From 160d7894d933fec4d7b11ca4c252670e098ab1fc Mon Sep 17 00:00:00 2001 From: Derek Tang Date: Wed, 20 Mar 2024 22:59:28 -0400 Subject: [PATCH 1/2] public ecr --- .github/workflows/ci.yml | 39 +++++++++++++++++++++------------------ 1 file changed, 21 insertions(+), 18 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4e06763..0075dac 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,30 +1,25 @@ name: analysis core ci - on: - workflow_dispatch: - + workflow_dispatch: pull_request: types: - opened - - synchronize - + - synchronize push: branches: - master - permissions: id-token: write contents: read - jobs: lint: if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }} runs-on: ubuntu-latest env: - REPO_DIR : /opt/analysis-core + REPO_DIR: /opt/analysis-core steps: - uses: actions/checkout@v4 @@ -64,8 +59,18 @@ jobs: needs: docker-build runs-on: ubuntu-latest steps: + - uses: actions/download-artifact@v4 + with: + name: image-artifact + path: /tmp + + - id: get-hash + run: | + FULL_SHA=${{ github.sha }} + echo "SHORT_SHA=${FULL_SHA:0:7}" >> $GITHUB_OUTPUT + - env: - AWS_REGION : us-east-1 + AWS_REGION: us-east-1 uses: aws-actions/configure-aws-credentials@v4 with: role-to-assume: ${{ vars.AWS_ROLE }} @@ -73,17 +78,15 @@ jobs: - id: login-ecr uses: aws-actions/amazon-ecr-login@v2 - - - uses: actions/download-artifact@v4 with: - name: image-artifact - path: /tmp + registry-type: public - env: - AWS_REGISTRY : ${{ steps.login-ecr.outputs.registry }} - AWS_REPO : analysis-core - IMG_TAG : latest + AWS_REGISTRY: ${{ steps.login-ecr.outputs.registry }} + AWS_REGISTRY_ALIAS: k2y5k6e2 + AWS_REPO: analysis-core + IMG_TAG: ${{ steps.get-hash.outputs.SHORT_SHA }} run: | docker load --input /tmp/image.tar - docker image tag tmp-tag $AWS_REGISTRY/$AWS_REPO:$IMG_TAG - docker push $AWS_REGISTRY/$AWS_REPO:$IMG_TAG + docker image tag tmp-tag $AWS_REGISTRY/$AWS_REGISTRY_ALIAS/$AWS_REPO:$IMG_TAG + docker push $AWS_REGISTRY/$AWS_REGISTRY_ALIAS/$AWS_REPO:$IMG_TAG From 31861b160ec7bf03f8c5716fc171835bab619f65 Mon Sep 17 00:00:00 2001 From: Derek Tang Date: Sat, 23 Mar 2024 16:27:49 -0400 Subject: [PATCH 2/2] use tabs in pom --- pom.xml | 546 ++++++++++++++++++++++++++++---------------------------- 1 file changed, 273 insertions(+), 273 deletions(-) diff --git a/pom.xml b/pom.xml index bbaa856..4dde8d6 100644 --- a/pom.xml +++ b/pom.xml @@ -1,276 +1,276 @@ - 4.0.0 - - org.reactome.server.tools - analysis-core - 3.4.7 - jar - - The Reactome analysis-core extracts data from the graph-database to create the intermediate data format - to be kept in memory and used for the analysis-service - - - analysis-core - - - The European Bioinformatics Institute - https://www.ebi.ac.uk/ - - - - - gviteri - Guilherme Viteri - https://www.ebi.ac.uk - - - fabregat - Antonio Fabregat - - - - - org.reactome.maven - reactome-parent - 1.0.3 - - - - 11 - org.reactome.server.analysis.core.Main - - - - - - org.reactome.server.graph - graph-core - - - - - com.martiansoftware - jsap - - - - - junit - junit - test - - - - - com.esotericsoftware - kryo - - - - - com.fasterxml.jackson.core - jackson-databind - - - - - org.apache.httpcomponents - httpclient - - - - - org.apache.commons - commons-text - - - - - com.googlecode.concurrent-trees - concurrent-trees - - - - - colt - colt - - - - joda-time - joda-time - - - - org.springframework - spring-web - provided - - - - commons-fileupload - commons-fileupload - - - - commons-codec - commons-codec - - - - - analysis-core - - - - src/main/resources - true - - - - - - src/test/resources - true - - - - - - org.apache.maven.plugins - maven-resources-plugin - ${maven.resources.version} - - - - org.apache.maven.plugins - maven-compiler-plugin - ${maven.compiler.version} - - ${java.version} - ${java.version} - - - - - - org.apache.maven.plugins - maven-jar-plugin - ${maven.jar.version} - - - exec-jar - - jar - - - exec - - - - default-jar - - jar - - - - org/reactome/server/analysis/core/config/ReactomeNeo4jConfig.class - **/logback.xml - - - - - - - - org.springframework.boot - spring-boot-maven-plugin - ${spring-boot.version} - - ${start.class} - exec - - - - package - - repackage - - - - - - - org.apache.maven.plugins - maven-source-plugin - ${maven.source.version} - - - attach-sources - - jar - - - - - - - org.apache.maven.plugins - maven-checkstyle-plugin - 3.1.1 - - - - com.puppycrawl.tools - checkstyle - 8.44 - - - - - checkstyle-check - - check - - - - - checkstyle.xml - - UTF-8 - - - - - - - - - - nexus-ebi-repo - The EBI internal repository - https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/ - - true - - - false - - - - - - nexus-ebi-snapshot-repo - The EBI internal snapshot repository - https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/ - - false - - - true - - - + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> + 4.0.0 + + org.reactome.server.tools + analysis-core + 3.4.7 + jar + + The Reactome analysis-core extracts data from the graph-database to create the intermediate data format + to be kept in memory and used for the analysis-service + + + analysis-core + + + The European Bioinformatics Institute + https://www.ebi.ac.uk/ + + + + + gviteri + Guilherme Viteri + https://www.ebi.ac.uk + + + fabregat + Antonio Fabregat + + + + + org.reactome.maven + reactome-parent + 1.0.3 + + + + 11 + org.reactome.server.analysis.core.Main + + + + + + org.reactome.server.graph + graph-core + + + + + com.martiansoftware + jsap + + + + + junit + junit + test + + + + + com.esotericsoftware + kryo + + + + + com.fasterxml.jackson.core + jackson-databind + + + + + org.apache.httpcomponents + httpclient + + + + + org.apache.commons + commons-text + + + + + com.googlecode.concurrent-trees + concurrent-trees + + + + + colt + colt + + + + joda-time + joda-time + + + + org.springframework + spring-web + provided + + + + commons-fileupload + commons-fileupload + + + + commons-codec + commons-codec + + + + + analysis-core + + + + src/main/resources + true + + + + + + src/test/resources + true + + + + + + org.apache.maven.plugins + maven-resources-plugin + ${maven.resources.version} + + + + org.apache.maven.plugins + maven-compiler-plugin + ${maven.compiler.version} + + ${java.version} + ${java.version} + + + + + + org.apache.maven.plugins + maven-jar-plugin + ${maven.jar.version} + + + exec-jar + + jar + + + exec + + + + default-jar + + jar + + + + org/reactome/server/analysis/core/config/ReactomeNeo4jConfig.class + **/logback.xml + + + + + + + + org.springframework.boot + spring-boot-maven-plugin + ${spring-boot.version} + + ${start.class} + exec + + + + package + + repackage + + + + + + + org.apache.maven.plugins + maven-source-plugin + ${maven.source.version} + + + attach-sources + + jar + + + + + + + org.apache.maven.plugins + maven-checkstyle-plugin + 3.1.1 + + + + com.puppycrawl.tools + checkstyle + 8.44 + + + + + checkstyle-check + + check + + + + + checkstyle.xml + + UTF-8 + + + + + + + + + + nexus-ebi-repo + The EBI internal repository + https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/ + + true + + + false + + + + + + nexus-ebi-snapshot-repo + The EBI internal snapshot repository + https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/ + + false + + + true + + +