Merge branch 'main' of https://github.com/reactome/release-gtp2chebi-update

Author: jweiser

.dockerignore

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+.git
+.github
+
+.dockerignore
+.gitignore
+CHANGELOG.md
+Dockerfile
+Jenkinsfile
+README.md

.github/workflows/ci.yml

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+name: release-gtp2chebi-update ci
+
+on:
+    workflow_dispatch: 
+    pull_request:
+        types:
+            - opened
+            - synchronize 
+    push:
+        branches:
+            - main
+
+permissions:
+    id-token: write
+    contents: read
+
+jobs:
+    lint:
+        if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
+        runs-on: ubuntu-latest
+        env:
+            REPO_DIR: /opt/release-gtp2chebi-update
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Run lint
+              run: |
+                docker build --build-arg REPO_DIR="$REPO_DIR" --target setup-env -t lint-image .
+                docker run --name lint-container lint-image
+            
+            - name: Display lint errors
+              if: failure()
+              run: |
+                docker cp lint-container:"$REPO_DIR"/lint.log .
+                while IFS= read -r LINT_MSG; do echo "::warning::${LINT_MSG}"; done < lint.log
+                exit 1
+
+    docker-build:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+
+            - uses: docker/setup-buildx-action@v3
+            
+            - uses: docker/build-push-action@v5
+              with:
+                context: .
+                file: Dockerfile
+                tags: tmp-tag
+                outputs: type=docker,dest=/tmp/image.tar
+
+            - uses: actions/upload-artifact@v4
+              with:
+                name: image-artifact
+                path: /tmp/image.tar
+
+    docker-push:
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        needs: docker-build
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/download-artifact@v4
+              with:
+                name: image-artifact
+                path: /tmp
+
+            - id: get-hash
+              run: |
+                FULL_SHA=${{ github.sha }}
+                echo "SHORT_SHA=${FULL_SHA:0:7}" >> $GITHUB_OUTPUT
+            
+            - env:
+                AWS_REGION: us-east-1
+              uses: aws-actions/configure-aws-credentials@v4
+              with:
+                role-to-assume: ${{ vars.AWS_ROLE }}
+                aws-region: ${{ env.AWS_REGION }}
+    
+            - id: login-ecr
+              uses: aws-actions/amazon-ecr-login@v2
+              with:
+                registry-type: public
+
+            - env:
+                AWS_REGISTRY: ${{ steps.login-ecr.outputs.registry }}
+                AWS_REGISTRY_ALIAS: reactome
+                AWS_REPO: release-gtp2chebi-update
+                IMG_TAG: ${{ steps.get-hash.outputs.SHORT_SHA }}
+              run: |
+                AWS_URI=$AWS_REGISTRY/$AWS_REGISTRY_ALIAS/$AWS_REPO
+                docker load --input /tmp/image.tar
+                docker tag tmp-tag $AWS_URI:latest
+                docker push $AWS_URI:latest
+                docker tag $AWS_URI:latest $AWS_URI:$IMG_TAG
+                docker push $AWS_URI:$IMG_TAG
+

Dockerfile

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+ARG REPO_DIR=/opt/release-gtp2chebi-update
+
+
+# ===== stage 1 =====
+FROM maven:3.9.6-eclipse-temurin-11-focal AS setup-env
+
+ARG REPO_DIR
+
+WORKDIR ${REPO_DIR}
+
+COPY . .
+
+SHELL ["/bin/bash", "-c"]
+
+# run lint if container started
+ENTRYPOINT []
+
+CMD mvn -B -q checkstyle:check | \
+    grep -i --color=never '\.java\|failed to execute goal' > lint.log && \
+    exit 1 || \
+    exit 0
+
+
+# ===== stage 2 =====
+FROM setup-env AS build-jar
+
+RUN mvn clean package
+
+
+# ===== stage 3 =====
+FROM eclipse-temurin:11-jre-focal
+
+ARG REPO_DIR
+
+ARG JAR_FILE=target/gtp-chebi-mapping-jar-with-dependencies.jar
+
+WORKDIR ${REPO_DIR}
+
+COPY --from=build-jar ${REPO_DIR}/${JAR_FILE} ./target/
+

checkstyle.xml

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+<!DOCTYPE module PUBLIC
+        "-//Puppy Crawl//DTD Check Configuration 1.3//EN"
+        "https://checkstyle.org/dtds/configuration_1_3.dtd">
+<module name="Checker">
+    <module name="LineLength">
+        <property name="max" value="150"/>
+    </module>
+    <!-- Add more modules as needed -->
+</module>