Merge pull request #2470 from opencb/TASK-6413

TASK-6413 - Allow migrations from 3.0.0.1 to 3.2.x
opencb · Jul 1, 2024 · f7f19a0 · f7f19a0
2 parents de0568c + 31c5886
commit f7f19a0
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Showing 3 changed files with 24 additions and 50 deletions.
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/NoteMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_1_0/NoteMigration.java
@@ -6,34 +6,23 @@
 import com.mongodb.client.model.RenameCollectionOptions;
 import com.mongodb.client.model.Updates;
 import com.mongodb.client.result.UpdateResult;
-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.opencga.catalog.db.api.NoteDBAdaptor;
-import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptorFactory;
 import org.opencb.opencga.catalog.db.mongodb.OrganizationMongoDBAdaptorFactory;
-import org.opencb.opencga.catalog.exceptions.CatalogDBException;
-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.MigrationTool;
-import org.opencb.opencga.core.api.ParamConstants;
 import org.opencb.opencga.core.models.notes.Note;
 
-import java.util.Collections;
-import java.util.List;
-
 @Migration(id = "migrate_notes", description = "Migrate notes #TASK-5836", version = "3.1.0",
         language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20240315)
 public class NoteMigration extends MigrationTool {
 
     @Override
     protected void run() throws Exception {
-        IOManagerFactory ioManagerFactory = new IOManagerFactory();
-        dbAdaptorFactory = new MongoDBAdaptorFactory(configuration, ioManagerFactory);
         // First migrate to add the new values
-        MongoCollection<Document> collection = getMongoCollection(ParamConstants.ADMIN_ORGANIZATION, "notes");
+        MongoCollection<Document> collection = getMongoCollection(organizationId, "notes");
         Bson query = Filters.exists(NoteDBAdaptor.QueryParams.STUDY_UID.key(), false);
         Bson update = Updates.combine(
                 Updates.set(NoteDBAdaptor.QueryParams.STUDY_UID.key(), -1L),
@@ -43,41 +32,20 @@ protected void run() throws Exception {
         );
         UpdateResult updateResult = collection.updateMany(query, update);
         if (updateResult.getModifiedCount() == 0) {
-            // Check there are at least 2 organizations present
-            logger.info("Note data model could not be updated. Detected organizations are: {}", StringUtils.join(dbAdaptorFactory.getOrganizationIds(), ","));
-            if (dbAdaptorFactory.getOrganizationIds().size() == 2) {
-                logger.info("Nothing to migrate");
-                return;
-            } else {
-                throw new CatalogDBException("Notes could not be found to migrate.");
-            }
+            logger.info("Note data model could not be updated. Notes found in organization '{}': {}", organizationId, updateResult.getMatchedCount());
         }
-        renameNoteCollection(Collections.singletonList(ParamConstants.ADMIN_ORGANIZATION));
-
-        dbAdaptorFactory.close();
-        dbAdaptorFactory = new MongoDBAdaptorFactory(configuration, ioManagerFactory);
-        // We run it a second time because the first time it will only rename the "opencga" org as OpenCGA will not be able to know
-        // which other organizations are present in the installation (trying to fetch the information from "note" instead of old "notes")
-        List<String> organizationIds = dbAdaptorFactory.getOrganizationIds();
-        organizationIds.remove(ParamConstants.ADMIN_ORGANIZATION);
-        renameNoteCollection(organizationIds);
-
-        // Reload catalog manager to install missing indexes
-        catalogManager = new CatalogManager(configuration);
-        catalogManager.installIndexes(token);
-    }
 
-    private void renameNoteCollection(List<String> organizationIds) throws CatalogDBException {
+        // Rename Note collection
         RenameCollectionOptions options = new RenameCollectionOptions().dropTarget(true);
         // Rename collection
-        for (String organizationId : organizationIds) {
-            String databaseName = dbAdaptorFactory.getMongoDataStore(organizationId).getDatabaseName();
-            logger.info("Renaming notes collection for organization '{}' -> Database: '{}'", organizationId, databaseName);
-            MongoDataStore mongoDataStore = dbAdaptorFactory.getMongoDataStore(organizationId);
-            mongoDataStore.getDb().getCollection("notes").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_COLLECTION), options);
-            mongoDataStore.getDb().getCollection("notes_archive").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_ARCHIVE_COLLECTION), options);
-            mongoDataStore.getDb().getCollection("notes_deleted").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.DELETED_NOTE_COLLECTION), options);
-        }
+        String databaseName = dbAdaptorFactory.getMongoDataStore(organizationId).getDatabaseName();
+        logger.info("Renaming notes collection for organization '{}' -> Database: '{}'", organizationId, databaseName);
+        MongoDataStore mongoDataStore = dbAdaptorFactory.getMongoDataStore(organizationId);
+        mongoDataStore.getDb().getCollection("notes").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_COLLECTION), options);
+        mongoDataStore.getDb().getCollection("notes_archive").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.NOTE_ARCHIVE_COLLECTION), options);
+        mongoDataStore.getDb().getCollection("notes_deleted").renameCollection(new MongoNamespace(databaseName, OrganizationMongoDBAdaptorFactory.DELETED_NOTE_COLLECTION), options);
+
+        catalogManager.installIndexes(organizationId, token);
     }
 
 }
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
@@ -301,7 +301,7 @@ public void installIndexes(String token) throws CatalogException {
 
     public void installIndexes(String organizationId, String token) throws CatalogException {
         JwtPayload payload = userManager.validateToken(token);
-        String userId = payload.getUserId();
+        String userId = payload.getUserId(organizationId);
         if (!authorizationManager.isAtLeastOrganizationOwnerOrAdmin(organizationId, userId)) {
             throw CatalogAuthorizationException.notOrganizationOwnerOrAdmin();
         }

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
@@ -125,14 +125,20 @@ public void runMigration(String version, Collection<Migration.MigrationDomain> d
     public void runMigration(String version, Collection<Migration.MigrationDomain> domains,
                              Collection<Migration.MigrationLanguage> languages, boolean offline, String appHome, ObjectMap params,
                              String token) throws CatalogException, IOException {
-        // Migrate all organizations
-        for (String organizationId : dbAdaptorFactory.getOrganizationIds()) {
-            if (!ParamConstants.ADMIN_ORGANIZATION.equals(organizationId)) {
-                runMigration(organizationId, version, domains, languages, offline, appHome, params, token);
+        runMigration(ParamConstants.ADMIN_ORGANIZATION, version, domains, languages, offline, appHome, params, token);
+
+        // ***** Starts code to remove in future versions. Reload MongoDBAdaptorFactory to avoid Notes migration issue. *****/
+        try (MongoDBAdaptorFactory mongoDBAdaptorFactory = new MongoDBAdaptorFactory(configuration, catalogManager.getIoManagerFactory())) {
+            for (String organizationId : mongoDBAdaptorFactory.getOrganizationIds()) {
+                // ***** Finish code to remove in future versions. Reload MongoDBAdaptorFactory to avoid Notes migration issue. *****/
+
+                // Migrate all organizations
+    //        for (String organizationId : dbAdaptorFactory.getOrganizationIds()) {
+                if (!ParamConstants.ADMIN_ORGANIZATION.equals(organizationId)) {
+                    runMigration(organizationId, version, domains, languages, offline, appHome, params, token);
+                }
             }
         }
-        // Lastly, migrate the admin organization
-        runMigration(ParamConstants.ADMIN_ORGANIZATION, version, domains, languages, offline, appHome, params, token);
     }
 
     public void runMigration(String organizationId, String version, Collection<Migration.MigrationDomain> domains,