Merge pull request #2422 from opencb/TASK-5922

TASK-5922 - Organization info doesn't return array of projects
opencb · Apr 17, 2024 · bdc444d · bdc444d
2 parents 8879e3a + f5cb4d6
commit bdc444d
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Showing 8 changed files with 187 additions and 36 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
@@ -95,9 +95,9 @@ public static QueryParams getParam(String key) {
 //
     OpenCGAResult<Organization> insert(Organization organization, QueryOptions options)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException;
-//
-//    OpenCGAResult<Project> get(String userId, QueryOptions options) throws CatalogDBException;
-//
+
+    OpenCGAResult<Organization> get(String userId, QueryOptions options) throws CatalogDBException;
+
     OpenCGAResult<Organization> get(QueryOptions options) throws CatalogDBException;
 //
 //    OpenCGAResult incrementCurrentRelease(long projectId) throws CatalogDBException;

diff --git a/...talog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptor.java b/...talog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptor.java
@@ -99,11 +99,24 @@ Organization insert(ClientSession clientSession, Organization organization)
         return organization;
     }
 
+    @Override
+    public OpenCGAResult<Organization> get(String user, QueryOptions options) throws CatalogDBException {
+        return get(null, user, options);
+    }
+
     @Override
     public OpenCGAResult<Organization> get(QueryOptions options) throws CatalogDBException {
-        return get(null, options);
+        return get(null, null, options);
+    }
+
+    OpenCGAResult<Organization> get(ClientSession clientSession, String user, QueryOptions options) throws CatalogDBException {
+        long startTime = startQuery();
+        try (DBIterator<Organization> dbIterator = iterator(clientSession, user, options)) {
+            return endQuery(startTime, dbIterator);
+        }
     }
 
+
     @Override
     public OpenCGAResult<Organization> update(String organizationId, ObjectMap parameters, QueryOptions queryOptions)
             throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException {
@@ -139,11 +152,11 @@ private OpenCGAResult<Organization> privateUpdate(ClientSession clientSession, S
         List<Event> events = new ArrayList<>();
         logger.debug("Update organization. Query: {}, Update: {}", queryBson.toBsonDocument(), organizationUpdate.toBsonDocument());
 
-        // Update study admins need to be before because we need to fetch the previous owner/admins in case of an update on these fields.
+        // Update study admins need to be executed before the actual update because we need to fetch the previous owner/admins in case
+        // of an update on these fields.
         updateStudyAdmins(clientSession, parameters, queryOptions);
         DataResult<?> updateResult = organizationCollection.update(clientSession, queryBson, organizationUpdate, null);
 
-
         if (updateResult.getNumMatches() == 0) {
             throw new CatalogDBException("Organization not found");
         }
@@ -161,7 +174,7 @@ private void updateStudyAdmins(ClientSession clientSession, ObjectMap parameters
             return;
         }
 
-        Organization organization = get(clientSession, OrganizationManager.INCLUDE_ORGANIZATION_ADMINS).first();
+        Organization organization = get(clientSession, null, OrganizationManager.INCLUDE_ORGANIZATION_ADMINS).first();
 
         if (parameters.containsKey(QueryParams.OWNER.key())) {
             // Owner has changed
@@ -234,7 +247,7 @@ private UpdateDocument getValidatedUpdateParams(ClientSession clientSession, Obj
                 throw new CatalogDBException("Could not update owner. User not found.");
             }
             // Fetch current owner
-            Organization organization = get(clientSession, OrganizationManager.INCLUDE_ORGANIZATION_ADMINS).first();
+            Organization organization = get(clientSession, null, OrganizationManager.INCLUDE_ORGANIZATION_ADMINS).first();
             if (owner.equals(organization.getOwner())) {
                 logger.warn("Organization owner is already '{}'.", owner);
             } else {
@@ -299,26 +312,19 @@ private UpdateDocument getValidatedUpdateParams(ClientSession clientSession, Obj
         return document;
     }
 
-    OpenCGAResult<Organization> get(ClientSession clientSession, QueryOptions options) throws CatalogDBException {
-        long startTime = startQuery();
-        try (DBIterator<Organization> dbIterator = iterator(clientSession, options)) {
-            return endQuery(startTime, dbIterator);
-        }
-    }
-
     @Override
     public OpenCGAResult<Organization> delete(Organization organization) throws CatalogDBException {
         return null;
     }
 
     @Override
     public DBIterator<Organization> iterator(QueryOptions options) throws CatalogDBException {
-        return iterator(null, options);
+        return iterator(null, null, options);
     }
 
-    public DBIterator<Organization> iterator(ClientSession clientSession, QueryOptions options) throws CatalogDBException {
+    public DBIterator<Organization> iterator(ClientSession clientSession, String user, QueryOptions options) throws CatalogDBException {
         MongoDBIterator<Document> mongoCursor = getMongoCursor(clientSession, options);
-        return new OrganizationCatalogMongoDBIterator<>(mongoCursor, clientSession, organizationConverter, dbAdaptorFactory, options);
+        return new OrganizationCatalogMongoDBIterator<>(mongoCursor, clientSession, organizationConverter, dbAdaptorFactory, options, user);
     }
 
     private MongoDBIterator<Document> getMongoCursor(ClientSession clientSession, QueryOptions options) {
@@ -338,7 +344,7 @@ private MongoDBIterator<Document> getMongoCursor(ClientSession clientSession, Qu
     }
 
     public List<String> 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<String> members = new ArrayList<>(organization.getAdmins().size() + 1);
         if (StringUtils.isNotEmpty(organization.getOwner())) {
             members.add(organization.getOwner());

diff --git a/...ga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java b/...ga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java
@@ -542,18 +542,27 @@ public OpenCGAResult<Project> get(Query query, QueryOptions options, String user
     }
 
     @Override
-    public OpenCGAResult<Document> nativeGet(Query query, QueryOptions options) throws CatalogDBException {
+    public OpenCGAResult nativeGet(Query query, QueryOptions options) throws CatalogDBException {
+        return nativeGet(null, query, options);
+    }
+
+    public OpenCGAResult<Document> nativeGet(ClientSession clientSession, Query query, QueryOptions options) throws CatalogDBException {
         long startTime = startQuery();
-        try (DBIterator<Document> dbIterator = nativeIterator(query, options)) {
+        try (DBIterator<Document> dbIterator = nativeIterator(clientSession, query, options)) {
             return endQuery(startTime, dbIterator);
         }
     }
 
     @Override
     public OpenCGAResult nativeGet(Query query, QueryOptions options, String user)
             throws CatalogDBException, CatalogAuthorizationException {
+        return nativeGet(null, query, options, user);
+    }
+
+    public OpenCGAResult<Document> nativeGet(ClientSession clientSession, Query query, QueryOptions options, String user)
+            throws CatalogDBException, CatalogAuthorizationException {
         long startTime = startQuery();
-        try (DBIterator<Document> dbIterator = nativeIterator(query, options, user)) {
+        try (DBIterator<Document> dbIterator = nativeIterator(clientSession, query, options, user)) {
             return endQuery(startTime, dbIterator);
         }
     }
@@ -570,11 +579,15 @@ public DBIterator<Project> 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<Document> mongoCursor = getMongoCursor(null, query, queryOptions);
-        return new ProjectCatalogMongoDBIterator<>(mongoCursor, null, null, dbAdaptorFactory, options, null);
+        MongoDBIterator<Document> mongoCursor = getMongoCursor(clientSession, query, queryOptions);
+        return new ProjectCatalogMongoDBIterator<>(mongoCursor, clientSession, null, dbAdaptorFactory, options, null);
     }
 
     @Override
@@ -587,11 +600,16 @@ public DBIterator<Project> 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<Document> mongoCursor = getMongoCursor(null, query, queryOptions, user);
-        return new ProjectCatalogMongoDBIterator<>(mongoCursor, null, null, dbAdaptorFactory, options, user);
+        MongoDBIterator<Document> mongoCursor = getMongoCursor(clientSession, query, queryOptions, user);
+        return new ProjectCatalogMongoDBIterator<>(mongoCursor, clientSession, null, dbAdaptorFactory, options, user);
     }
 
 //    private MongoDBIterator<Document> getMongoCursor(ClientSession clientSession, Query query, QueryOptions options, String user)

diff --git a/...src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/CatalogMongoDBIterator.java b/...src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/CatalogMongoDBIterator.java
@@ -183,25 +183,28 @@ protected QueryOptions createInnerQueryOptionsForVersionedEntity(QueryOptions op
     }
 
     protected boolean includeField(QueryOptions options, List<String> fields) {
-        Set<String> includedFields = new HashSet<>(fields);
         if (options.containsKey(QueryOptions.INCLUDE)) {
             List<String> currentIncludeList = options.getAsStringList(QueryOptions.INCLUDE);
             for (String include : currentIncludeList) {
-                if (includedFields.contains(include)) {
-                    return true;
+                for (String field : fields) {
+                    if (include.startsWith(field)) {
+                        return true;
+                    }
                 }
             }
             return false;
         } else if (options.containsKey(QueryOptions.EXCLUDE)) {
             List<String> currentExcludeList = options.getAsStringList(QueryOptions.EXCLUDE);
             for (String exclude : currentExcludeList) {
-                if (includedFields.contains(exclude)) {
-                    return false;
+                for (String field : fields) {
+                    if (exclude.equals(field)) {
+                        return false;
+                    }
                 }
+
             }
             return true;
         }
-
         return true;
     }
 

diff --git a/...a/org/opencb/opencga/catalog/db/mongodb/iterators/OrganizationCatalogMongoDBIterator.java b/...a/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;
@@ -11,7 +12,10 @@
 import org.opencb.opencga.catalog.db.mongodb.MigrationMongoDBAdaptor;
 import org.opencb.opencga.catalog.db.mongodb.NoteMongoDBAdaptor;
 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.catalog.exceptions.CatalogRuntimeException;
 import org.opencb.opencga.core.models.notes.Note;
 import org.opencb.opencga.core.response.OpenCGAResult;
 import org.slf4j.Logger;
@@ -23,24 +27,32 @@
 
 public class OrganizationCatalogMongoDBIterator<E> extends CatalogMongoDBIterator<E> {
 
+    private final String user;
+
     private final QueryOptions options;
+    private final QueryOptions projectOptions;
 
     private final Queue<Document> organizationListBuffer;
-    private final NoteMongoDBAdaptor noteMongoDBAdaptor;
     private final MigrationMongoDBAdaptor migrationDBAdaptor;
+    private final ProjectMongoDBAdaptor projectMongoDBAdaptor;
+    private final NoteMongoDBAdaptor noteMongoDBAdaptor;
 
     private final Logger logger;
 
 
     public OrganizationCatalogMongoDBIterator(MongoDBIterator<Document> mongoCursor, ClientSession clientSession,
                                          GenericDocumentComplexConverter<E> converter, OrganizationMongoDBAdaptorFactory dbAdaptorFactory,
-                                         QueryOptions options) {
+                                         QueryOptions options, String user) {
         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.noteMongoDBAdaptor = dbAdaptorFactory.getCatalogNotesDBAdaptor();
+        this.projectMongoDBAdaptor = dbAdaptorFactory.getCatalogProjectDBAdaptor();
 
         this.organizationListBuffer = new LinkedList<>();
         this.logger = LoggerFactory.getLogger(OrganizationCatalogMongoDBIterator.class);
@@ -72,6 +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<String> migrationFields = Arrays.asList(OrganizationDBAdaptor.QueryParams.INTERNAL.key(),
@@ -100,7 +113,24 @@ private void fetchNextBatch() {
                         OpenCGAResult<Document> 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 + "'.");
+                    }
+                }
+
+                List<String> projectField = Collections.singletonList(OrganizationDBAdaptor.QueryParams.PROJECTS.key());
+                if (includeField(options, projectField)) {
+                    OpenCGAResult<Document> openCGAResult = null;
+                    try {
+                        if (StringUtils.isNotEmpty(user)) {
+                            openCGAResult = projectMongoDBAdaptor.nativeGet(clientSession, new Query(), projectOptions, user);
+                        } else {
+                            openCGAResult = projectMongoDBAdaptor.nativeGet(clientSession, new Query(), projectOptions);
+                        }
+                        organizationDocument.put(OrganizationDBAdaptor.QueryParams.PROJECTS.key(), openCGAResult.getResults());
+                    } catch (CatalogAuthorizationException 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 + "'.");
                     }
                 }
             }

diff --git a/...-catalog/src/main/java/org/opencb/opencga/catalog/exceptions/CatalogRuntimeException.java b/...-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, "");
+    }
+
+
+}
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
@@ -134,7 +134,7 @@ public OpenCGAResult<Organization> get(String organizationId, QueryOptions optio
             QueryOptions queryOptions = ParamUtils.defaultObject(options, QueryOptions::new);
             boolean isOrgAdmin = authorizationManager.isAtLeastOrganizationOwnerOrAdmin(organizationId, userId);
             queryOptions.put(OrganizationDBAdaptor.IS_ORGANIZATION_ADMIN_OPTION, isOrgAdmin);
-            queryResult = getOrganizationDBAdaptor(organizationId).get(queryOptions);
+            queryResult = getOrganizationDBAdaptor(organizationId).get(userId, queryOptions);
         } catch (CatalogException e) {
             auditManager.auditInfo(organizationId, userId, Enums.Resource.ORGANIZATION, organizationId, "", "", "", auditParams,
                     new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError()));