From 050b14e6f4e24a57293de888654c109ee4d42314 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 26 Sep 2024 21:23:51 +0200 Subject: [PATCH 1/5] Prepare release in hotfix branch release-5.2.x --- cellbase-app/pom.xml | 2 +- cellbase-client/pom.xml | 2 +- cellbase-core/pom.xml | 2 +- cellbase-lib/pom.xml | 2 +- cellbase-server/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml index df777079c..4b05d287c 100644 --- a/cellbase-app/pom.xml +++ b/cellbase-app/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.1 + 6.2.2-SNAPSHOT ../pom.xml diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml index 2e9b1262a..f4ecc8458 100644 --- a/cellbase-client/pom.xml +++ b/cellbase-client/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.1 + 6.2.2-SNAPSHOT ../pom.xml diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml index 183634a92..1a35c185c 100644 --- a/cellbase-core/pom.xml +++ b/cellbase-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.1 + 6.2.2-SNAPSHOT ../pom.xml diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml index 0ccb570c2..c1ed6f6ba 100644 --- a/cellbase-lib/pom.xml +++ b/cellbase-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.1 + 6.2.2-SNAPSHOT ../pom.xml diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml index 96319c7cb..2bee90c83 100644 --- a/cellbase-server/pom.xml +++ b/cellbase-server/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.1 + 6.2.2-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 6c047d1a2..f44762ec0 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.1 + 6.2.2-SNAPSHOT pom CellBase project From 737568dcc29ac54245df972a7dd0ffd6e2517667 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Tue, 1 Oct 2024 11:42:24 +0200 Subject: [PATCH 2/5] core: fix configuration file by resolving conflics messages, #TASK-7030 --- cellbase-core/src/main/resources/configuration.yml | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/cellbase-core/src/main/resources/configuration.yml b/cellbase-core/src/main/resources/configuration.yml index 6e651f00d..84378507b 100644 --- a/cellbase-core/src/main/resources/configuration.yml +++ b/cellbase-core/src/main/resources/configuration.yml @@ -106,13 +106,6 @@ download: clinvar: # host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2021-07.xml.gz # host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2022-02.xml.gz -<<<<<<< HEAD - host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2022-11.xml.gz - clinvarVariation: -# host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_2021-07.xml.gz -# host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_2022-02.xml.gz - host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_2022-11.xml.gz -======= # host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2022-11.xml.gz host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/RCV_xml_old_format/ClinVarFullRelease_2024-05.xml.gz version: 2024-05 @@ -122,7 +115,6 @@ download: # host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_2022-11.xml.gz host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/VCV_xml_old_format/ClinVarVariationRelease_2024-05.xml.gz version: 2024-05 ->>>>>>> release-6.2.x clinvarSummary: host: http://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz clinvarVariationAllele: @@ -147,15 +139,10 @@ download: genomicSuperDups: host: http://hgdownload.cse.ucsc.edu/goldenPath gwasCatalog: -<<<<<<< HEAD - host: http://resources.opencb.org/opencb/cellbase/data/gwas/gwas_catalog_v1.0.2-associations_e106_r2022-05-17.tsv - version: "1.0.2 associations_e106_r2022-05-17" -======= #host: http://resources.opencb.org/opencb/cellbase/data/gwas/gwas_catalog_v1.0.2-associations_e106_r2022-05-17.tsv host: "https://ftp.ebi.ac.uk/pub/databases/gwas/releases/2024/05/20/gwas-catalog-associations_ontology-annotated.tsv" #version: "1.0.2 associations_e106_r2022-05-17" version: "2024-05-20" ->>>>>>> release-6.2.x hpo: host: https://ci.monarchinitiative.org/view/hpo/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/phenotype_to_genes.txt disgenet: From 836965e02a1e888791b810f8d50025e7ba8a02f8 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 1 Oct 2024 12:00:39 +0200 Subject: [PATCH 3/5] cicd: Adapt pull-request-approve workflow to the new SDLC --- .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 d339f65b9..ba378d3ab 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}" >> $GITHUB_OUTPUT env: diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh index 16ae8c471..fd9626a79 100644 --- a/.github/workflows/scripts/get-xetabase-branch.sh +++ b/.github/workflows/scripts/get-xetabase-branch.sh @@ -19,11 +19,11 @@ get_xetabase_branch() { return 0 fi - # Check if the branch name starts with "release-" and follows the patterns "release-a.b.x" or "release-a.b.c.x" - if [[ "$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=${BASH_REMATCH[1]} - # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR + # Calculate the XETABASE_MAJOR by subtracting 4 from MAJOR of cellbase XETABASE_MAJOR=$((MAJOR - 4)) # Check if the XETABASE_MAJOR is negative if (( XETABASE_MAJOR < 0 )); then From 15efe18c2a3578458cb3536e7e1dd076573a44aa Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 8 Oct 2024 09:21:57 +0200 Subject: [PATCH 4/5] Prepare release 6.2.2 --- cellbase-app/pom.xml | 2 +- cellbase-client/pom.xml | 2 +- cellbase-core/pom.xml | 2 +- cellbase-lib/pom.xml | 2 +- cellbase-server/pom.xml | 2 +- pom.xml | 6 +++--- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml index 4b05d287c..468e4c05d 100644 --- a/cellbase-app/pom.xml +++ b/cellbase-app/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2-SNAPSHOT + 6.2.2 ../pom.xml diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml index f4ecc8458..b519e5ec3 100644 --- a/cellbase-client/pom.xml +++ b/cellbase-client/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2-SNAPSHOT + 6.2.2 ../pom.xml diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml index 1a35c185c..e9d96cdbf 100644 --- a/cellbase-core/pom.xml +++ b/cellbase-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2-SNAPSHOT + 6.2.2 ../pom.xml diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml index c1ed6f6ba..7ae048359 100644 --- a/cellbase-lib/pom.xml +++ b/cellbase-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2-SNAPSHOT + 6.2.2 ../pom.xml diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml index 2bee90c83..a772dc2b0 100644 --- a/cellbase-server/pom.xml +++ b/cellbase-server/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2-SNAPSHOT + 6.2.2 ../pom.xml diff --git a/pom.xml b/pom.xml index f44762ec0..293345749 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2-SNAPSHOT + 6.2.2 pom CellBase project @@ -23,8 +23,8 @@ ${project.version} - 5.2.2-SNAPSHOT - 3.2.2-SNAPSHOT + 5.2.2 + 3.2.2 0.1.0 2.11.4 From 55dd516bbc9d88cab918fd410a4b35594e1a0300 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 8 Oct 2024 16:39:09 +0200 Subject: [PATCH 5/5] Prepare Port Patch 2.2.2 -> 2.3.0 #TASK-7038 --- cellbase-app/pom.xml | 2 +- cellbase-client/pom.xml | 2 +- cellbase-core/pom.xml | 2 +- cellbase-lib/pom.xml | 2 +- cellbase-server/pom.xml | 2 +- pom.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml index 468e4c05d..aed90e989 100644 --- a/cellbase-app/pom.xml +++ b/cellbase-app/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2 + 6.3.0-SNAPSHOT ../pom.xml diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml index b519e5ec3..7424c21bb 100644 --- a/cellbase-client/pom.xml +++ b/cellbase-client/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2 + 6.3.0-SNAPSHOT ../pom.xml diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml index e9d96cdbf..7c74e13d9 100644 --- a/cellbase-core/pom.xml +++ b/cellbase-core/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2 + 6.3.0-SNAPSHOT ../pom.xml diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml index 7ae048359..a181ccf4a 100644 --- a/cellbase-lib/pom.xml +++ b/cellbase-lib/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2 + 6.3.0-SNAPSHOT ../pom.xml diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml index a772dc2b0..fe4509c6f 100644 --- a/cellbase-server/pom.xml +++ b/cellbase-server/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2 + 6.3.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index c63760959..72d8a41e0 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ org.opencb.cellbase cellbase - 6.2.2 + 6.3.0-SNAPSHOT pom CellBase project