From 32710deff1a0b8ed8826273bf7781d8e18bed831 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 8 Mar 2024 17:07:25 +0100 Subject: [PATCH 01/13] Prepare cicd release --- .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 86bcb471976..93b011f556f 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -23,7 +23,7 @@ jobs: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: - cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build.outputs.version }} + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init secrets: inherit deploy-python: From b49d9e16ffedeedf576530359c5fa3e4af662759 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 19:06:22 +0200 Subject: [PATCH 02/13] pom: Release 3.1.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop/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 d43f173b4ff..a82fde15ccc 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 67bd1fa34e0..6dcf364e559 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 11535022d1b..ff10c269d7f 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index c9461e9c4de..ce253ddc6ae 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index adb57573b45..215d392ce1c 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 0153566efea..432db00c834 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3cbbbb2fa89..eda14c31ea1 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 804b83e792b..7632ed6d65f 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index a31567cb3bc..cc692c6fcea 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index ff97332afff..bae503e0e91 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 12c0f24a27b..0dffe6806ff 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index e63a1dfcc78..deac888af82 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 85caa7da48e..661d9416a8f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 719b5cf072a..358590f69f6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index a8a16269d93..394e6c90e16 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index a2d228c120d..58aac8414c5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index eab3b7f565e..8c00149ba90 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 1292ba96965..45370142854 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 4b4ab70de2b..82a3d1f0fdc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index b9f0fcc7696..c4839e1c646 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index d48ef593c4d..8d09832b15a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index cddf51ec925..0326f2479f3 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 943b2ff3eb8..7d97161a5e3 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 891225e9311..054ab3bc9de 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index f89a8783b7f..c3f5166b7fd 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 70f7e126a02..12981fefe10 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 1b5cc6907e7..09ddd09943d 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.1.1-SNAPSHOT + 3.1.0-SNAPSHOT pom OpenCGA From a0b8d919ee01a0d5d14492924b77f159f4b0a416 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 26 Sep 2024 10:23:00 +0200 Subject: [PATCH 03/13] cli: Error message Active token detected. Please logout first. #TASK-6992 --- .../opencga/app/cli/main/custom/CustomUsersCommandExecutor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomUsersCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomUsersCommandExecutor.java index bfef1fbca25..c608f5e2c1a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomUsersCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomUsersCommandExecutor.java @@ -77,7 +77,7 @@ public RestResponse login(CustomUsersCommandOptions.Logi String token = session.getSession().getToken(); String errorMsg = "Missing password. "; if (StringUtils.isNotEmpty(token)) { - errorMsg += "Active token detected "; + errorMsg += "Active token detected. Please logout first."; } CommandLineUtils.error(errorMsg); } From 92ff7a77913069d2644b6942883342c282358c56 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 26 Sep 2024 16:25:30 +0200 Subject: [PATCH 04/13] cli: Ensure that the client has the session token #TASK-6992 --- .../opencga/app/cli/main/processors/CommandProcessor.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/processors/CommandProcessor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/processors/CommandProcessor.java index ef06e2c8944..8c43c340ab6 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/processors/CommandProcessor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/processors/CommandProcessor.java @@ -136,9 +136,13 @@ private boolean checkAutoRefresh(OpencgaCommandExecutor commandExecutor) { public void loadSessionStudies(OpencgaCommandExecutor commandExecutor) { Session session = commandExecutor.getSessionManager().getSession(); - logger.debug("Loading session studies using token: " - + session.getToken()); OpenCGAClient openCGAClient = commandExecutor.getOpenCGAClient(); + logger.debug("openCGAClient Token: " + openCGAClient.getToken()); + if(StringUtils.isEmpty(openCGAClient.getToken())) { + openCGAClient.setToken(session.getToken()); + } + logger.debug("Loading session studies using token: " + + openCGAClient.getToken()); try { // Query the server to retrieve the studies of user projects RestResponse res = openCGAClient.getProjectClient().search(new ObjectMap()); From bd4ca990010e9f3f4001ff12db2a3549a00ce880 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 26 Sep 2024 16:41:28 +0200 Subject: [PATCH 05/13] Prepare release in hotfix branch release-3.2.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop/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 44dfcada226..0660ed5c025 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 7c86232e020..b84866dec25 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 32968f648dc..fd3439b6958 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 7af1fa42fb8..263ca0aab22 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 3aad7a17509..64ddb73f732 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 93b53c60ad9..7e67b3bf646 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index dfd75099282..711d461f9b8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 9a48c3cf8e0..9ccd85aef8f 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index ff1b502532f..20f1f1a0fb0 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index d2ef8e6ef94..a069ebc96c4 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 16196aae558..3ef37d0def2 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.1 + 3.2.2-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 bc904deccc8..cbbf5918cd6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.1 + 3.2.2-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 bf109e1371e..fd5b14d8ede 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.1 + 3.2.2-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 f6cb60ee7af..b3f07e1633b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.1 + 3.2.2-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 ebc420d03a1..9342f980100 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.1 + 3.2.2-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 2a4381a8c66..e39ccb54cbb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.1 + 3.2.2-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 91cc355092a..1f4eaf4eb07 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.1 + 3.2.2-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 abd28d36f1a..3be574c25e1 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.1 + 3.2.2-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 d5e8de35cc4..71956a9a81b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.1 + 3.2.2-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 616d8c0d0da..f896e5442b5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.1 + 3.2.2-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 beac4cdb3ce..f2089e1b584 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.1 + 3.2.2-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 477bc94cc09..0b81ae06188 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 69c94b8b2fd..14c33d3e3dc 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index f69ed9ee435..524b5ae6041 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 5e77d32e404..a26e01a35c0 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index dccd304226c..26f0cfc4bac 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index cba85a598b8..3bb7b819bb0 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.1 + 3.2.2-SNAPSHOT pom OpenCGA From 724afa9acd8141c7794c0e4df33d2e2fc17a8b7f Mon Sep 17 00:00:00 2001 From: pfurio Date: Thu, 26 Sep 2024 16:43:11 +0200 Subject: [PATCH 06/13] app: fix cohort-sample reference migration, #TASK-6998 --- .../SyncCohortsAndSamplesMigration.java | 27 +++++++++++++++---- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_6/SyncCohortsAndSamplesMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_6/SyncCohortsAndSamplesMigration.java index edfdbb7c828..d0d0cc931c3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_6/SyncCohortsAndSamplesMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_6/SyncCohortsAndSamplesMigration.java @@ -9,20 +9,24 @@ import org.bson.conversions.Bson; import org.opencb.opencga.catalog.db.api.CohortDBAdaptor; import org.opencb.opencga.catalog.db.api.SampleDBAdaptor; +import org.opencb.opencga.catalog.db.api.StudyDBAdaptor; import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor; import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptorFactory; import org.opencb.opencga.catalog.migration.Migration; import org.opencb.opencga.catalog.migration.MigrationTool; +import java.util.HashMap; import java.util.List; +import java.util.Map; import java.util.stream.Collectors; @Migration(id = "syncCohortsAndSamplesMigration" , - description = "Sync array of samples from cohort with array of cohortIds from Sample", + description = "Sync array of samples from cohort with array of cohortIds from Sample.", version = "2.12.6", domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, - date = 20240621 + date = 20240621, + patch = 2 // TASK-6998 ) public class SyncCohortsAndSamplesMigration extends MigrationTool { @@ -31,8 +35,18 @@ protected void run() throws Exception { MongoCollection sampleCollection = getMongoCollection(MongoDBAdaptorFactory.SAMPLE_COLLECTION); MongoCollection sampleArchiveCollection = getMongoCollection(MongoDBAdaptorFactory.SAMPLE_ARCHIVE_COLLECTION); + // Fill map study uid - fqn + Map uidFqnMap = new HashMap<>(); + Bson studyProjection = Projections.include(StudyDBAdaptor.QueryParams.UID.key(), StudyDBAdaptor.QueryParams.FQN.key()); + queryMongo(MongoDBAdaptorFactory.STUDY_COLLECTION, new Document(), studyProjection, study -> { + long studyUid = study.get(StudyDBAdaptor.QueryParams.UID.key(), Number.class).longValue(); + String studyFqn = study.getString(StudyDBAdaptor.QueryParams.FQN.key()); + uidFqnMap.put(studyUid, studyFqn); + }); + queryMongo(MongoDBAdaptorFactory.COHORT_COLLECTION, new Document(), - Projections.include(CohortDBAdaptor.QueryParams.ID.key(), CohortDBAdaptor.QueryParams.SAMPLES.key()), + Projections.include(CohortDBAdaptor.QueryParams.ID.key(), CohortDBAdaptor.QueryParams.SAMPLES.key(), + CohortDBAdaptor.QueryParams.STUDY_UID.key()), cohortDoc -> { String cohortId = cohortDoc.getString(CohortDBAdaptor.QueryParams.ID.key()); List samples = cohortDoc.getList(CohortDBAdaptor.QueryParams.SAMPLES.key(), Document.class); @@ -50,8 +64,11 @@ protected void run() throws Exception { long addedMissingCohort = sampleCollection.updateMany(query, update).getModifiedCount(); sampleArchiveCollection.updateMany(query, update); + long studyUid = cohortDoc.get(CohortDBAdaptor.QueryParams.STUDY_UID.key(), Number.class).longValue(); + // Ensure there aren't any samples pointing to this cohort that are not in the samples array query = Filters.and( + Filters.eq(SampleDBAdaptor.QueryParams.STUDY_UID.key(), studyUid), Filters.nin(SampleDBAdaptor.QueryParams.UID.key(), sampleUids), Filters.eq(SampleDBAdaptor.QueryParams.COHORT_IDS.key(), cohortId), Filters.eq(MongoDBAdaptor.LAST_OF_VERSION, true) @@ -61,10 +78,10 @@ protected void run() throws Exception { sampleArchiveCollection.updateMany(query, update); if (addedMissingCohort > 0 || removedNonAssociatedCohort > 0) { - logger.info("Fixed cohort '{}' references. " + logger.info("Fixed cohort '{}' references from study '{}'. " + "Added missing reference to {} samples. " + "Removed non-associated reference from {} samples.", - cohortId, addedMissingCohort, removedNonAssociatedCohort); + cohortId, uidFqnMap.get(studyUid), addedMissingCohort, removedNonAssociatedCohort); } } }); From ee5f048fbb8f4ae6c715d2b93c05aeb49d3c9e6a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 26 Sep 2024 21:32:23 +0200 Subject: [PATCH 07/13] Fix pull request approve #TASK-6992 --- .github/workflows/pull-request-approved.yml | 2 +- .github/workflows/scripts/get-xetabase-branch.sh | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml index a39ff011460..eb0e45fadce 100644 --- a/.github/workflows/pull-request-approved.yml +++ b/.github/workflows/pull-request-approved.yml @@ -24,7 +24,7 @@ jobs: chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}" echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}" - xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }}) + xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }}) echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY} echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT env: diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index a1eb7e529c6..90ab2c75747 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -19,11 +19,11 @@ get_xetabase_branch() { return 0 fi - # Check if the branch name starts with "release-" and follows the patterns "release-a.b.x" or "release-a.b.c.x" - if [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.([0-9]+)\.x$ ]]; then + # Check if the branch name starts with "release-" and follows the patterns "release-a.x.x" or "release-a.b.x" + if [[ "$input_branch" =~ ^release-([0-9]+)\.x\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]]; then # Extract the MAJOR part of the branch name MAJOR=${BASH_REMATCH[1]} - # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR + # Calculate the XETABASE_MAJOR by subtracting 1 from MAJOR of opencga XETABASE_MAJOR=$((MAJOR - 1)) # Check if the XETABASE_MAJOR is negative if (( XETABASE_MAJOR < 0 )); then From 3456609d33f8618cd310cef84eefee05ee3abbe4 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 27 Sep 2024 09:44:23 +0200 Subject: [PATCH 08/13] Update versions of the libraries #TASK-6992 --- pom.xml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/pom.xml b/pom.xml index 3bb7b819bb0..92abd71dbb6 100644 --- a/pom.xml +++ b/pom.xml @@ -43,12 +43,12 @@ - 3.2.1 - 3.2.1 - 6.2.1 - 3.2.1 - 5.2.1 - 3.2.1 + 3.2.2-SNAPSHOT + 3.2.2-SNAPSHOT + 6.2.2-SNAPSHOT + 3.2.2-SNAPSHOT + 5.2.2-SNAPSHOT + 3.2.2-SNAPSHOT 0.2.0 From a2369a05d8f427b49fec81210fa6b53a42ccf8f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Tue, 1 Oct 2024 17:53:55 +0100 Subject: [PATCH 09/13] app: Fix NPE at DetectIllegalConcurrentFileLoadingsMigration #TASK-6983 --- .../storage/DetectIllegalConcurrentFileLoadingsMigration.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_5/storage/DetectIllegalConcurrentFileLoadingsMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_5/storage/DetectIllegalConcurrentFileLoadingsMigration.java index c407cd82bbd..60ac81ab85e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_5/storage/DetectIllegalConcurrentFileLoadingsMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_5/storage/DetectIllegalConcurrentFileLoadingsMigration.java @@ -145,7 +145,7 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag metadataManager.getFileName(studyId, file), file); } } - } else if (sampleMetadata.getSampleIndexStatus(Optional.of(sampleMetadata.getSampleIndexVersion()).orElse(-1)) == TaskMetadata.Status.READY) { + } else if (sampleMetadata.getSampleIndexStatus(Optional.ofNullable(sampleMetadata.getSampleIndexVersion()).orElse(-1)) == TaskMetadata.Status.READY) { for (Integer fileId : sampleMetadata.getFiles()) { if (affectedFiles.contains(fileId)) { FileMetadata fileMetadata = metadataManager.getFileMetadata(studyId, fileId); From 1495e234fb53da73755dcbad9da2291d8886f02b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Fri, 4 Oct 2024 12:21:34 +0100 Subject: [PATCH 10/13] app: Imrpove logs at DetectIllegalConcurrentFileLoadingsMigration #TASK-6983 --- ...llegalConcurrentFileLoadingsMigration.java | 41 +++++++++++++------ 1 file changed, 29 insertions(+), 12 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_5/storage/DetectIllegalConcurrentFileLoadingsMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_5/storage/DetectIllegalConcurrentFileLoadingsMigration.java index 60ac81ab85e..347866e38d1 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_5/storage/DetectIllegalConcurrentFileLoadingsMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_12_5/storage/DetectIllegalConcurrentFileLoadingsMigration.java @@ -1,5 +1,6 @@ package org.opencb.opencga.app.migrations.v2_12_5.storage; +import org.apache.commons.lang3.tuple.Pair; import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; @@ -67,6 +68,8 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag if (fileSets.isEmpty()) { logger.info("No concurrent file loadings found in study '{}'", study); return; + } else { + logger.info("Found {} sets of files with shared samples in study '{}'", fileSets.size(), study); } Map fileTasks = new HashMap<>(); @@ -85,10 +88,12 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag } } - Set> fileSetsToInvalidate = new HashSet<>(); - Set affectedFiles = new HashSet<>(); - Set affectedSamples = new HashSet<>(); for (Set fileSet : fileSets) { + Set affectedFiles = new HashSet<>(); + Set affectedSamples = new HashSet<>(); + Set invalidFiles = new HashSet<>(); + Set invalidSampleIndexes = new HashSet<>(); + // Check if any task from this file set overlaps in time List tasks = new ArrayList<>(); for (Integer fileId : fileSet) { @@ -97,8 +102,11 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag tasks.add(task); } } - if (tasks.size() > 1) { - logger.info("Found {} tasks loading files {}", tasks.size(), fileSet); + if (tasks.size() <= 1) { + continue; + } else { + logger.info("--------------------"); + logger.info("Found {} tasks loading files {} in study {}", tasks.size(), fileSet, study); for (int i = 0; i < tasks.size(); i++) { TaskMetadata task1 = tasks.get(i); Date task1start = task1.getStatus().firstKey(); @@ -108,8 +116,7 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag Date task2start = task2.getStatus().firstKey(); Date task2end = task2.getStatus().lastKey(); if (task1start.before(task2end) && task1end.after(task2start)) { - fileSetsToInvalidate.add(fileSet); - affectedFiles.addAll(task1.getFileIds()); + affectedFiles.addAll(fileSet); List task1Files = task1.getFileIds().stream().map(fileId -> "'" + metadataManager.getFileName(studyId, fileId) + "'(" + fileId + ")").collect(Collectors.toList()); List task2Files = task2.getFileIds().stream().map(fileId -> "'" + metadataManager.getFileName(studyId, fileId) + "'(" + fileId + ")").collect(Collectors.toList()); @@ -131,8 +138,6 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag } } - Set invalidFiles = new HashSet<>(); - List invalidSampleIndexes = new ArrayList<>(); for (Integer sampleId : affectedSamples) { String sampleName = metadataManager.getSampleName(studyId, sampleId); SampleMetadata sampleMetadata = metadataManager.getSampleMetadata(studyId, sampleId); @@ -195,6 +200,8 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag } } } else { + logger.info("Sample '{}'({}) sample index is not in READY status. Invalidate to ensure rebuild", sampleName, sampleId); + logger.info(" - Invalidating sample index for sample '{}'({})", sampleName, sampleId); invalidSampleIndexes.add(sampleId); } } @@ -210,9 +217,19 @@ private void checkStudy(VariantStorageEngine engine, String study) throws Storag invalidSamples.addAll(metadataManager.getSampleIdsFromFileId(studyId, fileId)); } - logger.info("Affected files: {}", invalidFiles); - logger.info("Affected samples: {}", invalidSamples); - logger.info("Affected sample indexes: {}", invalidSampleIndexes); + logger.info("Study '{}'", study); + List> invalidFilesPairs = invalidFiles.stream() + .map(fileId -> Pair.of(metadataManager.getFileName(studyId, fileId), fileId)) + .collect(Collectors.toList()); + logger.info("Affected files: {}", invalidFilesPairs); + List> invalidSamplesPairs = invalidSamples.stream() + .map(sampleId -> Pair.of(metadataManager.getSampleName(studyId, sampleId), sampleId)) + .collect(Collectors.toList()); + logger.info("Affected samples: {}", invalidSamplesPairs); + List> invalidSampleIndexesPairs = invalidSampleIndexes.stream() + .map(sampleId -> Pair.of(metadataManager.getSampleName(studyId, sampleId), sampleId)) + .collect(Collectors.toList()); + logger.info("Affected sample indexes: {}", invalidSampleIndexesPairs); } } else { ObjectMap event = new ObjectMap() From 6689e77001c2465dcac7fa433e2811005535ba91 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 8 Oct 2024 10:03:35 +0200 Subject: [PATCH 11/13] Prepare release 3.2.2 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 10 +++++----- 27 files changed, 31 insertions(+), 31 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 0660ed5c025..09abf6e8a0a 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index b84866dec25..88ca5093bf2 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index fd3439b6958..e76c2600a5b 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 263ca0aab22..b92a75c0c2f 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 64ddb73f732..d95852a2a9e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 7e67b3bf646..8c8de33f6f8 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 711d461f9b8..3aa1a1ba140 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 9ccd85aef8f..62147506368 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 20f1f1a0fb0..1b7ca0552be 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index a069ebc96c4..97e71ad6767 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 3ef37d0def2..c887850d638 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.2-SNAPSHOT + 3.2.2 ../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 cbbf5918cd6..9b76b158426 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.2-SNAPSHOT + 3.2.2 ../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 fd5b14d8ede..2b9f10b4c61 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.2-SNAPSHOT + 3.2.2 ../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 b3f07e1633b..75de5cb3b59 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.2-SNAPSHOT + 3.2.2 ../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 9342f980100..99aa6bff987 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.2-SNAPSHOT + 3.2.2 ../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 e39ccb54cbb..6fcf4f6e119 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.2-SNAPSHOT + 3.2.2 ../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 1f4eaf4eb07..78ccb0c6fd6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.2-SNAPSHOT + 3.2.2 ../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 3be574c25e1..ddbea242efc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.2-SNAPSHOT + 3.2.2 ../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 71956a9a81b..13bd26d95e1 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.2-SNAPSHOT + 3.2.2 ../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 f896e5442b5..ef4661e6415 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.2-SNAPSHOT + 3.2.2 ../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 f2089e1b584..ac902e5cc34 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.2-SNAPSHOT + 3.2.2 ../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 0b81ae06188..3fb30139c00 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 14c33d3e3dc..aa5e1185fb3 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 524b5ae6041..91135571ce7 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index a26e01a35c0..7fb55b3543e 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 26f0cfc4bac..203fa2bef90 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 ../pom.xml diff --git a/pom.xml b/pom.xml index 92abd71dbb6..dedae4eaa39 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2-SNAPSHOT + 3.2.2 pom OpenCGA @@ -45,10 +45,10 @@ 3.2.2-SNAPSHOT 3.2.2-SNAPSHOT - 6.2.2-SNAPSHOT - 3.2.2-SNAPSHOT - 5.2.2-SNAPSHOT - 3.2.2-SNAPSHOT + 6.2.2 + 3.2.2 + 5.2.2 + 3.2.2 0.2.0 From e0d3af8ea57af1649db3dfe37bc1bd841b25d55c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 8 Oct 2024 11:55:01 +0200 Subject: [PATCH 12/13] Prepare release 3.2.2 --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index dedae4eaa39..4605dafa638 100644 --- a/pom.xml +++ b/pom.xml @@ -43,8 +43,8 @@ - 3.2.2-SNAPSHOT - 3.2.2-SNAPSHOT + 3.2.2 + 3.2.2 6.2.2 3.2.2 5.2.2 From a29dd0eef4f9236909a9fd9755ee882170cc81ad Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 8 Oct 2024 16:42:06 +0200 Subject: [PATCH 13/13] Prepare Port Patch 2.2.2 -> 2.3.0 #TASK-7038 --- 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 09abf6e8a0a..da118995989 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 88ca5093bf2..81cd804f3e8 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index e76c2600a5b..6b0951aa721 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index b92a75c0c2f..e18ab8949ad 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index d95852a2a9e..379849dd1a5 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 8c8de33f6f8..741360749ad 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 3aa1a1ba140..babb08f4107 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 62147506368..bdfa34a64b8 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 1b7ca0552be..9c27d061dff 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 97e71ad6767..cd5cb2c0888 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index c887850d638..80157147a92 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.2 + 3.3.0-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 9b76b158426..53b33f3c76a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.2 + 3.3.0-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 2b9f10b4c61..4e02eee65a2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.2 + 3.3.0-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 75de5cb3b59..7cda3125ff5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.2 + 3.3.0-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 99aa6bff987..b81b3599ad9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.2.2 + 3.3.0-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 6fcf4f6e119..2f2b0d32157 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.2 + 3.3.0-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 78ccb0c6fd6..ddc5d8e9792 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.2 + 3.3.0-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 ddbea242efc..f1b656e0c2b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.2 + 3.3.0-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 13bd26d95e1..00c4dddb2f2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.2 + 3.3.0-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 ef4661e6415..9dfa1bb4023 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.2 + 3.3.0-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 ac902e5cc34..d6c2eecf171 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.2.2 + 3.3.0-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 3fb30139c00..6462be6cfa4 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index aa5e1185fb3..7e2f40af775 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 91135571ce7..e4c020243bd 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 7fb55b3543e..2fdd79ef9f3 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 203fa2bef90..d2a279f522d 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 4605dafa638..6d529d46c55 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.2.2 + 3.3.0-SNAPSHOT pom OpenCGA