From f58cbd338f562de5bddad6b0cf1a50aa63a6967b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 9 Jan 2024 11:35:50 +0100 Subject: [PATCH 1/9] pom: updated versions #TASK-4437 --- pom.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index 0de0a7fdc99..ec05c5ced24 100644 --- a/pom.xml +++ b/pom.xml @@ -52,22 +52,22 @@ 0.2.0 - 2.11.4 + 2.14.3 2.30.1 4.4 1.7.7 3.11.4 1.28.1 - 1.7.32 + 1.7.36 2.17.2 8.8.2 0.11.2 9.4.17.v20190418 19.0 - 2.23.0 + 3.0.5 4.3.1 4.8.2 - 3.12.0 + 3.14.0 2.5 1.7 0.9.10 From 8f386008fea90c6fd9a52c5f0228bf29fce80872 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 9 Jan 2024 11:50:57 +0100 Subject: [PATCH 2/9] pom: Delete mapper-asl pom #TASK-4437 --- opencga-server/pom.xml | 4 ---- .../org/opencb/opencga/server/rest/ProjectWSServerTest.java | 2 +- .../org/opencb/opencga/server/rest/UserWSServerTest.java | 2 +- .../opencb/opencga/server/rest/VariableSetWSServerTest.java | 2 +- pom.xml | 5 ----- 5 files changed, 3 insertions(+), 12 deletions(-) diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 19845c9f6e5..a823bf691ce 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -106,10 +106,6 @@ com.fasterxml.jackson.core jackson-core - - org.codehaus.jackson - jackson-mapper-asl - com.google.protobuf protobuf-java diff --git a/opencga-server/src/test/java/org/opencb/opencga/server/rest/ProjectWSServerTest.java b/opencga-server/src/test/java/org/opencb/opencga/server/rest/ProjectWSServerTest.java index 518e867eaa5..04b5c77257d 100644 --- a/opencga-server/src/test/java/org/opencb/opencga/server/rest/ProjectWSServerTest.java +++ b/opencga-server/src/test/java/org/opencb/opencga/server/rest/ProjectWSServerTest.java @@ -146,7 +146,7 @@ public void modifyProject(long projectId, String sessionId) { System.out.println("\nJSON RESPONSE"); System.out.println(s); try { - org.codehaus.jackson.map.ObjectMapper objectMapper = new org.codehaus.jackson.map.ObjectMapper(); + ObjectMapper objectMapper = new ObjectMapper(); QueryResponse queryResponse = objectMapper.readValue(s, QueryResponse.class); //Map userData = objectMapper.readValue(s, Map.class); assertEquals("Expected [], actual [" + queryResponse.getError() + "]", "", queryResponse.getError()); diff --git a/opencga-server/src/test/java/org/opencb/opencga/server/rest/UserWSServerTest.java b/opencga-server/src/test/java/org/opencb/opencga/server/rest/UserWSServerTest.java index 2494c5cb1ad..c6a535628d7 100644 --- a/opencga-server/src/test/java/org/opencb/opencga/server/rest/UserWSServerTest.java +++ b/opencga-server/src/test/java/org/opencb/opencga/server/rest/UserWSServerTest.java @@ -16,7 +16,7 @@ package org.opencb.opencga.server.rest; -import org.codehaus.jackson.map.ObjectMapper; +import com.fasterxml.jackson.databind.ObjectMapper; import org.junit.experimental.categories.Category; import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.commons.datastore.core.QueryResponse; diff --git a/opencga-server/src/test/java/org/opencb/opencga/server/rest/VariableSetWSServerTest.java b/opencga-server/src/test/java/org/opencb/opencga/server/rest/VariableSetWSServerTest.java index 177a529004a..e746b1f7070 100644 --- a/opencga-server/src/test/java/org/opencb/opencga/server/rest/VariableSetWSServerTest.java +++ b/opencga-server/src/test/java/org/opencb/opencga/server/rest/VariableSetWSServerTest.java @@ -16,7 +16,7 @@ package org.opencb.opencga.server.rest; -import org.codehaus.jackson.map.ObjectMapper; +import com.fasterxml.jackson.databind.ObjectMapper; import org.junit.*; import org.junit.experimental.categories.Category; import org.junit.rules.ExpectedException; diff --git a/pom.xml b/pom.xml index ec05c5ced24..44d2b38212f 100644 --- a/pom.xml +++ b/pom.xml @@ -931,11 +931,6 @@ log4j ${log4j.version} - - org.codehaus.jackson - jackson-mapper-asl - ${jackson-codehaus.version} - org.codehaus.jackson jackson-core-asl From 55d9694f9e1de8f7cdc33841e9065ec1d2671f7c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 15 Jan 2024 12:30:21 +0100 Subject: [PATCH 3/9] pom opencga-app: Remove duplicated dependencies #TASK-4437 --- opencga-app/pom.xml | 14 +++++++++----- pom.xml | 5 +++++ 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 7e86ac13394..3562884db36 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -56,6 +56,10 @@ org.opencb.opencga opencga-master + + org.opencb.opencga + opencga-test + org.opencb.opencga opencga-client @@ -495,11 +499,11 @@ - - - - - + diff --git a/pom.xml b/pom.xml index 44d2b38212f..202c15d7048 100644 --- a/pom.xml +++ b/pom.xml @@ -249,6 +249,11 @@ opencga-storage-app ${project.version} + + org.opencb.opencga + opencga-test + ${project.version} + org.opencb.opencga opencga-storage-core From 20c4c2d1df24e711a8aa7ae0a977e3915d4a3f8f Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 15 Jan 2024 12:33:42 +0100 Subject: [PATCH 4/9] pom: Check sonar.scanner.force-deprecated-java-version fix sonar issue --- pom.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pom.xml b/pom.xml index 202c15d7048..674df17a7ff 100644 --- a/pom.xml +++ b/pom.xml @@ -146,6 +146,13 @@ 1.7.24 2.5-20081211 + + + true 2.23.0 From 56b64e68b021599c5bfe04f5baa6519cecb85e67 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 15 Jan 2024 14:00:20 +0100 Subject: [PATCH 5/9] test-analysis.yml: Update java version to 17 #TASK-5475 --- .github/workflows/test-analysis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index b2b5105877b..6a83e6e556c 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -27,7 +27,7 @@ jobs: uses: actions/setup-java@v3 with: distribution: 'temurin' - java-version: '11' + java-version: '17' cache: 'maven' - name: Install dependencies branches run: | From cabac0438722ccfbcc56b54a8a61c1db910ab459 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 15 Jan 2024 16:30:33 +0100 Subject: [PATCH 6/9] pom: Restore htsjdk version #TASK-4437 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 674df17a7ff..1f78cee2441 100644 --- a/pom.xml +++ b/pom.xml @@ -64,7 +64,7 @@ 0.11.2 9.4.17.v20190418 19.0 - 3.0.5 + 2.23.0 4.3.1 4.8.2 3.14.0 From f2c7d35fea34287273586b66b67999af43941577 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 24 Jan 2024 13:39:05 +0100 Subject: [PATCH 7/9] Fix OpenCB repository versions to conform to XetaBase 2.0.0 version #TASK-5444 --- 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-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/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 | 14 +++++++------- 21 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index d2910773818..35da9a4f99b 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 3562884db36..739465b22ef 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index d55580e9771..633389bd8dd 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 719034642cd..e8e9c753dd4 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 68060d55ac2..80cf5324837 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 760d7322c7d..dd8e2ad01d4 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 312572202db..8152c26eaf4 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index a823bf691ce..10f4fcb69b1 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index de4e12b5310..b20c1d8115b 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 - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index d242fe2d96c..35e2805dc98 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 - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 33d63a614fa..b9deeb49386 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 - 2.13.0-SNAPSHOT + 3.0.0-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 0843289ccfe..26f5e773f14 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 - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 65c4454d0ca..2ef5c79bb53 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 85bd2644a77..5a162302e74 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index afae54a1eed..ee2c708c193 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index e756e8671f3..9d9c1350046 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 7c572c7e0c3..cd9556e2d70 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index e910f2f9a13..c2d67f4046c 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 - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 3cf09aff1db..221a9b348c6 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 7e3c399852a..131840a3d34 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 1f78cee2441..d021df05c45 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.13.0-SNAPSHOT + 3.0.0-SNAPSHOT pom OpenCGA @@ -43,12 +43,12 @@ - 2.13.0_dev - 2.13.0_dev - 5.9.0-SNAPSHOT - 2.13.0-SNAPSHOT - 4.13.0-SNAPSHOT - 2.13.0-SNAPSHOT + 3.0.0_dev + 3.0.0_dev + 6.0.0-SNAPSHOT + 3.0.0-SNAPSHOT + 5.0.0-SNAPSHOT + 3.0.0-SNAPSHOT 0.2.0 From 8bc93c2102a64e3aa9a7fd0bde3dd6a2a1d58260 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 25 Jan 2024 14:08:08 +0100 Subject: [PATCH 8/9] pom: Update maven war plugin to 3.4.0 and add lombok dependency #TASK-5475 --- opencga-server/pom.xml | 1 - pom.xml | 14 ++++++++++++++ 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 1d95c4801af..1f0d99c6362 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -252,7 +252,6 @@ maven-war-plugin - 2.6 ${opencga.war.name}