index 675d8f0c9bb..f9d9f038ae1 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -62,7 +61,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, interpretation, clinicalAnalysis, clinicalAnalyses, interpretations, annotationSet, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinicalAnalyses, clinicalAnalysis, interpretation, interpretations, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 771d7d16480..e510a05eba8 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +37,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohort, cohorts, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index dc1ad726ed4..de04b212196 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -37,7 +36,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, members, families, annotationSet, family, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, families, family, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 52d5b80e3f6..41ff659c258 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +53,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, files, annotationSet, file, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, file, files, folder, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index b134810eeb3..a6053502605 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -31,7 +30,7 @@ #' [*]: Required parameter #' @export -setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) { +setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/ga4gh/reads/search: diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index ab204922c49..9a3bc092adc 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +37,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individuals, individual, annotationSet, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, annotationSet, individual, individuals, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index c48e3ae9691..df80a2c29cc 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index 8fd2202e69f..8da8f31ca44 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 868d718b61c..ecd586a9ed7 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Organization-methods.R b/opencga-client/src/main/R/R/Organization-methods.R index fd5681c5378..3efaf5eec2f 100644 --- a/opencga-client/src/main/R/R/Organization-methods.R +++ b/opencga-client/src/main/R/R/Organization-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -34,7 +33,7 @@ #' [*]: Required parameter #' @export -setMethod("organizationClient", "OpencgaR", function(OpencgaR, organization, id, endpointName, params=NULL, ...) { +setMethod("organizationClient", "OpencgaR", function(OpencgaR, id, organization, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/organizations/create: diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index 6f9d0bebb47..b23b8043f55 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 41235ecea72..380d33ea815 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index b61ca7558ca..a5434ddb451 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +37,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, samples, annotationSet, sample, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, members, sample, samples, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 81f0e582a7c..95104111011 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -49,7 +48,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, members, group, id, variableSet, templateId, study, studies, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, group, id, members, studies, study, templateId, variableSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index 4b6e2d76c67..ffc1c599ca9 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, users, filterId, user, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/anonymous: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 8bc5c25558b..95fba46fac9 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,6 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-04-29 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index a74cbd784c4..928fd361341 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -37,7 +37,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +45,6 @@ /** * This class contains methods for the Admin webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: admin */ public class AdminClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index 5d3cef8c796..ca1e1ecc744 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -49,7 +48,6 @@ /** * This class contains methods for the Alignment webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: analysis/alignment */ public class AlignmentClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index f12aa75b765..976ea17a4f6 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -55,7 +55,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -64,7 +63,6 @@ /** * This class contains methods for the ClinicalAnalysis webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: analysis/clinical */ public class ClinicalAnalysisClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalClient.java deleted file mode 100644 index 67bb142fc41..00000000000 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalClient.java +++ /dev/null @@ -1,914 +0,0 @@ -/* -* Copyright 2015-2022 OpenCB -* -* Licensed under the Apache License, Version 2.0 (the "License"); -* you may not use this file except in compliance with the License. -* You may obtain a copy of the License at -* -* http://www.apache.org/licenses/LICENSE-2.0 -* -* Unless required by applicable law or agreed to in writing, software -* distributed under the License is distributed on an "AS IS" BASIS, -* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -* See the License for the specific language governing permissions and -* limitations under the License. -*/ - -package org.opencb.opencga.client.rest.clients; - -import org.opencb.biodata.models.clinical.interpretation.ClinicalVariant; -import org.opencb.commons.datastore.core.FacetField; -import org.opencb.commons.datastore.core.ObjectMap; -import org.opencb.opencga.client.config.ClientConfiguration; -import org.opencb.opencga.client.exceptions.ClientException; -import org.opencb.opencga.client.rest.AbstractParentClient; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByGeneSummary; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByIndividual; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByIndividualSummary; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByVariant; -import org.opencb.opencga.core.models.analysis.knockout.KnockoutByVariantSummary; -import org.opencb.opencga.core.models.analysis.knockout.RgaKnockoutByGene; -import org.opencb.opencga.core.models.clinical.CancerTieringInterpretationAnalysisParams; -import org.opencb.opencga.core.models.clinical.ClinicalAnalysis; -import org.opencb.opencga.core.models.clinical.ClinicalAnalysisAclUpdateParams; -import org.opencb.opencga.core.models.clinical.ClinicalAnalysisCreateParams; -import org.opencb.opencga.core.models.clinical.ClinicalAnalysisUpdateParams; -import org.opencb.opencga.core.models.clinical.Interpretation; -import org.opencb.opencga.core.models.clinical.InterpretationCreateParams; -import org.opencb.opencga.core.models.clinical.InterpretationUpdateParams; -import org.opencb.opencga.core.models.clinical.RgaAnalysisParams; -import org.opencb.opencga.core.models.clinical.TeamInterpretationAnalysisParams; -import org.opencb.opencga.core.models.clinical.TieringInterpretationAnalysisParams; -import org.opencb.opencga.core.models.clinical.ZettaInterpretationAnalysisParams; -import org.opencb.opencga.core.models.job.Job; -import org.opencb.opencga.core.models.study.configuration.ClinicalAnalysisStudyConfiguration; -import org.opencb.opencga.core.response.RestResponse; - - -/* -* WARNING: AUTOGENERATED CODE -* -* This code was generated by a tool. -* Autogenerated on: 2022-08-02 08:25:32 ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x -* -* Manual changes to this file may cause unexpected behavior in your application. -* Manual changes to this file will be overwritten if the code is regenerated. -*/ - - -/** - * This class contains methods for the Clinical webservices. - * Client version: 2.3.3-SNAPSHOT [fb5e7ed17448243b10ddd619bdf973e4b20b0a74] ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x - * PATH: analysis/clinical - */ -public class ClinicalClient extends AbstractParentClient { - - public ClinicalClient(String token, ClientConfiguration configuration) { - super(token, configuration); - } - - /** - * Update the set of permissions granted for the member. - * @param members Comma separated list of user or group IDs. - * @param action Action to be performed [ADD, SET, REMOVE or RESET]. - * @param data JSON containing the parameters to add ACLs. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * propagate: Propagate permissions to related families, individuals, samples and files. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse updateAcl(String members, String action, ClinicalAnalysisAclUpdateParams data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("action", action); - params.put("body", data); - return execute("analysis", null, "clinical/acl", members, "update", params, POST, ObjectMap.class); - } - - /** - * Update Clinical Analysis configuration. - * @param data Configuration params to update. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse updateClinicalConfiguration(ClinicalAnalysisStudyConfiguration data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/clinical/configuration", null, "update", params, POST, ObjectMap.class); - } - - /** - * Create a new clinical analysis. - * @param data JSON containing clinical analysis information. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * skipCreateDefaultInterpretation: Flag to skip creating and initialise an empty default primary interpretation (Id will be - * '{clinicalAnalysisId}.1'). This flag is only considered if no Interpretation object is passed. - * includeResult: Flag indicating to include the created or updated document result in the response. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse create(ClinicalAnalysisCreateParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical", null, "create", params, POST, ClinicalAnalysis.class); - } - - /** - * Clinical Analysis distinct method. - * @param field Field for which to obtain the distinct values. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. - * uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. - * type: Clinical Analysis type. - * disorder: Clinical Analysis disorder. - * files: Clinical Analysis files. - * sample: Sample associated to the proband or any member of a family. - * individual: Proband or any member of a family. - * proband: Clinical Analysis proband. - * probandSamples: Clinical Analysis proband samples. - * family: Clinical Analysis family. - * familyMembers: Clinical Analysis family members. - * familyMemberSamples: Clinical Analysis family members samples. - * panels: Clinical Analysis panels. - * locked: Locked Clinical Analyses. - * analystId: Clinical Analysis analyst id. - * priority: Clinical Analysis priority. - * flags: Clinical Analysis flags. - * creationDate: Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * modificationDate: Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * dueDate: Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * qualityControlSummary: Clinical Analysis quality control summary. - * release: Release when it was created. - * status: Filter by status. - * internalStatus: Filter by internal status. - * deleted: Boolean to retrieve deleted entries. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse distinct(String field, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("field", field); - return execute("analysis", null, "clinical", null, "distinct", params, GET, ObjectMap.class); - } - - /** - * Interpretation distinct method. - * @param field Field for which to obtain the distinct values. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Interpretation IDs up to a maximum of 100. - * uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. - * clinicalAnalysisId: Clinical Analysis id. - * analystId: Analyst ID. - * methodName: Interpretation method name. - * panels: Interpretation panels. - * primaryFindings: Interpretation primary findings. - * secondaryFindings: Interpretation secondary findings. - * creationDate: Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * modificationDate: Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * status: Filter by status. - * internalStatus: Filter by internal status. - * release: Release when it was created. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse distinctInterpretation(String field, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("field", field); - return execute("analysis", null, "clinical/interpretation", null, "distinct", params, GET, ObjectMap.class); - } - - /** - * Search clinical interpretations. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * sort: Sort the results. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Interpretation IDs up to a maximum of 100. - * uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. - * clinicalAnalysisId: Clinical Analysis id. - * analystId: Analyst ID. - * methodName: Interpretation method name. - * panels: Interpretation panels. - * primaryFindings: Interpretation primary findings. - * secondaryFindings: Interpretation secondary findings. - * creationDate: Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * modificationDate: Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * status: Filter by status. - * internalStatus: Filter by internal status. - * release: Release when it was created. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse searchInterpretation(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/interpretation", null, "search", params, GET, Interpretation.class); - } - - /** - * Clinical interpretation information. - * @param interpretations Comma separated list of clinical interpretation IDs up to a maximum of 100. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * version: Comma separated list of interpretation versions. 'all' to get all the interpretation versions. Not supported if - * multiple interpretation ids are provided. - * deleted: Boolean to retrieve deleted entries. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse infoInterpretation(String interpretations, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/interpretation", interpretations, "info", params, GET, Interpretation.class); - } - - /** - * Run cancer tiering interpretation analysis. - * @param data Cancer tiering interpretation analysis params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runInterpreterCancerTiering(CancerTieringInterpretationAnalysisParams data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/interpreter/cancerTiering", null, "run", params, POST, Job.class); - } - - /** - * Run TEAM interpretation analysis. - * @param data TEAM interpretation analysis params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runInterpreterTeam(TeamInterpretationAnalysisParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/interpreter/team", null, "run", params, POST, Job.class); - } - - /** - * Run tiering interpretation analysis. - * @param data Tiering interpretation analysis params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runInterpreterTiering(TieringInterpretationAnalysisParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/interpreter/tiering", null, "run", params, POST, Job.class); - } - - /** - * Run Zetta interpretation analysis. - * @param data Zetta interpretation analysis params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runInterpreterZetta(ZettaInterpretationAnalysisParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/interpreter/zetta", null, "run", params, POST, Job.class); - } - - /** - * RGA aggregation stats. - * @param field List of fields separated by semicolons, e.g.: clinicalSignificances;type. For nested fields use >>, e.g.: - * type>>clinicalSignificances;knockoutType. - * @param params Map containing any of the following optional parameters. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse aggregationStatsRga(String field, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("field", field); - return execute("analysis", null, "clinical/rga", null, "aggregationStats", params, GET, FacetField.class); - } - - /** - * Query gene RGA. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * includeIndividual: Include only the comma separated list of individuals to the response. - * skipIndividual: Number of individuals to skip. - * limitIndividual: Limit number of individuals returned (default: 1000). - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse queryRgaGene(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/gene", null, "query", params, GET, RgaKnockoutByGene.class); - } - - /** - * RGA gene summary stats. - * @param params Map containing any of the following optional parameters. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse summaryRgaGene(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/gene", null, "summary", params, GET, KnockoutByGeneSummary.class); - } - - /** - * Generate Recessive Gene Analysis secondary index. - * @param data Recessive Gene Analysis index params. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. - * jobDescription: Job description. - * jobDependsOn: Comma separated list of existing job IDs the job will depend on. - * jobTags: Job tags. - * auxiliarIndex: Index auxiliar collection to improve performance assuming RGA is completely indexed. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse runRgaIndex(RgaAnalysisParams data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical/rga/index", null, "run", params, POST, Job.class); - } - - /** - * Query individual RGA. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse queryRgaIndividual(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/individual", null, "query", params, GET, KnockoutByIndividual.class); - } - - /** - * RGA individual summary stats. - * @param params Map containing any of the following optional parameters. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse summaryRgaIndividual(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/individual", null, "summary", params, GET, KnockoutByIndividualSummary.class); - } - - /** - * Query variant RGA. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * includeIndividual: Include only the comma separated list of individuals to the response. - * skipIndividual: Number of individuals to skip. - * limitIndividual: Limit number of individuals returned (default: 1000). - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse queryRgaVariant(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/variant", null, "query", params, GET, KnockoutByVariant.class); - } - - /** - * RGA variant summary stats. - * @param params Map containing any of the following optional parameters. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * sampleId: Filter by sample id. - * individualId: Filter by individual id. - * sex: Filter by sex. - * phenotypes: Filter by phenotypes. - * disorders: Filter by disorders. - * numParents: Filter by the number of parents registered. - * geneId: Filter by gene id. - * geneName: Filter by gene name. - * chromosome: Filter by chromosome. - * start: Filter by start position. - * end: Filter by end position. - * transcriptId: Filter by transcript id. - * variants: Filter by variant id. - * dbSnps: Filter by DB_SNP id. - * knockoutType: Filter by knockout type. - * filter: Filter by filter (PASS, NOT_PASS). - * type: Filter by variant type. - * clinicalSignificance: Filter by clinical significance. - * populationFrequency: Filter by population frequency. - * consequenceType: Filter by consequence type. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse summaryRgaVariant(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/rga/variant", null, "summary", params, GET, KnockoutByVariantSummary.class); - } - - /** - * Clinical analysis search. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. - * uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. - * type: Clinical Analysis type. - * disorder: Clinical Analysis disorder. - * files: Clinical Analysis files. - * sample: Sample associated to the proband or any member of a family. - * individual: Proband or any member of a family. - * proband: Clinical Analysis proband. - * probandSamples: Clinical Analysis proband samples. - * family: Clinical Analysis family. - * familyMembers: Clinical Analysis family members. - * familyMemberSamples: Clinical Analysis family members samples. - * panels: Clinical Analysis panels. - * locked: Locked Clinical Analyses. - * analystId: Clinical Analysis analyst id. - * priority: Clinical Analysis priority. - * flags: Clinical Analysis flags. - * creationDate: Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * modificationDate: Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * dueDate: Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * qualityControlSummary: Clinical Analysis quality control summary. - * release: Release when it was created. - * status: Filter by status. - * internalStatus: Filter by internal status. - * deleted: Boolean to retrieve deleted entries. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse search(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical", null, "search", params, GET, ClinicalAnalysis.class); - } - - /** - * Fetch actionable clinical variants. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * sample: Sample ID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse actionableVariant(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/variant", null, "actionable", params, GET, ClinicalVariant.class); - } - - /** - * Fetch clinical variants. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * limit: Number of results to be returned. - * skip: Number of results to skip. - * count: Get the total number of results matching the query. Deactivated by default. - * approximateCount: Get an approximate count, instead of an exact total count. Reduces execution time. - * approximateCountSamplingSize: Sampling size to get the approximate count. Larger values increase accuracy but also increase - * execution time. - * savedFilter: Use a saved filter at User level. - * id: List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T. - * region: List of regions, these can be just a single chromosome name or regions in the format chr:start-end, e.g.: - * 2,3:100000-200000. - * type: List of types, accepted values are SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION, - * DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL. - * study: Filter variants from the given studies, these can be either the numeric ID or the alias with the format - * organization@project:study. - * file: Filter variants from the files specified. This will set includeFile parameter when not provided. - * filter: Specify the FILTER for any of the files. If 'file' filter is provided, will match the file and the filter. e.g.: - * PASS,LowGQX. - * qual: Specify the QUAL for any of the files. If 'file' filter is provided, will match the file and the qual. e.g.: >123.4. - * fileData: Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file - * is specified, will use all files from "file" filter. e.g. AN>200 or file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can - * be combined. e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP. - * sample: Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This - * filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) - * operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) - * operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. - * 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, - * regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, - * HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with - * segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, - * compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . - * sampleData: Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will - * use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be - * combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. - * sampleAnnotation: Selects some samples using metadata information from Catalog. e.g. - * age>20;phenotype=hpo:123,hpo:456;name=smith. - * cohort: Select variants with calculated stats for the selected cohorts. - * cohortStatsRef: Reference Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * cohortStatsAlt: Alternate Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * cohortStatsMaf: Minor Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * cohortStatsMgf: Minor Genotype Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * cohortStatsPass: Filter PASS frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8. - * missingAlleles: Number of missing alleles: [{study:}]{cohort}[<|>|<=|>=]{number}. - * missingGenotypes: Number of missing genotypes: [{study:}]{cohort}[<|>|<=|>=]{number}. - * score: Filter by variant score: [{study:}]{score}[<|>|<=|>=]{number}. - * family: Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT). - * familyDisorder: Specify the disorder to use for the family segregation. - * familySegregation: Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, - * XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. - * familyMembers: Sub set of the members of a given family. - * familyProband: Specify the proband child to use for the family segregation. - * gene: List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' parameter. - * ct: List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' - * and 'protein_altering'. - * xref: List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, - * dbSNP, ClinVar, HPO, Cosmic, ... - * biotype: List of biotypes, e.g. protein_coding. - * proteinSubstitution: Protein substitution scores include SIFT and PolyPhen. You can query using the score - * {protein_score}[<|>|<=|>=]{number} or the description {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant. - * conservation: Filter by conservation score: {conservation_score}[<|>|<=|>=]{number} e.g. phastCons>0.5,phylop<0.1,gerp>0.1. - * populationFrequencyAlt: Alternate Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - * populationFrequencyRef: Reference Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - * populationFrequencyMaf: Population minor allele frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - * transcriptFlag: List of transcript flags. e.g. canonical, CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc, - * TSO500. - * geneTraitId: List of gene trait association id. e.g. "umls:C0007222" , "OMIM:269600". - * go: List of GO (Gene Ontology) terms. e.g. "GO:0002020". - * expression: List of tissues of interest. e.g. "lung". - * proteinKeyword: List of Uniprot protein variant annotation keywords. - * drug: List of drug names. - * functionalScore: Functional score: {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 , cadd_raw<=0.3. - * clinical: Clinical source: clinvar, cosmic. - * clinicalSignificance: Clinical significance: benign, likely_benign, likely_pathogenic, pathogenic. - * clinicalConfirmedStatus: Clinical confirmed status. - * customAnnotation: Custom annotation: {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}. - * panel: Filter by genes from the given disease panel. - * panelModeOfInheritance: Filter genes from specific panels that match certain mode of inheritance. Accepted values : [ - * autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, - * compoundHeterozygous ]. - * panelConfidence: Filter genes from specific panels that match certain confidence. Accepted values : [ high, medium, low, - * rejected ]. - * panelRoleInCancer: Filter genes from specific panels that match certain role in cancer. Accepted values : [ both, oncogene, - * tumorSuppressorGene, fusion ]. - * panelFeatureType: Filter elements from specific panels by type. Accepted values : [ gene, region, str, variant ]. - * panelIntersection: Intersect panel genes and regions with given genes and regions from que input query. This will prevent - * returning variants from regions out of the panel. - * trait: List of traits, based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies, descriptions,... - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse queryVariant(ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical/variant", null, "query", params, GET, ClinicalVariant.class); - } - - /** - * Returns the acl of the clinical analyses. If member is provided, it will only return the acl for the member. - * @param clinicalAnalyses Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * member: User or group ID. - * silent: Boolean to retrieve all possible entries that are queried for, false to raise an exception whenever one of the entries - * looked for cannot be shown for whichever reason. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse acl(String clinicalAnalyses, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical", clinicalAnalyses, "acl", params, GET, ObjectMap.class); - } - - /** - * Delete clinical analyses. - * @param clinicalAnalyses Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param params Map containing any of the following optional parameters. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * force: Force deletion if the ClinicalAnalysis contains interpretations or is locked. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse delete(String clinicalAnalyses, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical", clinicalAnalyses, "delete", params, DELETE, ClinicalAnalysis.class); - } - - /** - * Update clinical analysis attributes. - * @param clinicalAnalyses Comma separated list of clinical analysis IDs. - * @param data JSON containing clinical analysis information. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * commentsAction: Action to be performed if the array of comments is being updated. - * flagsAction: Action to be performed if the array of flags is being updated. - * filesAction: Action to be performed if the array of files is being updated. - * panelsAction: Action to be performed if the array of panels is being updated. - * includeResult: Flag indicating to include the created or updated document result in the response. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse update(String clinicalAnalyses, ClinicalAnalysisUpdateParams data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis", null, "clinical", clinicalAnalyses, "update", params, POST, ClinicalAnalysis.class); - } - - /** - * Clinical analysis info. - * @param clinicalAnalysis Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: Study [[organization@]project:]study where study and project can be either the ID or UUID. - * deleted: Boolean to retrieve deleted entries. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse info(String clinicalAnalysis, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis", null, "clinical", clinicalAnalysis, "info", params, GET, ClinicalAnalysis.class); - } - - /** - * Create a new Interpretation. - * @param clinicalAnalysis Clinical analysis ID. - * @param data JSON containing clinical interpretation information. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: [[organization@]project:]study id. - * setAs: Set interpretation as. - * includeResult: Flag indicating to include the created or updated document result in the response. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse createInterpretation(String clinicalAnalysis, InterpretationCreateParams data, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", null, "create", params, POST, Interpretation.class); - } - - /** - * Clear the fields of the main interpretation of the Clinical Analysis. - * @param clinicalAnalysis Clinical analysis ID. - * @param interpretations Interpretation IDs of the Clinical Analysis. - * @param params Map containing any of the following optional parameters. - * study: [[organization@]project:]study ID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse clearInterpretation(String clinicalAnalysis, String interpretations, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "clear", params, POST, - Interpretation.class); - } - - /** - * Delete interpretation. - * @param clinicalAnalysis Clinical analysis ID. - * @param interpretations Interpretation IDs of the Clinical Analysis. - * @param params Map containing any of the following optional parameters. - * study: [[organization@]project:]study ID. - * setAsPrimary: Interpretation id to set as primary from the list of secondaries in case of deleting the actual primary one. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse deleteInterpretation(String clinicalAnalysis, String interpretations, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "delete", params, DELETE, - Interpretation.class); - } - - /** - * Revert to a previous interpretation version. - * @param clinicalAnalysis Clinical analysis ID. - * @param interpretation Interpretation ID. - * @param version Version to revert to. - * @param params Map containing any of the following optional parameters. - * study: [[organization@]project:]study ID. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse revertInterpretation(String clinicalAnalysis, String interpretation, int version, ObjectMap params) - throws ClientException { - params = params != null ? params : new ObjectMap(); - params.putIfNotNull("version", version); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "revert", params, POST, - Interpretation.class); - } - - /** - * Update interpretation fields. - * @param clinicalAnalysis Clinical analysis ID. - * @param interpretation Interpretation ID. - * @param data JSON containing clinical interpretation information. - * @param params Map containing any of the following optional parameters. - * include: Fields included in the response, whole JSON path must be provided. - * exclude: Fields excluded in the response, whole JSON path must be provided. - * study: [[organization@]project:]study ID. - * primaryFindingsAction: Action to be performed if the array of primary findings is being updated. - * methodsAction: Action to be performed if the array of methods is being updated. - * secondaryFindingsAction: Action to be performed if the array of secondary findings is being updated. - * commentsAction: Action to be performed if the array of comments is being updated. To REMOVE or REPLACE, the date will need to - * be provided to identify the comment. - * panelsAction: Action to be performed if the array of panels is being updated. - * setAs: Set interpretation as. - * includeResult: Flag indicating to include the created or updated document result in the response. - * @return a RestResponse object. - * @throws ClientException ClientException if there is any server error. - */ - public RestResponse updateInterpretation(String clinicalAnalysis, String interpretation, InterpretationUpdateParams - data, ObjectMap params) throws ClientException { - params = params != null ? params : new ObjectMap(); - params.put("body", data); - return execute("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "update", params, POST, - Interpretation.class); - } -} diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 127e40de626..0bcb27158a8 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -36,7 +36,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +44,6 @@ /** * This class contains methods for the Cohort webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: cohorts */ public class CohortClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index d55854b6127..ead924800fa 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -44,7 +43,6 @@ /** * This class contains methods for the DiseasePanel webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: panels */ public class DiseasePanelClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 663903149db..368cf2eb4a5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -35,7 +35,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -44,7 +43,6 @@ /** * This class contains methods for the Family webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: families */ public class FamilyClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 0fe1fba1940..09cc5ab8c25 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -52,7 +51,6 @@ /** * This class contains methods for the File webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: files */ public class FileClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index 0e14eba34d8..e1eb10bd8a1 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -36,7 +35,6 @@ /** * This class contains methods for the GA4GH webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: ga4gh */ public class GA4GHClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index 5598bf2ec81..571f7b8953f 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -35,7 +35,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -44,7 +43,6 @@ /** * This class contains methods for the Individual webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: individuals */ public class IndividualClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 02037990104..523523ab4b3 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -36,7 +36,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +44,6 @@ /** * This class contains methods for the Job webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: jobs */ public class JobClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index 8826ff88f90..8401614fec4 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -37,7 +36,6 @@ /** * This class contains methods for the Meta webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: meta */ public class MetaClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java index e1ec2b30ebf..aebe0ba61f5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java @@ -33,7 +33,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -42,7 +41,6 @@ /** * This class contains methods for the Organization webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: organizations */ public class OrganizationClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 23b5a0f0afd..53ecaea4610 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -31,7 +31,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +39,6 @@ /** * This class contains methods for the Project webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: projects */ public class ProjectClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index 5f69fa0997a..811dcbfe08c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -35,7 +35,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -44,7 +43,6 @@ /** * This class contains methods for the Sample webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: samples */ public class SampleClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 02383dedf92..71e89be53fb 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -47,7 +47,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -56,7 +55,6 @@ /** * This class contains methods for the Study webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: studies */ public class StudyClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index bdadc50c29b..ee290b40d21 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +44,6 @@ /** * This class contains methods for the User webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: users */ public class UserClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index 58f15654b8d..93ae92a1d88 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -71,7 +70,6 @@ /** * This class contains methods for the Variant webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: analysis/variant */ public class VariantClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index 31b832fd1bd..9731eb2bcc0 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -59,7 +58,6 @@ /** * This class contains methods for the VariantOperation webservices. - * Client version: 3.1.0-SNAPSHOT * PATH: operation */ public class VariantOperationClient extends AbstractParentClient { diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 7fcab038434..d383816bf1d 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 1ec703a5d46..ed8a3bbfd92 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index e445a613946..7c5dc0a1945 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 6f9ac1e3c22..77eab098fce 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index 4343bc420dc..22e1396f73d 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index 245c24abe04..2373953dd6e 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index 0a085be817c..b58a521aa0e 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index 1bef974d359..a1eef8aa57f 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index ce94d506024..54b26ab6614 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 1d2aa95b0cc..9723d0f2581 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 6d9869452f1..2d87a490250 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Organization.js b/opencga-client/src/main/javascript/Organization.js index a429ccf6868..655ef3f691d 100644 --- a/opencga-client/src/main/javascript/Organization.js +++ b/opencga-client/src/main/javascript/Organization.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index e58af550ded..3c6fc5e3c66 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index f4ae4e29625..7d149016fbe 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index d13f1d427c3..c7d8fa7132c 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index e478e03db6f..07f92f42d1e 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index c341d110c64..ea198944e5c 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index a178fbbddcf..38408792d25 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,6 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-04-29 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index ead2235886b..7311fa7e5dd 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Admin(_ParentRestClient): """ This class contains methods for the 'Admin' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/admin """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index 313d3223ade..4924a3e1233 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Alignment(_ParentRestClient): """ This class contains methods for the 'Analysis - Alignment' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/analysis/alignment """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index d43bfa65210..e66873eba68 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class ClinicalAnalysis(_ParentRestClient): """ This class contains methods for the 'Analysis - Clinical' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/analysis/clinical """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_client.py deleted file mode 100644 index 3c42c2e0a16..00000000000 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_client.py +++ /dev/null @@ -1,1005 +0,0 @@ -""" -WARNING: AUTOGENERATED CODE - - This code was generated by a tool. - Autogenerated on: 2022-08-02 08:25:32 ->>>>>>> develop ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x - - Manual changes to this file may cause unexpected behavior in your application. - Manual changes to this file will be overwritten if the code is regenerated. -""" - -from pyopencga.rest_clients._parent_rest_clients import _ParentRestClient - - -class Clinical(_ParentRestClient): - """ - This class contains methods for the 'Analysis - Clinical' webservices - Client version: 2.3.3-SNAPSHOT [fb5e7ed17448243b10ddd619bdf973e4b20b0a74] ->>>>>>> develop ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x - PATH: /{apiVersion}/analysis/clinical - """ - - def __init__(self, configuration, token=None, login_handler=None, *args, **kwargs): - super(Clinical, self).__init__(configuration, token, login_handler, *args, **kwargs) - - def update_acl(self, members, action, data=None, **options): - """ - Update the set of permissions granted for the member. - PATH: /{apiVersion}/analysis/clinical/acl/{members}/update - - :param dict data: JSON containing the parameters to add ACLs. - (REQUIRED) - :param str action: Action to be performed [ADD, SET, REMOVE or RESET]. - (REQUIRED) - :param str members: Comma separated list of user or group IDs. - (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param bool propagate: Propagate permissions to related families, - individuals, samples and files. - """ - - options['action'] = action - return self._post(category='analysis', resource='update', subcategory='clinical/acl', second_query_id=members, data=data, **options) - - def update_clinical_configuration(self, data=None, **options): - """ - Update Clinical Analysis configuration. - PATH: /{apiVersion}/analysis/clinical/clinical/configuration/update - - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param dict data: Configuration params to update. - """ - - return self._post(category='analysis', resource='update', subcategory='clinical/clinical/configuration', data=data, **options) - - def create(self, data=None, **options): - """ - Create a new clinical analysis. - PATH: /{apiVersion}/analysis/clinical/create - - :param dict data: JSON containing clinical analysis information. - (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param bool skip_create_default_interpretation: Flag to skip creating - and initialise an empty default primary interpretation (Id will be - '{clinicalAnalysisId}.1'). This flag is only considered if no - Interpretation object is passed. - :param bool include_result: Flag indicating to include the created or - updated document result in the response. - """ - - return self._post(category='analysis', resource='create', subcategory='clinical', data=data, **options) - - def distinct(self, field, **options): - """ - Clinical Analysis distinct method. - PATH: /{apiVersion}/analysis/clinical/distinct - - :param str field: Field for which to obtain the distinct values. - (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str id: Comma separated list of Clinical Analysis IDs up to a - maximum of 100. - :param str uuid: Comma separated list of Clinical Analysis UUIDs up to - a maximum of 100. - :param str type: Clinical Analysis type. - :param str disorder: Clinical Analysis disorder. - :param str files: Clinical Analysis files. - :param str sample: Sample associated to the proband or any member of a - family. - :param str individual: Proband or any member of a family. - :param str proband: Clinical Analysis proband. - :param str proband_samples: Clinical Analysis proband samples. - :param str family: Clinical Analysis family. - :param str family_members: Clinical Analysis family members. - :param str family_member_samples: Clinical Analysis family members - samples. - :param str panels: Clinical Analysis panels. - :param bool locked: Locked Clinical Analyses. - :param str analyst_id: Clinical Analysis analyst id. - :param str priority: Clinical Analysis priority. - :param str flags: Clinical Analysis flags. - :param str creation_date: Clinical Analysis Creation date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str modification_date: Clinical Analysis Modification date. - Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str due_date: Clinical Analysis due date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str quality_control_summary: Clinical Analysis quality control - summary. - :param str release: Release when it was created. - :param str status: Filter by status. - :param str internal_status: Filter by internal status. - :param bool deleted: Boolean to retrieve deleted entries. - """ - - options['field'] = field - return self._get(category='analysis', resource='distinct', subcategory='clinical', **options) - - def distinct_interpretation(self, field, **options): - """ - Interpretation distinct method. - PATH: /{apiVersion}/analysis/clinical/interpretation/distinct - - :param str field: Field for which to obtain the distinct values. - (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str id: Comma separated list of Interpretation IDs up to a - maximum of 100. - :param str uuid: Comma separated list of Interpretation UUIDs up to a - maximum of 100. - :param str clinical_analysis_id: Clinical Analysis id. - :param str analyst_id: Analyst ID. - :param str method_name: Interpretation method name. - :param str panels: Interpretation panels. - :param str primary_findings: Interpretation primary findings. - :param str secondary_findings: Interpretation secondary findings. - :param str creation_date: Interpretation Creation date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str modification_date: Interpretation Modification date. - Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str status: Filter by status. - :param str internal_status: Filter by internal status. - :param str release: Release when it was created. - """ - - options['field'] = field - return self._get(category='analysis', resource='distinct', subcategory='clinical/interpretation', **options) - - def search_interpretation(self, **options): - """ - Search clinical interpretations. - PATH: /{apiVersion}/analysis/clinical/interpretation/search - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool sort: Sort the results. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str id: Comma separated list of Interpretation IDs up to a - maximum of 100. - :param str uuid: Comma separated list of Interpretation UUIDs up to a - maximum of 100. - :param str clinical_analysis_id: Clinical Analysis id. - :param str analyst_id: Analyst ID. - :param str method_name: Interpretation method name. - :param str panels: Interpretation panels. - :param str primary_findings: Interpretation primary findings. - :param str secondary_findings: Interpretation secondary findings. - :param str creation_date: Interpretation Creation date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str modification_date: Interpretation Modification date. - Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str status: Filter by status. - :param str internal_status: Filter by internal status. - :param str release: Release when it was created. - """ - - return self._get(category='analysis', resource='search', subcategory='clinical/interpretation', **options) - - def info_interpretation(self, interpretations, **options): - """ - Clinical interpretation information. - PATH: /{apiVersion}/analysis/clinical/interpretation/{interpretations}/info - - :param str interpretations: Comma separated list of clinical - interpretation IDs up to a maximum of 100. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str version: Comma separated list of interpretation versions. - 'all' to get all the interpretation versions. Not supported if - multiple interpretation ids are provided. - :param bool deleted: Boolean to retrieve deleted entries. - """ - - return self._get(category='analysis', resource='info', subcategory='clinical/interpretation', second_query_id=interpretations, **options) - - def run_interpreter_cancer_tiering(self, data=None, **options): - """ - Run cancer tiering interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/cancerTiering/run - - :param dict data: Cancer tiering interpretation analysis params. - (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/cancerTiering', data=data, **options) - - def run_interpreter_exomiser(self, data=None, **options): - """ - Run exomiser interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/exomiser/run - - :param dict data: Exomizer interpretation analysis params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/exomiser', data=data, **options) - - def run_interpreter_team(self, data=None, **options): - """ - Run TEAM interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/team/run - - :param dict data: TEAM interpretation analysis params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/team', data=data, **options) - - def run_interpreter_tiering(self, data=None, **options): - """ - Run tiering interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/tiering/run - - :param dict data: Tiering interpretation analysis params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/tiering', data=data, **options) - - def run_interpreter_zetta(self, data=None, **options): - """ - Run Zetta interpretation analysis. - PATH: /{apiVersion}/analysis/clinical/interpreter/zetta/run - - :param dict data: Zetta interpretation analysis params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/interpreter/zetta', data=data, **options) - - def aggregation_stats_rga(self, field, **options): - """ - RGA aggregation stats. - PATH: /{apiVersion}/analysis/clinical/rga/aggregationStats - - :param str field: List of fields separated by semicolons, e.g.: - clinicalSignificances;type. For nested fields use >>, e.g.: - type>>clinicalSignificances;knockoutType. (REQUIRED) - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - options['field'] = field - return self._get(category='analysis', resource='aggregationStats', subcategory='clinical/rga', **options) - - def query_rga_gene(self, **options): - """ - Query gene RGA. - PATH: /{apiVersion}/analysis/clinical/rga/gene/query - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str include_individual: Include only the comma separated list - of individuals to the response. - :param int skip_individual: Number of individuals to skip. - :param int limit_individual: Limit number of individuals returned - (default: 1000). - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='query', subcategory='clinical/rga/gene', **options) - - def summary_rga_gene(self, **options): - """ - RGA gene summary stats. - PATH: /{apiVersion}/analysis/clinical/rga/gene/summary - - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='summary', subcategory='clinical/rga/gene', **options) - - def run_rga_index(self, data=None, **options): - """ - Generate Recessive Gene Analysis secondary index. - PATH: /{apiVersion}/analysis/clinical/rga/index/run - - :param dict data: Recessive Gene Analysis index params. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str job_id: Job ID. It must be a unique string within the - study. An ID will be autogenerated automatically if not provided. - :param str job_description: Job description. - :param str job_depends_on: Comma separated list of existing job IDs - the job will depend on. - :param str job_tags: Job tags. - :param bool auxiliar_index: Index auxiliar collection to improve - performance assuming RGA is completely indexed. - """ - - return self._post(category='analysis', resource='run', subcategory='clinical/rga/index', data=data, **options) - - def query_rga_individual(self, **options): - """ - Query individual RGA. - PATH: /{apiVersion}/analysis/clinical/rga/individual/query - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='query', subcategory='clinical/rga/individual', **options) - - def summary_rga_individual(self, **options): - """ - RGA individual summary stats. - PATH: /{apiVersion}/analysis/clinical/rga/individual/summary - - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='summary', subcategory='clinical/rga/individual', **options) - - def query_rga_variant(self, **options): - """ - Query variant RGA. - PATH: /{apiVersion}/analysis/clinical/rga/variant/query - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str include_individual: Include only the comma separated list - of individuals to the response. - :param int skip_individual: Number of individuals to skip. - :param int limit_individual: Limit number of individuals returned - (default: 1000). - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='query', subcategory='clinical/rga/variant', **options) - - def summary_rga_variant(self, **options): - """ - RGA variant summary stats. - PATH: /{apiVersion}/analysis/clinical/rga/variant/summary - - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str sample_id: Filter by sample id. - :param str individual_id: Filter by individual id. - :param str sex: Filter by sex. - :param str phenotypes: Filter by phenotypes. - :param str disorders: Filter by disorders. - :param str num_parents: Filter by the number of parents registered. - :param str gene_id: Filter by gene id. - :param str gene_name: Filter by gene name. - :param str chromosome: Filter by chromosome. - :param str start: Filter by start position. - :param str end: Filter by end position. - :param str transcript_id: Filter by transcript id. - :param str variants: Filter by variant id. - :param str db_snps: Filter by DB_SNP id. - :param str knockout_type: Filter by knockout type. - :param str filter: Filter by filter (PASS, NOT_PASS). - :param str type: Filter by variant type. - :param str clinical_significance: Filter by clinical significance. - :param str population_frequency: Filter by population frequency. - :param str consequence_type: Filter by consequence type. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - """ - - return self._get(category='analysis', resource='summary', subcategory='clinical/rga/variant', **options) - - def search(self, **options): - """ - Clinical analysis search. - PATH: /{apiVersion}/analysis/clinical/search - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str id: Comma separated list of Clinical Analysis IDs up to a - maximum of 100. - :param str uuid: Comma separated list of Clinical Analysis UUIDs up to - a maximum of 100. - :param str type: Clinical Analysis type. - :param str disorder: Clinical Analysis disorder. - :param str files: Clinical Analysis files. - :param str sample: Sample associated to the proband or any member of a - family. - :param str individual: Proband or any member of a family. - :param str proband: Clinical Analysis proband. - :param str proband_samples: Clinical Analysis proband samples. - :param str family: Clinical Analysis family. - :param str family_members: Clinical Analysis family members. - :param str family_member_samples: Clinical Analysis family members - samples. - :param str panels: Clinical Analysis panels. - :param bool locked: Locked Clinical Analyses. - :param str analyst_id: Clinical Analysis analyst id. - :param str priority: Clinical Analysis priority. - :param str flags: Clinical Analysis flags. - :param str creation_date: Clinical Analysis Creation date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str modification_date: Clinical Analysis Modification date. - Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str due_date: Clinical Analysis due date. Format: - yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - :param str quality_control_summary: Clinical Analysis quality control - summary. - :param str release: Release when it was created. - :param str status: Filter by status. - :param str internal_status: Filter by internal status. - :param bool deleted: Boolean to retrieve deleted entries. - """ - - return self._get(category='analysis', resource='search', subcategory='clinical', **options) - - def actionable_variant(self, **options): - """ - Fetch actionable clinical variants. - PATH: /{apiVersion}/analysis/clinical/variant/actionable - - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str sample: Sample ID. - """ - - return self._get(category='analysis', resource='actionable', subcategory='clinical/variant', **options) - - def query_variant(self, **options): - """ - Fetch clinical variants. - PATH: /{apiVersion}/analysis/clinical/variant/query - - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param int limit: Number of results to be returned. - :param int skip: Number of results to skip. - :param bool count: Get the total number of results matching the query. - Deactivated by default. - :param bool approximate_count: Get an approximate count, instead of an - exact total count. Reduces execution time. - :param int approximate_count_sampling_size: Sampling size to get the - approximate count. Larger values increase accuracy but also - increase execution time. - :param str saved_filter: Use a saved filter at User level. - :param str id: List of IDs, these can be rs IDs (dbSNP) or variants in - the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T. - :param str region: List of regions, these can be just a single - chromosome name or regions in the format chr:start-end, e.g.: - 2,3:100000-200000. - :param str type: List of types, accepted values are SNV, MNV, INDEL, - SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION, - DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g. - SNV,INDEL. - :param str study: Filter variants from the given studies, these can be - either the numeric ID or the alias with the format - user@project:study. - :param str file: Filter variants from the files specified. This will - set includeFile parameter when not provided. - :param str filter: Specify the FILTER for any of the files. If 'file' - filter is provided, will match the file and the filter. e.g.: - PASS,LowGQX. - :param str qual: Specify the QUAL for any of the files. If 'file' - filter is provided, will match the file and the qual. e.g.: >123.4. - :param str file_data: Filter by file data (i.e. FILTER, QUAL and INFO - columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file - is specified, will use all files from 'file' filter. e.g. AN>200 or - file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined. - e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP. - :param str sample: Filter variants by sample genotype. This will - automatically set 'includeSample' parameter when not provided. This - filter accepts multiple 3 forms: 1) List of samples: Samples that - contain the main variant. Accepts AND (;) and OR (,) operators. - e.g. HG0097,HG0098 . 2) List of samples with genotypes: - {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. - HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will - also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice - versa. When filtering by multi-allelic genotypes, any secondary - allele will match, regardless of its position e.g. 1/2 will match - with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: - HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. - HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation - mode: {sample}:{segregation}. Only one sample accepted.Accepted - segregation modes: [ autosomalDominant, autosomalRecessive, - XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. Value is case insensitive. - e.g. HG0097:DeNovo Sample must have parents defined and indexed. . - :param str sample_data: Filter by any SampleData field from samples. - [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will - use all samples from 'sample' or 'genotype' filter. e.g. DP>200 or - HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be combined. - e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. - :param str sample_annotation: Selects some samples using metadata - information from Catalog. e.g. - age>20;phenotype=hpo:123,hpo:456;name=smith. - :param str cohort: Select variants with calculated stats for the - selected cohorts. - :param str cohort_stats_ref: Reference Allele Frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - :param str cohort_stats_alt: Alternate Allele Frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - :param str cohort_stats_maf: Minor Allele Frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - :param str cohort_stats_mgf: Minor Genotype Frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - :param str cohort_stats_pass: Filter PASS frequency: - [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8. - :param str missing_alleles: Number of missing alleles: - [{study:}]{cohort}[<|>|<=|>=]{number}. - :param str missing_genotypes: Number of missing genotypes: - [{study:}]{cohort}[<|>|<=|>=]{number}. - :param str score: Filter by variant score: - [{study:}]{score}[<|>|<=|>=]{number}. - :param str family: Filter variants where any of the samples from the - given family contains the variant (HET or HOM_ALT). - :param str family_disorder: Specify the disorder to use for the family - segregation. - :param str family_segregation: Filter by segregation mode from a given - family. Accepted values: [ autosomalDominant, autosomalRecessive, - XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - mendelianError, compoundHeterozygous ]. - :param str family_members: Sub set of the members of a given family. - :param str family_proband: Specify the proband child to use for the - family segregation. - :param str gene: List of genes, most gene IDs are accepted (HGNC, - Ensembl gene, ...). This is an alias to 'xref' parameter. - :param str ct: List of SO consequence types, e.g. - missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts - aliases 'loss_of_function' and 'protein_altering'. - :param str xref: List of any external reference, these can be genes, - proteins or variants. Accepted IDs include HGNC, Ensembl genes, - dbSNP, ClinVar, HPO, Cosmic, ... - :param str biotype: List of biotypes, e.g. protein_coding. - :param str protein_substitution: Protein substitution scores include - SIFT and PolyPhen. You can query using the score - {protein_score}[<|>|<=|>=]{number} or the description - {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant. - :param str conservation: Filter by conservation score: - {conservation_score}[<|>|<=|>=]{number} e.g. - phastCons>0.5,phylop<0.1,gerp>0.1. - :param str population_frequency_alt: Alternate Population Frequency: - {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - :param str population_frequency_ref: Reference Population Frequency: - {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01. - :param str population_frequency_maf: Population minor allele - frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. - 1000G:ALL<0.01. - :param str transcript_flag: List of transcript flags. e.g. canonical, - CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc, - TSO500. - :param str gene_trait_id: List of gene trait association id. e.g. - 'umls:C0007222' , 'OMIM:269600'. - :param str go: List of GO (Gene Ontology) terms. e.g. 'GO:0002020'. - :param str expression: List of tissues of interest. e.g. 'lung'. - :param str protein_keyword: List of Uniprot protein variant annotation - keywords. - :param str drug: List of drug names. - :param str functional_score: Functional score: - {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 , - cadd_raw<=0.3. - :param str clinical: Clinical source: clinvar, cosmic. - :param str clinical_significance: Clinical significance: benign, - likely_benign, likely_pathogenic, pathogenic. - :param bool clinical_confirmed_status: Clinical confirmed status. - :param str custom_annotation: Custom annotation: - {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}. - :param str panel: Filter by genes from the given disease panel. - :param str panel_mode_of_inheritance: Filter genes from specific - panels that match certain mode of inheritance. Accepted values : [ - autosomalDominant, autosomalRecessive, XLinkedDominant, - XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, - compoundHeterozygous ]. - :param str panel_confidence: Filter genes from specific panels that - match certain confidence. Accepted values : [ high, medium, low, - rejected ]. - :param str panel_role_in_cancer: Filter genes from specific panels - that match certain role in cancer. Accepted values : [ both, - oncogene, tumorSuppressorGene, fusion ]. - :param str panel_feature_type: Filter elements from specific panels by - type. Accepted values : [ gene, region, str, variant ]. - :param bool panel_intersection: Intersect panel genes and regions with - given genes and regions from que input query. This will prevent - returning variants from regions out of the panel. - :param str trait: List of traits, based on ClinVar, HPO, COSMIC, i.e.: - IDs, histologies, descriptions,... - """ - - return self._get(category='analysis', resource='query', subcategory='clinical/variant', **options) - - def acl(self, clinical_analyses, **options): - """ - Returns the acl of the clinical analyses. If member is provided, it - will only return the acl for the member. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalyses}/acl - - :param str clinical_analyses: Comma separated list of clinical - analysis IDs or names up to a maximum of 100. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str member: User or group ID. - :param bool silent: Boolean to retrieve all possible entries that are - queried for, false to raise an exception whenever one of the - entries looked for cannot be shown for whichever reason. - """ - - return self._get(category='analysis', resource='acl', subcategory='clinical', second_query_id=clinical_analyses, **options) - - def delete(self, clinical_analyses, **options): - """ - Delete clinical analyses. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalyses}/delete - - :param str clinical_analyses: Comma separated list of clinical - analysis IDs or names up to a maximum of 100. (REQUIRED) - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param bool force: Force deletion if the ClinicalAnalysis contains - interpretations or is locked. - """ - - return self._delete(category='analysis', resource='delete', subcategory='clinical', second_query_id=clinical_analyses, **options) - - def update(self, clinical_analyses, data=None, **options): - """ - Update clinical analysis attributes. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalyses}/update - - :param dict data: JSON containing clinical analysis information. - (REQUIRED) - :param str clinical_analyses: Comma separated list of clinical - analysis IDs. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param str comments_action: Action to be performed if the array of - comments is being updated. Allowed values: ['ADD', 'REMOVE', - 'REPLACE'] - :param str flags_action: Action to be performed if the array of flags - is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param str files_action: Action to be performed if the array of files - is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param str panels_action: Action to be performed if the array of - panels is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param bool include_result: Flag indicating to include the created or - updated document result in the response. - """ - - return self._post(category='analysis', resource='update', subcategory='clinical', second_query_id=clinical_analyses, data=data, **options) - - def info(self, clinical_analysis, **options): - """ - Clinical analysis info. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/info - - :param str clinical_analysis: Comma separated list of clinical - analysis IDs or names up to a maximum of 100. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: Study [[user@]project:]study where study and project - can be either the ID or UUID. - :param bool deleted: Boolean to retrieve deleted entries. - """ - - return self._get(category='analysis', resource='info', subcategory='clinical', second_query_id=clinical_analysis, **options) - - def create_interpretation(self, clinical_analysis, data=None, **options): - """ - Create a new Interpretation. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create - - :param dict data: JSON containing clinical interpretation information. - (REQUIRED) - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: [[user@]project:]study id. - :param str set_as: Set interpretation as. Allowed values: ['PRIMARY', - 'SECONDARY'] - :param bool include_result: Flag indicating to include the created or - updated document result in the response. - """ - - return self._post(category='analysis/clinical', resource='create', query_id=clinical_analysis, subcategory='interpretation', data=data, **options) - - def clear_interpretation(self, clinical_analysis, interpretations, **options): - """ - Clear the fields of the main interpretation of the Clinical Analysis. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/clear - - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str interpretations: Interpretation IDs of the Clinical - Analysis. (REQUIRED) - :param str study: [[user@]project:]study ID. - """ - - return self._post(category='analysis/clinical', resource='clear', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretations, **options) - - def delete_interpretation(self, clinical_analysis, interpretations, **options): - """ - Delete interpretation. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/delete - - :param str interpretations: Interpretation IDs of the Clinical - Analysis. (REQUIRED) - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str study: [[user@]project:]study ID. - :param str set_as_primary: Interpretation id to set as primary from - the list of secondaries in case of deleting the actual primary one. - """ - - return self._delete(category='analysis/clinical', resource='delete', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretations, **options) - - def revert_interpretation(self, clinical_analysis, interpretation, version, **options): - """ - Revert to a previous interpretation version. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/revert - - :param int version: Version to revert to. (REQUIRED) - :param str interpretation: Interpretation ID. (REQUIRED) - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str study: [[user@]project:]study ID. - """ - - options['version'] = version - return self._post(category='analysis/clinical', resource='revert', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretation, **options) - - def update_interpretation(self, clinical_analysis, interpretation, data=None, **options): - """ - Update interpretation fields. - PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update - - :param dict data: JSON containing clinical interpretation information. - (REQUIRED) - :param str interpretation: Interpretation ID. (REQUIRED) - :param str clinical_analysis: Clinical analysis ID. (REQUIRED) - :param str include: Fields included in the response, whole JSON path - must be provided. - :param str exclude: Fields excluded in the response, whole JSON path - must be provided. - :param str study: [[user@]project:]study ID. - :param str primary_findings_action: Action to be performed if the - array of primary findings is being updated. Allowed values: ['ADD', - 'SET', 'REMOVE', 'REPLACE'] - :param str methods_action: Action to be performed if the array of - methods is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param str secondary_findings_action: Action to be performed if the - array of secondary findings is being updated. Allowed values: - ['ADD', 'SET', 'REMOVE', 'REPLACE'] - :param str comments_action: Action to be performed if the array of - comments is being updated. To REMOVE or REPLACE, the date will need - to be provided to identify the comment. Allowed values: ['ADD', - 'REMOVE', 'REPLACE'] - :param str panels_action: Action to be performed if the array of - panels is being updated. Allowed values: ['ADD', 'SET', 'REMOVE'] - :param str set_as: Set interpretation as. Allowed values: ['PRIMARY', - 'SECONDARY'] - :param bool include_result: Flag indicating to include the created or - updated document result in the response. - """ - - return self._post(category='analysis/clinical', resource='update', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretation, data=data, **options) - diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 5772cf02ee5..f38109debed 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Cohort(_ParentRestClient): """ This class contains methods for the 'Cohorts' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/cohorts """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 0688b1f4c07..dff08d5a0f8 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class DiseasePanel(_ParentRestClient): """ This class contains methods for the 'Disease Panels' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/panels """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index e13a27bddf0..278c306bfe6 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Family(_ParentRestClient): """ This class contains methods for the 'Families' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/families """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 0d9c9655f4b..f922f15b910 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class File(_ParentRestClient): """ This class contains methods for the 'Files' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/files """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index c7e9bb9efeb..2b850d3c6fb 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class GA4GH(_ParentRestClient): """ This class contains methods for the 'GA4GH' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/ga4gh """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index a3c184edacd..515ca12ca0b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Individual(_ParentRestClient): """ This class contains methods for the 'Individuals' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/individuals """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 22d31ddfacd..459007a179f 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Job(_ParentRestClient): """ This class contains methods for the 'Jobs' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/jobs """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 130fa0aa824..39c13a7bcb7 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Meta(_ParentRestClient): """ This class contains methods for the 'Meta' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/meta """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py index 681e988c54d..a3124bfcf45 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Organization(_ParentRestClient): """ This class contains methods for the 'Organizations' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/organizations """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index 28bf4f3e914..dd650ac0f26 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Project(_ParentRestClient): """ This class contains methods for the 'Projects' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/projects """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index 8f6753319e5..6b10aac717f 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Sample(_ParentRestClient): """ This class contains methods for the 'Samples' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/samples """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index b6f496bf061..57826554192 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Study(_ParentRestClient): """ This class contains methods for the 'Studies' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/studies """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index 6bc479ff5f0..93451319d3d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class User(_ParentRestClient): """ This class contains methods for the 'Users' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/users """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index db47d5553a7..e1d63675309 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class Variant(_ParentRestClient): """ This class contains methods for the 'Analysis - Variant' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/analysis/variant """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index ffaa0dbb2e4..e726e9dd2db 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,6 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-04-29 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +13,6 @@ class VariantOperation(_ParentRestClient): """ This class contains methods for the 'Operations - Variant Storage' webservices - Client version: 3.1.0-SNAPSHOT PATH: /{apiVersion}/operation """ From 8386d44c8bc7387fa89c529e068c25d13d301c83 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Fri, 24 May 2024 08:51:48 +0100 Subject: [PATCH 55/59] client: Extract copyright from clients to a file. #TASK-6302 --- opencga-app/app/misc/clients/copyright.txt | 13 +++++++++ .../app/misc/clients/java_client_generator.py | 14 +--------- .../clients/javascript_client_generator.py | 12 ++------- .../app/misc/clients/rest_client_generator.py | 27 +++++++++++++++++++ .../server/generator/ClientsGenerator.java | 6 ++++- 5 files changed, 48 insertions(+), 24 deletions(-) create mode 100644 opencga-app/app/misc/clients/copyright.txt diff --git a/opencga-app/app/misc/clients/copyright.txt b/opencga-app/app/misc/clients/copyright.txt new file mode 100644 index 00000000000..5c551251867 --- /dev/null +++ b/opencga-app/app/misc/clients/copyright.txt @@ -0,0 +1,13 @@ +Copyright 2015-2024 OpenCB + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. \ No newline at end of file diff --git a/opencga-app/app/misc/clients/java_client_generator.py b/opencga-app/app/misc/clients/java_client_generator.py index d932d08eec6..f65a89983e9 100755 --- a/opencga-app/app/misc/clients/java_client_generator.py +++ b/opencga-app/app/misc/clients/java_client_generator.py @@ -36,19 +36,7 @@ def get_imports(self): headers = [] headers.append('/*') - headers.append('* Copyright 2015-' + str(date.today().year) + ' OpenCB') - headers.append('*') - headers.append('* Licensed under the Apache License, Version 2.0 (the "License");') - headers.append('* you may not use this file except in compliance with the License.') - headers.append('* You may obtain a copy of the License at') - headers.append('*') - headers.append('* http://www.apache.org/licenses/LICENSE-2.0') - headers.append('*') - headers.append('* Unless required by applicable law or agreed to in writing, software') - headers.append('* distributed under the License is distributed on an "AS IS" BASIS,') - headers.append('* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.') - headers.append('* See the License for the specific language governing permissions and') - headers.append('* limitations under the License.') + headers.append(self.get_copyright_message(prefix='* ')) headers.append('*/') headers.append('') # We need to calculate the Java package and no use: headers.append('package org.opencb.opencga.client.rest.clients;') diff --git a/opencga-app/app/misc/clients/javascript_client_generator.py b/opencga-app/app/misc/clients/javascript_client_generator.py index b6955e46fe4..2ac2fb88667 100644 --- a/opencga-app/app/misc/clients/javascript_client_generator.py +++ b/opencga-app/app/misc/clients/javascript_client_generator.py @@ -28,18 +28,10 @@ def __init__(self, server_url, output_dir): } def get_imports(self): + copyright = self.get_copyright_message(prefix=' * ') auto_msg = "\n * ".join(self.get_autogenerated_message()) return (f'/**\n' - f' * Copyright 2015-2020 OpenCB\n' - f' * Licensed under the Apache License, Version 2.0 (the "License");\n' - f' * you may not use this file except in compliance with the License.\n' - f' * You may obtain a copy of the License at\n' - f' * http://www.apache.org/licenses/LICENSE-2.0\n' - f' * Unless required by applicable law or agreed to in writing, software\n' - f' * distributed under the License is distributed on an "AS IS" BASIS,\n' - f' * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n' - f' * See the License for the specific language governing permissions and\n' - f' * limitations under the License.\n' + f'{copyright}\n' f' * {auto_msg}' f' \n *\n**/\n\n' f'import OpenCGAParentClass from "./../opencga-parent-class.js";\n\n') diff --git a/opencga-app/app/misc/clients/rest_client_generator.py b/opencga-app/app/misc/clients/rest_client_generator.py index 5fa98d9be8d..53ed2bdfd8f 100644 --- a/opencga-app/app/misc/clients/rest_client_generator.py +++ b/opencga-app/app/misc/clients/rest_client_generator.py @@ -56,6 +56,33 @@ def __init__(self, rest_api_file, output_dir): 'Admin': 'Admin' } + @staticmethod + def get_copyright_message(prefix=""): + # copyright = [ + # 'Copyright 2015-2024 OpenCB', + # '', + # 'Licensed under the Apache License, Version 2.0 (the "License");', + # 'you may not use this file except in compliance with the License.', + # 'You may obtain a copy of the License at', + # '', + # ' http://www.apache.org/licenses/LICENSE-2.0', + # '', + # 'Unless required by applicable law or agreed to in writing, software', + # 'distributed under the License is distributed on an "AS IS" BASIS,', + # 'WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.', + # 'See the License for the specific language governing permissions and', + # 'limitations under the License.' + # ] + copyright_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'copyright.txt') + print("Reading from file: ", copyright_file) + with open(copyright_file, 'r') as file: + copyright = file.read().splitlines() + ## Add prefix to each line + if prefix: + for line in range(len(copyright)): + copyright[line] = (prefix + copyright[line]).rstrip() + return "\n".join(copyright) + @staticmethod def get_autogenerated_message(): return [ diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/ClientsGenerator.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/ClientsGenerator.java index b9082449a32..f94a917e20f 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/ClientsGenerator.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/ClientsGenerator.java @@ -54,14 +54,18 @@ private void generateLibrary(String clientsGeneratorDir, String language, String System.out.println("outDir " + outDir); String binary = clientsGeneratorDir + "/" + language + "_client_generator.py"; ProcessBuilder processBuilder = new ProcessBuilder("python3", binary, restFilePath, outDir); + System.out.println("python3 " + binary + " " + restFilePath + " " + outDir); Process p; try { p = processBuilder.start(); BufferedReader input = new BufferedReader(new InputStreamReader(p.getInputStream())); + BufferedReader error = new BufferedReader(new InputStreamReader(p.getErrorStream())); String line; while ((line = input.readLine()) != null) { logger.info("{} library generator: {}", language, line); - System.out.println(language + " library generator: " + line); + } + while ((line = error.readLine()) != null) { + logger.error("{} library generator: {}", language, line); } p.waitFor(); input.close(); From dcff2e390f6b1b4390e6057685ed42b5acb0d962 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Fri, 24 May 2024 09:40:30 +0100 Subject: [PATCH 56/59] client: Autogenerate clients. #TASK-6302 --- opencga-client/src/main/javascript/Admin.js | 7 +++++-- opencga-client/src/main/javascript/Alignment.js | 7 +++++-- opencga-client/src/main/javascript/ClinicalAnalysis.js | 7 +++++-- opencga-client/src/main/javascript/Cohort.js | 7 +++++-- opencga-client/src/main/javascript/DiseasePanel.js | 7 +++++-- opencga-client/src/main/javascript/Family.js | 7 +++++-- opencga-client/src/main/javascript/File.js | 7 +++++-- opencga-client/src/main/javascript/GA4GH.js | 7 +++++-- opencga-client/src/main/javascript/Individual.js | 7 +++++-- opencga-client/src/main/javascript/Job.js | 7 +++++-- opencga-client/src/main/javascript/Meta.js | 7 +++++-- opencga-client/src/main/javascript/Organization.js | 7 +++++-- opencga-client/src/main/javascript/Project.js | 7 +++++-- opencga-client/src/main/javascript/Sample.js | 7 +++++-- opencga-client/src/main/javascript/Study.js | 7 +++++-- opencga-client/src/main/javascript/User.js | 7 +++++-- opencga-client/src/main/javascript/Variant.js | 7 +++++-- opencga-client/src/main/javascript/VariantOperation.js | 7 +++++-- 18 files changed, 90 insertions(+), 36 deletions(-) diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index d383816bf1d..3f6204d4165 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index ed8a3bbfd92..0b374aab6a5 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 7c5dc0a1945..265e9e28a2b 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 77eab098fce..dcd44092cc6 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index 22e1396f73d..b23920896d2 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index 2373953dd6e..55a5ac0caf6 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index b58a521aa0e..80c275318ef 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index a1eef8aa57f..02af95b1363 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index 54b26ab6614..fb33520e6db 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 9723d0f2581..e9014ed296f 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 2d87a490250..0a536de0c03 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Organization.js b/opencga-client/src/main/javascript/Organization.js index 655ef3f691d..4385a545eb0 100644 --- a/opencga-client/src/main/javascript/Organization.js +++ b/opencga-client/src/main/javascript/Organization.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index 3c6fc5e3c66..524221df852 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index 7d149016fbe..48edf930fc8 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index c7d8fa7132c..1be4598d5bc 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index 07f92f42d1e..843416dd14e 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index ea198944e5c..177fdffdae3 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index 38408792d25..6f2ce1afafa 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -1,9 +1,12 @@ /** - * Copyright 2015-2020 OpenCB + * Copyright 2015-2024 OpenCB + * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. From f9291aef0b4d7607d8ba2cf09a4bc1237152535b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 24 May 2024 13:09:33 +0200 Subject: [PATCH 57/59] pom:Fix number version #TASK-6256 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 27 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 8e87f263f06..e0b30a8882d 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index bfbd58793b9..69ea6975e71 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 16647aebdec..b078878178e 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 832dde11be9..183d0de46d6 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index e18104a17bc..d309c1542dd 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index eb2c6d0f786..05ca25079e5 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 7e3925bb9fe..87f8dd26c76 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index be27dc552d0..3a54e9267c6 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6eb6c110bd5..b920b27a6bf 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 80c167215df..4ffcee0a682 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 2e2ee67cc27..14d41561c1f 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 2d5dbebf91b..2723f7bdd83 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 9708846e4f8..557b499da4a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 797c371a6a7..943104d930b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index 2d1922b3655..bc7929a5e5b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 803fee44a25..3ead859cde8 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 0a7cea85134..3aa6c664266 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 452570b992b..0afb37a331e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 7c6cbacda94..29d98c3fb1e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 0cca28f1721..35bfaf2b683 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 7e8d9e80136..b39ecfa1c28 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 10d9d270831..c799f4e1278 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index ac1e8071fb5..b9dc4e7afe0 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 69f063a9a44..e6f50d31070 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 0347eca3180..45b0e418665 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index da8d02db513..c8a06679244 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 181affb30a7..0d8e82fe5e3 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT pom OpenCGA From 39fed2253b2af85dae6cf961208b748244b9a231 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 29 May 2024 16:33:26 +0200 Subject: [PATCH 58/59] Prepare release 3.0.0.1 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 6 +++--- 27 files changed, 29 insertions(+), 29 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index e0b30a8882d..f360b51b820 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 69ea6975e71..a211147e294 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index b078878178e..4b0827a1058 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 183d0de46d6..b86efb944d4 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index d309c1542dd..ef56059fcb1 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 05ca25079e5..8942fdd2d11 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 87f8dd26c76..fb06b5d2b98 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 3a54e9267c6..846323d417d 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index b920b27a6bf..2715a9b06ac 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 4ffcee0a682..896868defdb 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 14d41561c1f..b62ec3d581f 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 2723f7bdd83..35d022c328d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 557b499da4a..48b48e0a406 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 943104d930b..b2ad7976f66 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index bc7929a5e5b..e10b7910ee9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 3ead859cde8..87a073c4d53 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 3aa6c664266..8da62fe6c4d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 0afb37a331e..298103a6ce9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 29d98c3fb1e..1062a0712d9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 35bfaf2b683..392730030fa 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index b39ecfa1c28..608cab88861 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index c799f4e1278..1b0e3907b90 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index b9dc4e7afe0..440a1fec50a 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index e6f50d31070..98bfb2231ee 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 45b0e418665..0615d0daa9b 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index c8a06679244..d43e29d0f30 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/pom.xml b/pom.xml index 0d8e82fe5e3..efdab0d6520 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 pom OpenCGA @@ -43,8 +43,8 @@ - 3.0.0 - 3.0.0 + + 3.0.0.1 6.0.0 3.0.0 5.0.0 From 79eafc9be1feae4ed488092c3e864aeaae71c57a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 10 Jun 2024 12:08:54 +0200 Subject: [PATCH 59/59] Prepare port patch #TASK-6281 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 27 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index f360b51b820..185192a6227 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index a211147e294..1c77750c7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 4b0827a1058..096c7abfae1 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index b86efb944d4..2582a5f2003 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index ef56059fcb1..16aff526b3e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 8942fdd2d11..73047a516e9 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index fb06b5d2b98..2348ef6f6f7 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 846323d417d..294acb88305 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 2715a9b06ac..1834d5c7e64 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 896868defdb..02953389c2d 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index b62ec3d581f..a7a2c8adbbb 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 35d022c328d..ea3dbc32689 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 48b48e0a406..927d616c88c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index b2ad7976f66..a84279ad4de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index e10b7910ee9..ea5b63a7b6f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 87a073c4d53..705f7b4104c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8da62fe6c4d..19c1294d041 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 298103a6ce9..3675d760a35 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 1062a0712d9..ee08e659ae7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 392730030fa..ffd41bdf7ca 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 608cab88861..435818c24cf 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 1b0e3907b90..495de2ebf89 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 440a1fec50a..7de2add12c5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 98bfb2231ee..d6d92f43dda 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 0615d0daa9b..2cbf9a9aa24 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index d43e29d0f30..76a6360d5e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index efdab0d6520..a15be286fbd 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT pom OpenCGA