From 149577b9f6af15e8341867f6879cd7a2b05022e7 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 29 May 2024 16:33:31 +0200 Subject: [PATCH 01/16] Prepare new development version 3.0.0.2-SNAPSHOT --- 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 f360b51b82..eb4825ee88 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index a211147e29..92d7e27fc3 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 4b0827a105..dba2d4ff1a 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index b86efb944d..8a221b55fe 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index ef56059fcb..f2ea05a986 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 8942fdd2d1..acaffb174f 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index fb06b5d2b9..d0d14e9506 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 846323d417..f93f5ffd04 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 2715a9b06a..fd9869835d 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 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 896868defd..640a4a655e 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 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index b62ec3d581..74320f628a 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 + 3.0.0.2-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 35d022c328..e2f710f5e7 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 + 3.0.0.2-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 48b48e0a40..614ad7332c 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 + 3.0.0.2-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 b2ad7976f6..f768ed47aa 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 + 3.0.0.2-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 e10b7910ee..75f6adc95e 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 + 3.0.0.2-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 87a073c4d5..46993e19f5 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 + 3.0.0.2-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 8da62fe6c4..bf1c0dc3a0 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 + 3.0.0.2-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 298103a6ce..87b41711fa 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 + 3.0.0.2-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 1062a0712d..2bb2e0fea4 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 + 3.0.0.2-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 392730030f..bb429c443f 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 + 3.0.0.2-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 608cab8886..e029d3b5bf 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 + 3.0.0.2-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 1b0e3907b9..b2648803b3 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 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 440a1fec50..b4258b03d3 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 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 98bfb2231e..5a605a0565 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 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 0615d0daa9..33ffd81655 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index d43e29d0f3..711d494413 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index efdab0d652..0c2ea552a9 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.0.0.2-SNAPSHOT pom OpenCGA From 27f590664c4d05e5361f4d99aa632e2e46e4820b Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 21 Oct 2024 09:43:13 +0200 Subject: [PATCH 02/16] app: allow changing the organization id during main migration,#TASK-7118 --- .../executors/MigrationCommandExecutor.java | 2 +- .../options/MigrationCommandOptions.java | 4 + .../v3/v3_0_0/OrganizationMigration.java | 74 +++++++++++++++++-- 3 files changed, 71 insertions(+), 9 deletions(-) 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 3f5f7cee80..1a52874866 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 @@ -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); organizationMigration.execute(); } diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/options/MigrationCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/options/MigrationCommandOptions.java index a306f222c3..7d42b1e77c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/options/MigrationCommandOptions.java +++ b/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") diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index d1f749bafe..46e7878275 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -1,10 +1,7 @@ package org.opencb.opencga.app.migrations.v3.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.model.*; import com.mongodb.client.result.DeleteResult; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.StringUtils; @@ -17,12 +14,15 @@ 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.CatalogDBException; 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.managers.CatalogManager; import org.opencb.opencga.catalog.migration.Migration; import org.opencb.opencga.catalog.migration.MigrationTool; +import org.opencb.opencga.catalog.utils.FqnUtils; +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.config.Configuration; @@ -62,10 +62,12 @@ private enum MigrationStatus { ERROR } - public OrganizationMigration(Configuration configuration, String adminPassword, String userId) throws CatalogException { + public OrganizationMigration(Configuration configuration, String adminPassword, String userId, String organizationId) + throws CatalogException { this.configuration = configuration; this.adminPassword = adminPassword; this.userId = userId; + this.organizationId = organizationId; this.status = checkAndInit(); } @@ -193,7 +195,10 @@ private MigrationStatus checkAndInit() throws CatalogException { this.userIdsToDiscardData = new HashSet<>(); } - this.organizationId = this.userId; + if (StringUtils.isEmpty(this.organizationId)) { + this.organizationId = this.userId; + } + ParamUtils.checkIdentifier(this.organizationId, "Organization id"); this.catalogManager = new CatalogManager(configuration); return MigrationStatus.PENDING_MIGRATION; } @@ -360,6 +365,10 @@ protected void run() throws Exception { CatalogIOManager ioManager = new CatalogIOManager(configuration); + Map organizationOwnerMap = new HashMap<>(); + organizationOwnerMap.put(ParamConstants.ADMIN_ORGANIZATION, ParamConstants.OPENCGA_USER_ID); + organizationOwnerMap.put(this.organizationId, this.userId); + // Loop over all organizations to perform additional data model changes for (String organizationId : mongoDBAdaptorFactory.getOrganizationIds()) { ioManager.createOrganization(organizationId); @@ -400,13 +409,14 @@ protected void run() throws Exception { } // Add owner as admin of every study and remove _ownerId field + String ownerId = organizationOwnerMap.get(organizationId); 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.$.userIds", organizationId) + Updates.push("groups.$.userIds", ownerId) )); } @@ -434,16 +444,64 @@ protected void run() throws Exception { // Set organization counter, owner and authOrigins orgCol.updateOne(Filters.eq("id", organizationId), Updates.combine( Updates.set("_idCounter", counter), - Updates.set("owner", organizationId), + Updates.set("owner", ownerId), Updates.set("configuration.authenticationOrigins", authOrigins) )); } + // If the user didn't want to use the userId as the new organization id, we then need to change all the fqn's + if (!this.organizationId.equals(this.userId)) { + changeFqns(); + } + // Skip current migration for both organizations catalogManager.getMigrationManager().skipPendingMigrations(ParamConstants.ADMIN_ORGANIZATION, opencgaToken); catalogManager.getMigrationManager().skipPendingMigrations(organizationId, opencgaToken); } + private void changeFqns() throws CatalogDBException { + this.dbAdaptorFactory = this.mongoDBAdaptorFactory; + + // Change project fqn's + for (String projectCol : Arrays.asList(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION, + OrganizationMongoDBAdaptorFactory.DELETED_PROJECT_COLLECTION)) { + migrateCollection(projectCol, new Document(), Projections.include("_id", "id"), (document, bulk) -> { + String projectId = document.getString("id"); + String projectFqn = FqnUtils.buildFqn(this.organizationId, projectId); + bulk.add(new UpdateOneModel<>( + Filters.eq("_id", document.get("_id")), + new Document("$set", new Document("fqn", projectFqn))) + ); + }); + } + + MongoDatabase database = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb(); + MongoCollection jobCollection = database.getCollection(OrganizationMongoDBAdaptorFactory.JOB_COLLECTION); + MongoCollection jobDeletedCollection = database.getCollection(OrganizationMongoDBAdaptorFactory.DELETED_JOB_COLLECTION); + + // Change study fqn's + for (String studyCol : Arrays.asList(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION, + OrganizationMongoDBAdaptorFactory.DELETED_STUDY_COLLECTION)) { + migrateCollection(studyCol, new Document(), Projections.include("_id", "uid", "fqn"), (document, bulk) -> { + long studyUid = document.get("uid", Number.class).longValue(); + + String oldStudyFqn = document.getString("fqn"); + FqnUtils.FQN oldFqnInstance = FqnUtils.parse(oldStudyFqn); + String newFqn = FqnUtils.buildFqn(this.organizationId, oldFqnInstance.getProject(), oldFqnInstance.getStudy()); + bulk.add(new UpdateOneModel<>( + Filters.eq("_id", document.get("_id")), + new Document("$set", new Document("fqn", newFqn))) + ); + + // Change fqn in all jobs that were pointing to this study + Bson jobQuery = Filters.eq("studyUid", studyUid); + Bson update = Updates.set("study.id", newFqn); + jobCollection.updateMany(jobQuery, update); + jobDeletedCollection.updateMany(jobQuery, update); + }); + } + } + Set> getAvailableMigrations() { Reflections reflections = new Reflections(new ConfigurationBuilder() .setScanners( From 1f25e7adfd6f5c4a6d8baf8b71e2c7f536380cbc Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 21 Oct 2024 15:37:25 +0200 Subject: [PATCH 03/16] Adapt pom to the new SDLC #TASK-7118 --- 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/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 | 4 ++-- 27 files changed, 28 insertions(+), 28 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index eb4825ee88..314766dc1d 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 92d7e27fc3..eaa503dd09 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index dba2d4ff1a..f6f5768166 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 8a221b55fe..909598e048 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f2ea05a986..c173e0eb19 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index acaffb174f..43f0f3f65b 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index d0d14e9506..bc7eeae241 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f93f5ffd04..1b1e16acbc 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index fd9869835d..8b4822ad6e 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 - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 640a4a655e..0c0bf1c727 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 - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 74320f628a..20cd38689a 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 e2f710f5e7..3d0375fea0 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 614ad7332c..6837051499 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 f768ed47aa..b5852968a7 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 75f6adc95e..5e097253ee 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 46993e19f5..88200e3425 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 bf1c0dc3a0..2d94efc52f 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 87b41711fa..0b50aadf33 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 2bb2e0fea4..25941e5afe 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 bb429c443f..91438cbe32 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 e029d3b5bf..0026c0c4ba 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 - 3.0.0.2-SNAPSHOT + 3.0.1-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 b2648803b3..d824df6b12 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 - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index b4258b03d3..470344d436 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 - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 5a605a0565..215850fd9b 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 - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 33ffd81655..b2e665c34f 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 711d494413..0ef882d8ac 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 0c2ea552a9..cc351a473d 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.2-SNAPSHOT + 3.0.1-SNAPSHOT pom OpenCGA @@ -44,7 +44,7 @@ - 3.0.0.1 + 3.0.1 6.0.0 3.0.0 5.0.0 From acac916e782ea8557c902bb6b22bc9d29c293d83 Mon Sep 17 00:00:00 2001 From: pfurio Date: Tue, 22 Oct 2024 16:23:36 +0200 Subject: [PATCH 04/16] app: store old fqn in attributes before migration, #TASK-7118 --- .../v3/v3_0_0/OrganizationMigration.java | 28 ++++++++++++++++--- 1 file changed, 24 insertions(+), 4 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index 46e7878275..b42b85c18b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -24,6 +24,7 @@ import org.opencb.opencga.catalog.utils.FqnUtils; import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.core.api.ParamConstants; +import org.opencb.opencga.core.common.TimeUtils; import org.opencb.opencga.core.config.AuthenticationOrigin; import org.opencb.opencga.core.config.Configuration; import org.opencb.opencga.core.models.migration.MigrationRun; @@ -461,16 +462,23 @@ protected void run() throws Exception { private void changeFqns() throws CatalogDBException { this.dbAdaptorFactory = this.mongoDBAdaptorFactory; + String date = TimeUtils.getTime(); // Change project fqn's for (String projectCol : Arrays.asList(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION, OrganizationMongoDBAdaptorFactory.DELETED_PROJECT_COLLECTION)) { - migrateCollection(projectCol, new Document(), Projections.include("_id", "id"), (document, bulk) -> { + migrateCollection(projectCol, new Document(), Projections.include("_id", "id", "fqn"), (document, bulk) -> { + String currentFqn = document.getString("fqn"); String projectId = document.getString("id"); String projectFqn = FqnUtils.buildFqn(this.organizationId, projectId); bulk.add(new UpdateOneModel<>( Filters.eq("_id", document.get("_id")), - new Document("$set", new Document("fqn", projectFqn))) + new Document("$set", new Document() + .append("fqn", projectFqn) + .append("attributes.OPENCGA.3_0_0", new Document() + .append("date", date) + .append("oldFqn", currentFqn) + ))) ); }); } @@ -490,12 +498,24 @@ private void changeFqns() throws CatalogDBException { String newFqn = FqnUtils.buildFqn(this.organizationId, oldFqnInstance.getProject(), oldFqnInstance.getStudy()); bulk.add(new UpdateOneModel<>( Filters.eq("_id", document.get("_id")), - new Document("$set", new Document("fqn", newFqn))) + new Document("$set", new Document() + .append("fqn", newFqn) + .append("attributes.OPENCGA.3_0_0", new Document() + .append("date", date) + .append("oldFqn", oldStudyFqn) + ) + )) ); // Change fqn in all jobs that were pointing to this study Bson jobQuery = Filters.eq("studyUid", studyUid); - Bson update = Updates.set("study.id", newFqn); + Bson update = new Document("$set", new Document() + .append("study.id", newFqn) + .append("attributes.OPENCGA.3_0_0", new Document() + .append("date", date) + .append("oldStudyFqn", oldStudyFqn) + ) + ); jobCollection.updateMany(jobQuery, update); jobDeletedCollection.updateMany(jobQuery, update); }); From d2c80732611df83ee8f62b32fe1d505fab8e9213 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 23 Oct 2024 10:45:15 +0100 Subject: [PATCH 05/16] app: Ensure project.internal.datastores.variant is defined when changing organizationId #TASK-7118 --- .../manager/VariantStorageManager.java | 3 +- .../v3/v3_0_0/OrganizationMigration.java | 66 ++++++++++++++++--- .../catalog/migration/MigrationTool.java | 12 +++- 3 files changed, 68 insertions(+), 13 deletions(-) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java index 847a2bb1ac..b8322bbcb8 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java @@ -1726,8 +1726,7 @@ 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()); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index b42b85c18b..25215778dd 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -9,6 +9,7 @@ import org.bson.conversions.Bson; import org.opencb.commons.datastore.mongodb.MongoDataStore; import org.opencb.commons.utils.CryptoUtils; +import org.opencb.opencga.analysis.variant.manager.VariantStorageManager; import org.opencb.opencga.catalog.auth.authentication.CatalogAuthenticationManager; import org.opencb.opencga.catalog.db.api.StudyDBAdaptor; import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptorFactory; @@ -20,6 +21,7 @@ import org.opencb.opencga.catalog.io.CatalogIOManager; 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.catalog.utils.FqnUtils; import org.opencb.opencga.catalog.utils.ParamUtils; @@ -29,12 +31,17 @@ 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.opencb.opencga.core.models.project.DataStore; +import org.opencb.opencga.storage.core.StorageEngineFactory; +import org.opencb.opencga.storage.core.exceptions.StorageEngineException; +import org.opencb.opencga.storage.core.variant.VariantStorageEngine; 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.io.IOException; import java.lang.reflect.Modifier; import java.net.URL; import java.nio.file.Files; @@ -452,6 +459,8 @@ protected void run() throws Exception { // If the user didn't want to use the userId as the new organization id, we then need to change all the fqn's if (!this.organizationId.equals(this.userId)) { + logger.info("New organization id '{}' is different from original userId '{}'. Changing FQN's from projects and studies" + , this.organizationId, this.userId); changeFqns(); } @@ -460,26 +469,62 @@ protected void run() throws Exception { catalogManager.getMigrationManager().skipPendingMigrations(organizationId, opencgaToken); } - private void changeFqns() throws CatalogDBException { + private void changeFqns() throws CatalogDBException, MigrationException { this.dbAdaptorFactory = this.mongoDBAdaptorFactory; String date = TimeUtils.getTime(); + StorageEngineFactory storageEngineFactory = StorageEngineFactory.get(readStorageConfiguration()); + // Change project fqn's for (String projectCol : Arrays.asList(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION, OrganizationMongoDBAdaptorFactory.DELETED_PROJECT_COLLECTION)) { - migrateCollection(projectCol, new Document(), Projections.include("_id", "id", "fqn"), (document, bulk) -> { - String currentFqn = document.getString("fqn"); + migrateCollection(projectCol, new Document(), Projections.include("_id", "id", "fqn", "internal.datastores.variant"), (document, bulk) -> { + String oldFqn = document.getString("fqn"); String projectId = document.getString("id"); - String projectFqn = FqnUtils.buildFqn(this.organizationId, projectId); + String newFqn = FqnUtils.buildFqn(this.organizationId, projectId); + logger.info("Changing project fqn from '{}' to '{}'", oldFqn, newFqn); + + Document set = new Document() + .append("fqn", newFqn) + .append("attributes.OPENCGA.3_0_0", new Document() + .append("date", date) + .append("oldFqn", oldFqn) + ); + + Document internal = document.get("internal", Document.class); + if (internal != null) { + Document datastores = internal.get("datastores", Document.class); + if (datastores != null) { + Document variant = datastores.get("variant", Document.class); + if (variant == null) { + DataStore dataStore = VariantStorageManager.defaultDataStore(configuration.getDatabasePrefix(), oldFqn); + logger.info("Undefined variant \"internal.datastores.variant\" at project '{}'.", oldFqn); + + // Update only if the project exists in the variant storage + try (VariantStorageEngine variantStorageEngine = storageEngineFactory + .getVariantStorageEngine(dataStore.getStorageEngine(), dataStore.getDbName())) { + if (variantStorageEngine.getMetadataManager().exists()) { + logger.info("Project exists in the variant storage. Setting variant data store: {}", dataStore); + set.append("internal.datastores.variant", new Document() + .append("storageEngine", dataStore.getStorageEngine()) + .append("dbName", dataStore.getDbName()) + .append("options", new Document())); + } else { + logger.info("Project does not exist in the variant storage. Skipping"); + } + } catch (StorageEngineException | IOException e) { + throw new RuntimeException(e); + } + + } + } + } + bulk.add(new UpdateOneModel<>( Filters.eq("_id", document.get("_id")), - new Document("$set", new Document() - .append("fqn", projectFqn) - .append("attributes.OPENCGA.3_0_0", new Document() - .append("date", date) - .append("oldFqn", currentFqn) - ))) + new Document("$set", set)) ); + logger.info("-------"); }); } @@ -496,6 +541,7 @@ private void changeFqns() throws CatalogDBException { String oldStudyFqn = document.getString("fqn"); FqnUtils.FQN oldFqnInstance = FqnUtils.parse(oldStudyFqn); String newFqn = FqnUtils.buildFqn(this.organizationId, oldFqnInstance.getProject(), oldFqnInstance.getStudy()); + logger.info("Changing study fqn from '{}' to '{}'", oldStudyFqn, newFqn); bulk.add(new UpdateOneModel<>( Filters.eq("_id", document.get("_id")), new Document("$set", new Document() 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 f46e54277d..dd162c0635 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 @@ -151,7 +151,17 @@ protected final void migrateCollection(MongoCollection 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(); From bfe19252a8356dc0a220c0f2152ce5c3aa098e9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 24 Oct 2024 16:07:17 +0100 Subject: [PATCH 06/16] app: Fix NPE. Add appHome to OrganizationMigration. #TASK-7118 --- .../admin/executors/MigrationCommandExecutor.java | 2 +- .../migrations/v3/v3_0_0/OrganizationMigration.java | 12 +++++++++--- 2 files changed, 10 insertions(+), 4 deletions(-) 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 1a52874866..5fdada19a9 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 @@ -70,7 +70,7 @@ private void runMigrationToV3() throws Exception { setCatalogDatabaseCredentials(options, options.commonOptions); OrganizationMigration organizationMigration = new OrganizationMigration(configuration, options.commonOptions.adminPassword, - options.user, options.organizationId); + options.user, options.organizationId, Paths.get(appHome)); organizationMigration.execute(); } diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index 25215778dd..26780bc506 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -9,6 +9,7 @@ import org.bson.conversions.Bson; import org.opencb.commons.datastore.mongodb.MongoDataStore; import org.opencb.commons.utils.CryptoUtils; +import org.opencb.commons.utils.FileUtils; import org.opencb.opencga.analysis.variant.manager.VariantStorageManager; import org.opencb.opencga.catalog.auth.authentication.CatalogAuthenticationManager; import org.opencb.opencga.catalog.db.api.StudyDBAdaptor; @@ -45,6 +46,7 @@ import java.lang.reflect.Modifier; import java.net.URL; import java.nio.file.Files; +import java.nio.file.Path; import java.nio.file.Paths; import java.security.NoSuchAlgorithmException; import java.util.*; @@ -70,21 +72,25 @@ private enum MigrationStatus { ERROR } - public OrganizationMigration(Configuration configuration, String adminPassword, String userId, String organizationId) - throws CatalogException { + public OrganizationMigration(Configuration configuration, String adminPassword, String userId, String organizationId, Path appHome) + throws CatalogException, IOException { this.configuration = configuration; this.adminPassword = adminPassword; this.userId = userId; this.organizationId = organizationId; + this.appHome = appHome; this.status = checkAndInit(); } - private MigrationStatus checkAndInit() throws CatalogException { + private MigrationStatus checkAndInit() throws CatalogException, IOException { this.oldDatabase = configuration.getDatabasePrefix() + "_catalog"; this.mongoDBAdaptorFactory = new MongoDBAdaptorFactory(configuration); this.oldDatastore = mongoDBAdaptorFactory.getMongoManager().get(oldDatabase, mongoDBAdaptorFactory.getMongoDbConfiguration()); + FileUtils.checkDirectory(appHome); + readStorageConfiguration(); + MongoCollection userCol = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION); FindIterable iterable = userCol.find(Filters.eq("id", ParamConstants.OPENCGA_USER_ID)); try (MongoCursor cursor = iterable.cursor()) { From 85671b9143458d5a6986bd9ce5eb2a6103450fa0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Fri, 25 Oct 2024 16:15:59 +0100 Subject: [PATCH 07/16] app: Rename StudyMetadata.name to match the new fqn. #TASK-7118 --- .../v3/v3_0_0/OrganizationMigration.java | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index 26780bc506..3d3d98d9ca 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -52,6 +52,8 @@ import java.util.*; import java.util.stream.Collectors; +import static org.opencb.opencga.core.config.storage.StorageConfiguration.Mode.READ_ONLY; + @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 { @@ -65,6 +67,7 @@ public class OrganizationMigration extends MigrationTool { private Set userIdsToDiscardData; private MigrationStatus status; + private boolean changeOrganizationId; private enum MigrationStatus { MIGRATED, @@ -212,6 +215,11 @@ private MigrationStatus checkAndInit() throws CatalogException, IOException { if (StringUtils.isEmpty(this.organizationId)) { this.organizationId = this.userId; } + changeOrganizationId = !this.organizationId.equals(this.userId); + if (changeOrganizationId && readStorageConfiguration().getMode() == READ_ONLY) { + throw new CatalogException("Cannot change organization id when storage is in read-only mode"); + } + ParamUtils.checkIdentifier(this.organizationId, "Organization id"); this.catalogManager = new CatalogManager(configuration); return MigrationStatus.PENDING_MIGRATION; @@ -464,7 +472,7 @@ protected void run() throws Exception { } // If the user didn't want to use the userId as the new organization id, we then need to change all the fqn's - if (!this.organizationId.equals(this.userId)) { + if (changeOrganizationId) { logger.info("New organization id '{}' is different from original userId '{}'. Changing FQN's from projects and studies" , this.organizationId, this.userId); changeFqns(); @@ -515,6 +523,13 @@ private void changeFqns() throws CatalogDBException, MigrationException { .append("storageEngine", dataStore.getStorageEngine()) .append("dbName", dataStore.getDbName()) .append("options", new Document())); + variantStorageEngine.getMetadataManager().updateStudyMetadata(oldFqn, studyMetadata -> { + studyMetadata.setName(newFqn); + studyMetadata.getAttributes().put("OPENCGA.3_0_0", new Document() + .append("date", date) + .append("oldFqn", oldFqn) + ); + }); } else { logger.info("Project does not exist in the variant storage. Skipping"); } From f73fbc16b4c12e68cb3f2b94ec6e7de2ddc12714 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Mon, 28 Oct 2024 14:11:43 +0000 Subject: [PATCH 08/16] app: Fix rename storage studyFqn #TASK-7118 --- .../v3/v3_0_0/OrganizationMigration.java | 33 +++++++++++-------- 1 file changed, 19 insertions(+), 14 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index 3d3d98d9ca..58e50f750b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -493,16 +493,16 @@ private void changeFqns() throws CatalogDBException, MigrationException { for (String projectCol : Arrays.asList(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION, OrganizationMongoDBAdaptorFactory.DELETED_PROJECT_COLLECTION)) { migrateCollection(projectCol, new Document(), Projections.include("_id", "id", "fqn", "internal.datastores.variant"), (document, bulk) -> { - String oldFqn = document.getString("fqn"); String projectId = document.getString("id"); - String newFqn = FqnUtils.buildFqn(this.organizationId, projectId); - logger.info("Changing project fqn from '{}' to '{}'", oldFqn, newFqn); + String oldProjectFqn = document.getString("fqn"); + String newProjectFqn = FqnUtils.buildFqn(this.organizationId, projectId); + logger.info("Changing project fqn from '{}' to '{}'", oldProjectFqn, newProjectFqn); Document set = new Document() - .append("fqn", newFqn) + .append("fqn", newProjectFqn) .append("attributes.OPENCGA.3_0_0", new Document() .append("date", date) - .append("oldFqn", oldFqn) + .append("oldFqn", oldProjectFqn) ); Document internal = document.get("internal", Document.class); @@ -511,8 +511,8 @@ private void changeFqns() throws CatalogDBException, MigrationException { if (datastores != null) { Document variant = datastores.get("variant", Document.class); if (variant == null) { - DataStore dataStore = VariantStorageManager.defaultDataStore(configuration.getDatabasePrefix(), oldFqn); - logger.info("Undefined variant \"internal.datastores.variant\" at project '{}'.", oldFqn); + DataStore dataStore = VariantStorageManager.defaultDataStore(configuration.getDatabasePrefix(), oldProjectFqn); + logger.info("Undefined variant \"internal.datastores.variant\" at project '{}'.", oldProjectFqn); // Update only if the project exists in the variant storage try (VariantStorageEngine variantStorageEngine = storageEngineFactory @@ -523,13 +523,18 @@ private void changeFqns() throws CatalogDBException, MigrationException { .append("storageEngine", dataStore.getStorageEngine()) .append("dbName", dataStore.getDbName()) .append("options", new Document())); - variantStorageEngine.getMetadataManager().updateStudyMetadata(oldFqn, studyMetadata -> { - studyMetadata.setName(newFqn); - studyMetadata.getAttributes().put("OPENCGA.3_0_0", new Document() - .append("date", date) - .append("oldFqn", oldFqn) - ); - }); + + for (String oldStudyFqn : variantStorageEngine.getMetadataManager().getStudies().keySet()) { + String newStudyFqn = FqnUtils.buildFqn(this.organizationId, projectId, FqnUtils.parse(oldStudyFqn).getStudy()); + logger.info("Changing study fqn from '{}' to '{}'", oldStudyFqn, newStudyFqn); + variantStorageEngine.getMetadataManager().updateStudyMetadata(oldStudyFqn, studyMetadata -> { + studyMetadata.setName(newStudyFqn); + studyMetadata.getAttributes().put("OPENCGA.3_0_0", new Document() + .append("date", date) + .append("oldFqn", oldStudyFqn) + ); + }); + } } else { logger.info("Project does not exist in the variant storage. Skipping"); } From d796b3d082a3d9f33490660db5a1487e219aab8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Mon, 28 Oct 2024 14:12:59 +0000 Subject: [PATCH 09/16] app: Ensure OrganizationMigration is marked as "manual" to avoid automatic execution. #TASK-7118 --- .../opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index 58e50f750b..0ff69f25a0 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -55,7 +55,7 @@ import static org.opencb.opencga.core.config.storage.StorageConfiguration.Mode.READ_ONLY; @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) + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20231212, manual = true) public class OrganizationMigration extends MigrationTool { private final Configuration configuration; private final String adminPassword; From f45c22306e333867d6753d082b1ffc970ecdff59 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 30 Oct 2024 19:59:49 +0100 Subject: [PATCH 10/16] Prepare release 3.0.1 --- 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/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 314766dc1d..43b1160fe2 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index eaa503dd09..c4dfcb85e4 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index f6f5768166..fadfdd92a1 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 909598e048..0ca39ca098 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index c173e0eb19..8963d152c2 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 43f0f3f65b..80cc54dcb2 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index bc7eeae241..fce3eef301 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 1b1e16acbc..c35e769d46 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 8b4822ad6e..7f5ba7e7ca 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 - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 0c0bf1c727..9de3546a3e 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 - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 20cd38689a..8182135dd4 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 3d0375fea0..31dd086e2b 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 6837051499..e95b3ba1c0 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 b5852968a7..66034e11b8 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 5e097253ee..27d4d67362 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 88200e3425..5ef22584c7 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 2d94efc52f..cedc3c90e9 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 0b50aadf33..d75d126306 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 25941e5afe..5faf374ce1 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 91438cbe32..e2dc27a8fd 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 0026c0c4ba..87b718d629 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 - 3.0.1-SNAPSHOT + 3.0.1 ../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 d824df6b12..e2561199b0 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 - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 470344d436..1c008fe8fa 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 - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 215850fd9b..0c614d54af 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 - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index b2e665c34f..7a177fdf3e 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 0ef882d8ac..37d0589acb 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/pom.xml b/pom.xml index cc351a473d..a9c566886a 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1-SNAPSHOT + 3.0.1 pom OpenCGA From e2c126162d16203a05fcd1a48b8e56125ae71860 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 30 Oct 2024 19:59:54 +0100 Subject: [PATCH 11/16] Prepare new development version 3.0.2-SNAPSHOT --- 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 43b1160fe2..b87b735227 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index c4dfcb85e4..9888d9eff1 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index fadfdd92a1..9b90d1abe8 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 0ca39ca098..e79ddeca00 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 8963d152c2..d14ae03e2d 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 80cc54dcb2..7fdcef9359 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index fce3eef301..4b28c21116 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index c35e769d46..2b17811efd 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 7f5ba7e7ca..2ea3d81f94 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 - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9de3546a3e..d9eac96485 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 - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 8182135dd4..4c272f5582 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 - 3.0.1 + 3.0.2-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 31dd086e2b..d8175c811e 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 - 3.0.1 + 3.0.2-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 e95b3ba1c0..b9497bf885 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 - 3.0.1 + 3.0.2-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 66034e11b8..2e8fc54913 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 - 3.0.1 + 3.0.2-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 27d4d67362..4c3be0aacf 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 - 3.0.1 + 3.0.2-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 5ef22584c7..3f28c2c77a 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 - 3.0.1 + 3.0.2-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 cedc3c90e9..016818d607 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 - 3.0.1 + 3.0.2-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 d75d126306..fa81312adc 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 - 3.0.1 + 3.0.2-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 5faf374ce1..94fd573d1c 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 - 3.0.1 + 3.0.2-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 e2dc27a8fd..78becbf80e 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 - 3.0.1 + 3.0.2-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 87b718d629..5f7d8651c9 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 - 3.0.1 + 3.0.2-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 e2561199b0..01b610468f 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 - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 1c008fe8fa..9ef4161339 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 - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 0c614d54af..8fc3460884 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 - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 7a177fdf3e..9298492d10 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 37d0589acb..923d0bc200 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index a9c566886a..39db4b7cfc 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.0.2-SNAPSHOT pom OpenCGA From 345a6f2889f1f039e2c21f195482b0a9424807f0 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 30 Oct 2024 20:24:12 +0100 Subject: [PATCH 12/16] Prepare release 3.0.2 --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 39db4b7cfc..f68aa475a8 100644 --- a/pom.xml +++ b/pom.xml @@ -43,8 +43,8 @@ - - 3.0.1 + 3.0.2 + 3.0.2 6.0.0 3.0.0 5.0.0 From 3863e5ecf597b7f922348f4dd2c0d43d24e0f5f4 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 30 Oct 2024 20:27:51 +0100 Subject: [PATCH 13/16] Prepare release 3.0.1 --- .github/workflows/release.yml | 26 +++++++++---------- 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-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../pom.xml | 2 +- .../pom.xml | 2 +- .../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 +- .../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-hadoop/pom.xml | 2 +- .../opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 6 ++--- 28 files changed, 42 insertions(+), 42 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 86bcb47197..33aa540ca2 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -12,19 +12,19 @@ jobs: 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 - with: - maven_opts: -P hdp3.1 -Dopencga.war.name=opencga - secrets: inherit - - deploy-docker: - 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 --tag ${{ needs.build.outputs.version }} - secrets: inherit +# deploy-maven: +# uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop +# needs: build +# with: +# maven_opts: -P hdp3.1 -Dopencga.war.name=opencga +# secrets: inherit +# +# deploy-docker: +# 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 --tag ${{ needs.build.outputs.version }} +# secrets: inherit deploy-python: uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index b87b735227..43b1160fe2 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 9888d9eff1..c4dfcb85e4 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 9b90d1abe8..fadfdd92a1 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index e79ddeca00..0ca39ca098 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index d14ae03e2d..8963d152c2 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 7fdcef9359..80cc54dcb2 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 4b28c21116..fce3eef301 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 2b17811efd..c35e769d46 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 2ea3d81f94..7f5ba7e7ca 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 - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index d9eac96485..9de3546a3e 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 - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 4c272f5582..8182135dd4 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 d8175c811e..31dd086e2b 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 b9497bf885..e95b3ba1c0 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 2e8fc54913..66034e11b8 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 4c3be0aacf..27d4d67362 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 3f28c2c77a..5ef22584c7 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 016818d607..cedc3c90e9 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 fa81312adc..d75d126306 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 94fd573d1c..5faf374ce1 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 78becbf80e..e2dc27a8fd 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 5f7d8651c9..87b718d629 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 - 3.0.2-SNAPSHOT + 3.0.1 ../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 01b610468f..e2561199b0 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 - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 9ef4161339..1c008fe8fa 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 - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 8fc3460884..0c614d54af 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 - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 9298492d10..7a177fdf3e 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 923d0bc200..37d0589acb 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 ../pom.xml diff --git a/pom.xml b/pom.xml index f68aa475a8..a19afedca3 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.2-SNAPSHOT + 3.0.1 pom OpenCGA @@ -43,8 +43,8 @@ - 3.0.2 - 3.0.2 + 3.0.1 + 3.0.1 6.0.0 3.0.0 5.0.0 From 1269834c23a3ec3aa55d107f9d7941c983b1973c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 30 Oct 2024 20:31:57 +0100 Subject: [PATCH 14/16] Prepare release 3.0.1 --- .github/workflows/release.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 33aa540ca2..f283f1a003 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -36,7 +36,8 @@ jobs: release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build, deploy-maven, deploy-docker, deploy-python ] + # needs: [ build, deploy-maven, deploy-docker, deploy-python ] + needs: build with: artifact: build-folder file: | From 40484f00b63075f6415207c40ea95b75a04e1a70 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 30 Oct 2024 20:32:32 +0100 Subject: [PATCH 15/16] Prepare release 3.0.1 --- .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 f283f1a003..c02f0d3833 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -37,7 +37,7 @@ jobs: release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop # needs: [ build, deploy-maven, deploy-docker, deploy-python ] - needs: build + needs: deploy-python with: artifact: build-folder file: | From cd27755e4740562d971f1efdcfc0fc4bd99d8b8f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 5 Nov 2024 18:35:26 +0100 Subject: [PATCH 16/16] Prepare Port Patch 3.0.1 -> 3.4.0 Xetabase 2.0.1 -> 2.4.0 --- 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/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 43b1160fe2..7ac4af0923 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index c4dfcb85e4..7aed855b51 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index fadfdd92a1..e28e69b462 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 0ca39ca098..68d77922ca 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 8963d152c2..a43011299c 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 80cc54dcb2..6707b15204 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index fce3eef301..6b57d5a3f3 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index c35e769d46..053c5892bb 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 7f5ba7e7ca..9d3555928b 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 - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9de3546a3e..c9bd1a8856 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 - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 8182135dd4..7aa897d4e9 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 - 3.0.1 + 3.4.0-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 31dd086e2b..864aac19c1 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 - 3.0.1 + 3.4.0-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 e95b3ba1c0..e98d6d2626 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 - 3.0.1 + 3.4.0-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 66034e11b8..9f92738cf9 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 - 3.0.1 + 3.4.0-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 27d4d67362..f2bdb5f8e9 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 - 3.0.1 + 3.4.0-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 5ef22584c7..f79e2ca383 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 - 3.0.1 + 3.4.0-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 cedc3c90e9..2e243830f9 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 - 3.0.1 + 3.4.0-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 d75d126306..1c5876905e 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 - 3.0.1 + 3.4.0-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 5faf374ce1..991c499dc8 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 - 3.0.1 + 3.4.0-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 e2dc27a8fd..a960e1a068 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 - 3.0.1 + 3.4.0-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 87b718d629..ae6332feb3 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 - 3.0.1 + 3.4.0-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 e2561199b0..db8d5b9aec 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 - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 1c008fe8fa..80807b54c5 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 - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 0c614d54af..3dd2a91dd4 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 - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 7a177fdf3e..40b18f7559 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 37d0589acb..8b5c1157ef 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index a19afedca3..bf6c0adb10 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.1 + 3.4.0-SNAPSHOT pom OpenCGA