From 73ab330bdf5ddc96a7a2ca0a6a5ca2c4b7189864 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 23 Mar 2023 11:14:13 +0100 Subject: [PATCH 01/10] Prepare next release 2.7.2-SNAPSHOT --- .github/workflows/test-analysis.yml | 11 +++-------- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 4 ++-- 6 files changed, 9 insertions(+), 14 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 913524da..3ba05432 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -1,5 +1,4 @@ name: Build and test the project - on: workflow_call: inputs: @@ -20,12 +19,9 @@ on: required: true SSH_TESTING_SERVER_PASSWORD: required: true - env: - xb_version: "1.5.1" - + xb_version: "1.5.2" jobs: - test: name: Test and push Sonar analysis runs-on: ubuntu-22.04 @@ -51,14 +47,13 @@ jobs: with: name: workdir path: "**/target/site" - publish-test: name: Publish test results runs-on: ubuntu-22.04 needs: test strategy: matrix: - module: [ "biodata-tools","biodata-models" ] + module: ["biodata-tools", "biodata-models"] steps: - name: Download result dir uses: actions/download-artifact@v3 @@ -73,4 +68,4 @@ jobs: port: ${{ secrets.SSH_TESTING_SERVER_PORT}} username: ${{ secrets.SSH_TESTING_SERVER_USER }} password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }} - concurrency: 2 \ No newline at end of file + concurrency: 2 diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index 0e1122eb..045f9332 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.7.1 + 2.7.2-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 43c7163c..a754dfdc 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.7.1 + 2.7.2-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 6bd3cd59..a7b3b84b 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.7.1 + 2.7.2-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index b0a2ec64..d749d44d 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.7.1 + 2.7.2-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index cd6759a7..62ac7177 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.7.1 + 2.7.2-SNAPSHOT pom Biodata Biological entities and their equivalents in different file formats typically used in bioinformatics @@ -34,7 +34,7 @@ - 4.7.1 + 4.7.2-SNAPSHOT 4.4 1.7.7 3.11.4 From 0ad483cc7da5a09f7d8393a8da2bdc8eebb33896 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 19 Apr 2023 23:08:32 +0200 Subject: [PATCH 02/10] Prepare new development branch release-2.8.x --- .github/workflows/test-analysis.yml | 2 +- biodata-external/pom.xml | 2 +- biodata-formats/pom.xml | 2 +- biodata-models/pom.xml | 2 +- biodata-tools/pom.xml | 2 +- pom.xml | 4 ++-- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 0a8239e7..6c94ab41 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -20,7 +20,7 @@ on: SSH_TESTING_SERVER_PASSWORD: required: true env: - xb_version: "1.7.0" + xb_version: "1.6.1" jobs: test: name: Test and push Sonar analysis diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index 47f5cd08..6adefb4b 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -6,7 +6,7 @@ biodata org.opencb.biodata - 2.9.0-SNAPSHOT + 2.8.1-SNAPSHOT ../pom.xml diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index f2b19d8f..d5f1fb39 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.9.0-SNAPSHOT + 2.8.1-SNAPSHOT ../pom.xml diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index f5d4624a..23cc5168 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.9.0-SNAPSHOT + 2.8.1-SNAPSHOT ../pom.xml diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 6019c1d0..73002058 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -22,7 +22,7 @@ org.opencb.biodata biodata - 2.9.0-SNAPSHOT + 2.8.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index f4513aac..e7b22c08 100644 --- a/pom.xml +++ b/pom.xml @@ -20,7 +20,7 @@ org.opencb.biodata biodata - 2.9.0-SNAPSHOT + 2.8.1-SNAPSHOT pom Biodata Biological entities and their equivalents in different file formats typically used in bioinformatics @@ -34,7 +34,7 @@ - 4.8.0-SNAPSHOT + 4.7.2-SNAPSHOT 4.4 1.7.7 3.11.4 From 4a8bc8f5bf540fbf41fa8712afa537942d4546b2 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 4 May 2023 21:07:56 +0200 Subject: [PATCH 03/10] pom:several dependency cleanups #TASK-2095 --- biodata-external/pom.xml | 4 +- biodata-formats/pom.xml | 48 ++++++++++--- biodata-models/pom.xml | 30 ++++++--- biodata-tools/pom.xml | 92 +++++++++++++++++-------- pom.xml | 141 ++++++++++++++++++++++++++++++++++----- 5 files changed, 252 insertions(+), 63 deletions(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index 045f9332..2bae88fc 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -19,8 +19,8 @@ avro - org.opencb.commons - commons-datastore-core + com.fasterxml.jackson.core + jackson-databind diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index a754dfdc..3a48e01a 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -34,31 +34,63 @@ org.opencb.biodata biodata-models - + + org.opencb.commons + commons-lib + jakarta.xml.bind jakarta.xml.bind-api - 2.3.3 com.sun.xml.bind jaxb-impl - 2.3.3 runtime net.sourceforge.owlapi owlapi-oboformat - 5.1.13 - junit - junit + org.slf4j + slf4j-api + + + com.fasterxml.jackson.core + jackson-annotations + + + com.fasterxml.jackson.core + jackson-databind + + + com.fasterxml.jackson.core + jackson-core + + + org.apache.commons + commons-lang3 + + + com.google.guava + guava + + + org.apache.commons + commons-collections4 + + + com.github.samtools + htsjdk + + + org.codehaus.jackson + jackson-mapper-asl test - org.slf4j - slf4j-simple + junit + junit test diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index a7b3b84b..81be1b5b 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -38,11 +38,14 @@ org.opencb.commons commons-datastore-core - org.apache.commons commons-collections4 + + org.apache.commons + commons-lang3 + com.github.samtools htsjdk @@ -56,17 +59,28 @@ protobuf-java - io.grpc - grpc-all + com.google.code.findbugs + jsr305 - junit - junit - test + org.slf4j + slf4j-api - org.slf4j - slf4j-simple + com.fasterxml.jackson.core + jackson-annotations + + + com.fasterxml.jackson.core + jackson-databind + + + org.codehaus.jackson + jackson-mapper-asl + + + junit + junit test diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index d749d44d..8a6be31b 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -34,6 +34,10 @@ org.opencb.biodata biodata-formats + + org.opencb.biodata + biodata-models + org.opencb.commons commons-datastore-core @@ -41,44 +45,81 @@ org.opencb.ga4gh ga4gh - 0.6.0a5 - - - org.apache.avro - avro-ipc - - - - log4j - log4j - 1.2.17 + org.opencb.commons + commons-lib com.databricks SnpEff - 4.3.1 - - - junit - junit - - - com.github.samtools - htsjdk - - org.rocksdb rocksdbjni - 4.5.1 org.biojava biojava-alignment + + org.biojava + biojava-core + + + org.slf4j + slf4j-api + + + com.fasterxml.jackson.core + jackson-annotations + + + com.fasterxml.jackson.core + jackson-databind + + + com.fasterxml.jackson.core + jackson-core + + + org.apache.commons + commons-lang3 + + + org.apache.commons + commons-collections4 + + + org.codehaus.jackson + jackson-mapper-asl + + + com.google.guava + guava + + + com.github.samtools + htsjdk + + + org.apache.avro + avro + + + com.google.protobuf + protobuf-java + + + com.google.code.findbugs + jsr305 + + + + commons-io + commons-io + test + org.opencb.biodata biodata-models @@ -91,11 +132,6 @@ junit test - - org.slf4j - slf4j-simple - test - diff --git a/pom.xml b/pom.xml index 62ac7177..22d1b4a2 100644 --- a/pom.xml +++ b/pom.xml @@ -35,18 +35,30 @@ 4.7.2-SNAPSHOT + 2.11.4 4.4 1.7.7 3.11.4 1.28.1 2.23.0 1.7.32 - + 3.0.2 + 3.12.0 opencb https://sonarcloud.io - + 1.9.13 1.8 UTF-8 + 22.0 + 2.4 + 5.0.0 + 0.6.0a5 + 4.3.1 + 4.5.1 + 2.3.3 + 5.1.13 + 2.3.3 + 4.1.0 @@ -121,6 +133,36 @@ + + jakarta.xml.bind + jakarta.xml.bind-api + ${jakarta.xml.bind-api.version} + + + org.rocksdb + rocksdbjni + ${rocksdbjni.version} + + + org.opencb.ga4gh + ga4gh + ${ga4gh.version} + + + org.rocksdb + rocksdbjni + ${rocksdbjni.version} + + + com.databricks + SnpEff + ${SnpEff.version} + + + org.opencb.commons + commons-lib + ${java-common-libs.version} + org.opencb.biodata biodata-formats @@ -135,30 +177,49 @@ org.opencb.commons commons-lib ${java-common-libs.version} - - - org.apache.logging.log4j - log4j-slf4j-impl - - org.opencb.commons commons-datastore-core ${java-common-libs.version} - - - org.apache.logging.log4j - log4j-slf4j-impl - - - + com.google.guava + guava + ${guava.version} + + com.github.samtools htsjdk ${htsjdk.version} + + com.fasterxml.jackson.core + jackson-core + ${jackson.version} + + + com.fasterxml.jackson.core + jackson-databind + ${jackson.version} + + + com.fasterxml.jackson.core + jackson-annotations + ${jackson.version} + + + + org.apache.commons + commons-lang3 + ${commons-lang.version} + + + org.codehaus.jackson + jackson-mapper-asl + ${jackson-mapper.version} + + org.apache.avro avro @@ -179,10 +240,20 @@ grpc-all ${grpc.version} + + org.slf4j + slf4j-api + ${slf4j.version} + + + com.google.code.findbugs + jsr305 + ${jsr.version} + org.biojava biojava-alignment - 4.1.0 + ${biojava-alignment.version} org.apache.logging.log4j @@ -198,6 +269,16 @@ + + commons-io + commons-io + ${commons-io.version} + + + org.biojava + biojava-core + ${biojava-core.version} + junit junit @@ -212,7 +293,17 @@ test true - + + com.sun.xml.bind + jaxb-impl + ${jaxb-impl.version} + + + net.sourceforge.owlapi + owlapi-oboformat + ${owlapi-oboformat.version} + + @@ -224,6 +315,22 @@ + + org.apache.maven.plugins + maven-dependency-plugin + 3.5.0 + + + analyze + + analyze-only + + + true + + + + org.apache.maven.plugins maven-compiler-plugin From fa0f873cd1a2eaf6344f5b8338e22c724d9ed4e4 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 5 May 2023 00:01:39 +0200 Subject: [PATCH 04/10] pom: Dependency cleanups #TASK-2095 --- pom.xml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index 22d1b4a2..cfb5aa7b 100644 --- a/pom.xml +++ b/pom.xml @@ -34,6 +34,7 @@ + 4.7.2-SNAPSHOT 2.11.4 4.4 @@ -44,11 +45,7 @@ 1.7.32 3.0.2 3.12.0 - opencb - https://sonarcloud.io 1.9.13 - 1.8 - UTF-8 22.0 2.4 5.0.0 @@ -59,6 +56,11 @@ 5.1.13 2.3.3 4.1.0 + + opencb + https://sonarcloud.io + 1.8 + UTF-8 From 02d8e7f11717a3819d9a73ac480086d81185c83c Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 5 May 2023 01:23:47 +0100 Subject: [PATCH 05/10] pom: minor style changes --- biodata-tools/pom.xml | 14 +++++++------- pom.xml | 44 +++++++++++++++++++------------------------ 2 files changed, 26 insertions(+), 32 deletions(-) diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index 8a6be31b..e147cf4b 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -42,14 +42,14 @@ org.opencb.commons commons-datastore-core - - org.opencb.ga4gh - ga4gh - org.opencb.commons commons-lib + + org.opencb.ga4gh + ga4gh + com.databricks SnpEff @@ -72,15 +72,15 @@ com.fasterxml.jackson.core - jackson-annotations + jackson-core com.fasterxml.jackson.core - jackson-databind + jackson-annotations com.fasterxml.jackson.core - jackson-core + jackson-databind org.apache.commons diff --git a/pom.xml b/pom.xml index cfb5aa7b..31f46566 100644 --- a/pom.xml +++ b/pom.xml @@ -34,7 +34,7 @@ - + 4.7.2-SNAPSHOT 2.11.4 4.4 @@ -56,6 +56,7 @@ 5.1.13 2.3.3 4.1.0 + 4.13.2 opencb https://sonarcloud.io @@ -284,7 +285,7 @@ junit junit - 4.13.2 + ${junit.version} test @@ -305,34 +306,11 @@ owlapi-oboformat ${owlapi-oboformat.version} - - - - - - - - - org.apache.maven.plugins - maven-dependency-plugin - 3.5.0 - - - analyze - - analyze-only - - - true - - - - org.apache.maven.plugins maven-compiler-plugin @@ -399,6 +377,22 @@ + + org.apache.maven.plugins + maven-dependency-plugin + 3.5.0 + + + analyze + + analyze-only + + + true + + + + From 28e5e45beb744e45614f5e043034373fcb036c43 Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 5 May 2023 14:18:21 +0100 Subject: [PATCH 06/10] pom: minor style changes --- pom.xml | 54 +++++++++++++++++++++++++++--------------------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/pom.xml b/pom.xml index 100737a6..d60ec949 100644 --- a/pom.xml +++ b/pom.xml @@ -143,31 +143,7 @@ - - jakarta.xml.bind - jakarta.xml.bind-api - ${jakarta.xml.bind-api.version} - - - org.rocksdb - rocksdbjni - ${rocksdbjni.version} - - - org.opencb.ga4gh - ga4gh - ${ga4gh.version} - - - org.rocksdb - rocksdbjni - ${rocksdbjni.version} - - - com.databricks - SnpEff - ${SnpEff.version} - + org.opencb.commons commons-lib @@ -193,6 +169,32 @@ commons-datastore-core ${java-common-libs.version} + + jakarta.xml.bind + jakarta.xml.bind-api + ${jakarta.xml.bind-api.version} + + + org.rocksdb + rocksdbjni + ${rocksdbjni.version} + + + org.opencb.ga4gh + ga4gh + ${ga4gh.version} + + + + org.rocksdb + rocksdbjni + ${rocksdbjni.version} + + + com.databricks + SnpEff + ${SnpEff.version} + com.google.guava guava @@ -218,7 +220,6 @@ jackson-annotations ${jackson.version} - org.apache.commons commons-lang3 @@ -229,7 +230,6 @@ jackson-mapper-asl ${jackson-mapper.version} - org.apache.avro avro From 6555f52f45c50ff065844a50d64fbd6abcc30160 Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 5 May 2023 14:37:11 +0100 Subject: [PATCH 07/10] pm: downgrade guava to 22.0 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index d60ec949..c53246db 100644 --- a/pom.xml +++ b/pom.xml @@ -46,7 +46,7 @@ 3.0.2 3.12.0 1.9.13 - 22.0 + 19.0 2.4 5.0.0 0.6.0a5 From bfb4ec59e1736115c4ab3e71331c6c1630d82591 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 11 Oct 2023 15:35:54 +0200 Subject: [PATCH 08/10] clean pom TASK-2095 --- biodata-formats/pom.xml | 1 + biodata-tools/pom.xml | 1 + 2 files changed, 2 insertions(+) diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 560ea3da..ab4b86c5 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -38,6 +38,7 @@ org.opencb.commons commons-lib + jakarta.xml.bind jakarta.xml.bind-api diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index cb90dd90..7a5fc420 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -50,6 +50,7 @@ org.opencb.ga4gh ga4gh + com.databricks SnpEff From e5184081f2e2a93552562fd110a87ff3b996a2bc Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 13 Oct 2023 16:11:06 +0100 Subject: [PATCH 09/10] pom: upgrade dependency plugin version --- biodata-formats/pom.xml | 4 ++++ pom.xml | 10 ++++++---- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index 1f8b2f46..b3ae1990 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -84,6 +84,10 @@ com.github.samtools htsjdk + + org.apache.avro + avro + org.codehaus.jackson jackson-mapper-asl diff --git a/pom.xml b/pom.xml index b915aaea..ab1bbdb7 100644 --- a/pom.xml +++ b/pom.xml @@ -15,13 +15,16 @@ ~ limitations under the License. --> - + 4.0.0 org.opencb.biodata biodata 2.12.0-SNAPSHOT pom + Biodata Biological entities and their equivalents in different file formats typically used in bioinformatics https://github.com/opencb/biodata/wiki @@ -36,7 +39,6 @@ 4.12.0-SNAPSHOT - 2.11.4 4.4 1.7.7 @@ -201,7 +203,7 @@ guava ${guava.version} - + com.github.samtools htsjdk ${htsjdk.version} @@ -388,7 +390,7 @@ org.apache.maven.plugins maven-dependency-plugin - 3.5.0 + 3.6.0 analyze From d0f7d6eb3a96958f94af281424634c6869615018 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 19 Oct 2023 12:52:45 +0200 Subject: [PATCH 10/10] pom: Added develop dependencies to review #TASK-2095 --- biodata-external/pom.xml | 5 +++++ biodata-formats/pom.xml | 6 ++++++ biodata-models/pom.xml | 10 ++++++++++ biodata-tools/pom.xml | 12 +++++++++++- pom.xml | 9 +++++++++ 5 files changed, 41 insertions(+), 1 deletion(-) diff --git a/biodata-external/pom.xml b/biodata-external/pom.xml index 38faf4ec..b3b44270 100644 --- a/biodata-external/pom.xml +++ b/biodata-external/pom.xml @@ -22,6 +22,11 @@ com.fasterxml.jackson.core jackson-databind + + + org.opencb.commons + commons-datastore-core + diff --git a/biodata-formats/pom.xml b/biodata-formats/pom.xml index b3ae1990..af86394c 100644 --- a/biodata-formats/pom.xml +++ b/biodata-formats/pom.xml @@ -98,6 +98,12 @@ junit test + + + org.slf4j + slf4j-simple + test + diff --git a/biodata-models/pom.xml b/biodata-models/pom.xml index 23246435..83c7b456 100644 --- a/biodata-models/pom.xml +++ b/biodata-models/pom.xml @@ -83,6 +83,16 @@ junit test + + + io.grpc + grpc-all + + + org.slf4j + slf4j-simple + test + diff --git a/biodata-tools/pom.xml b/biodata-tools/pom.xml index ddaddba5..4cc34f6e 100644 --- a/biodata-tools/pom.xml +++ b/biodata-tools/pom.xml @@ -50,7 +50,6 @@ org.opencb.ga4gh ga4gh - com.databricks SnpEff @@ -133,6 +132,17 @@ junit test + + + + log4j + log4j + + + org.slf4j + slf4j-simple + test + diff --git a/pom.xml b/pom.xml index ab1bbdb7..d522cbd3 100644 --- a/pom.xml +++ b/pom.xml @@ -65,6 +65,7 @@ https://sonarcloud.io 1.8 UTF-8 + 1.2.17 @@ -316,6 +317,11 @@ owlapi-oboformat ${owlapi-oboformat.version} + + log4j + log4j + ${log4j.version} + @@ -399,6 +405,9 @@ true + + * +