TASK-7175 - Port Patch 2.0.1 -> 2.4.0

opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java

@@ -1757,8 +1757,7 @@ public static DataStore defaultDataStore(CatalogManager catalogManager, Project
         return defaultDataStore(catalogManager.getConfiguration().getDatabasePrefix(), project.getFqn());
     }
 
-    public static DataStore defaultDataStore(String databasePrefix, String projectFqnStr)
-            throws CatalogException {
+    public static DataStore defaultDataStore(String databasePrefix, String projectFqnStr) {
         CatalogFqn projectFqn = CatalogFqn.extractFqnFromProjectFqn(projectFqnStr);
 
         String dbName = buildDatabaseName(databasePrefix, projectFqn.getOrganizationId(), projectFqn.getProjectId());

opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java

@@ -70,7 +70,7 @@ private void runMigrationToV3() throws Exception {
         setCatalogDatabaseCredentials(options, options.commonOptions);
 
         OrganizationMigration organizationMigration = new OrganizationMigration(configuration, options.commonOptions.adminPassword,
-                options.user);
+                options.user, options.organizationId, Paths.get(appHome));
         organizationMigration.execute();
     }
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/options/MigrationCommandOptions.java

@@ -46,6 +46,10 @@ public class OrganizationMigrationCommandOptions extends AdminCliOptionsParser.C
         @Parameter(names = {"--user"}, description = "User whose data is going to be migrated. If more than one user of type FULL contains"
                 + " projects and studies, only the one provided will keep the data and will be fully migrated.")
         public String user;
+
+        @Parameter(names = {"--organization-id"}, description = "Optional parameter to specify how the new organization will be named." +
+                " By default, if not provided, the organization id will match the user id that is currently owning the data.")
+        public String organizationId;
     }
 
     @Parameters(commandNames = {"summary"}, commandDescription = "Obtain migrations status summary")

opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java

@@ -1,15 +1,21 @@
 package org.opencb.opencga.app.migrations.v3.v3_0_0;
 
+import org.opencb.opencga.catalog.exceptions.CatalogException;
 import org.opencb.opencga.catalog.migration.Migration;
 import org.opencb.opencga.catalog.migration.MigrationTool;
 import org.opencb.opencga.core.config.Configuration;
 
+import java.io.IOException;
+import java.nio.file.Path;
+
 @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,
-        deprecatedSince = "3.1.0")
+        manual = true, deprecatedSince = "3.1.0")
+
 public class OrganizationMigration extends MigrationTool {
 
-    public OrganizationMigration(Configuration configuration, String adminPassword, String userId) {
+    public OrganizationMigration(Configuration configuration, String adminPassword, String userId,
+                                 String organizationId, Path appHome) throws CatalogException, IOException {
     }
 
     @Override

opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java

@@ -153,7 +153,17 @@ protected final void migrateCollection(MongoCollection<Document> inputCollection
                 .cursor()) {
             while (it.hasNext()) {
                 Document document = it.next();
-                migrateFunc.accept(document, list);
+                try {
+                    migrateFunc.accept(document, list);
+                } catch (Exception e) {
+                    try {
+                        logger.error("Error migrating document: {}", document.toJson());
+                    } catch (Exception e1) {
+                        e.addSuppressed(e1);
+                        logger.error("Error migrating document: {}", e.getMessage());
+                    }
+                    throw e;
+                }
 
                 if (list.size() >= batchSize) {
                     count += list.size();