From 22b412bdb87966592c08080d4e0d37addb5d08aa Mon Sep 17 00:00:00 2001 From: Derek Tang Date: Wed, 28 Feb 2024 13:57:15 -0500 Subject: [PATCH 1/3] initial ci --- .dockerignore | 9 ++++ .github/workflows/ci.yml | 89 ++++++++++++++++++++++++++++++++++++++++ Dockerfile | 39 ++++++++++++++++++ checkstyle.xml | 9 ++++ pom.xml | 31 +++++++++++++- 5 files changed, 175 insertions(+), 2 deletions(-) create mode 100644 .dockerignore create mode 100644 .github/workflows/ci.yml create mode 100644 Dockerfile create mode 100644 checkstyle.xml diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..8f4925a --- /dev/null +++ b/.dockerignore @@ -0,0 +1,9 @@ +.git +.github + +.dockerignore +.gitignore +Dockerfile +Jenkinsfile +OrthoinferenceOverview.png +README.md diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..f4e50ef --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,89 @@ +name: release-orthoinference ci + + +on: + workflow_dispatch: + + pull_request: + types: + - opened + - synchronize + + push: + branches: + - main + + +permissions: + id-token: write + contents: read + + +jobs: + lint: + if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }} + runs-on: ubuntu-latest + env: + REPO_DIR : /opt/release-orthoinference + steps: + - uses: actions/checkout@v4 + + - name: Run lint + run: | + docker build --build-arg REPO_DIR="$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: + - 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 + + - uses: actions/download-artifact@v4 + with: + name: image-artifact + path: /tmp + + - env: + AWS_REGISTRY : ${{ steps.login-ecr.outputs.registry }} + AWS_REPO : release-orthoinference + IMG_TAG : latest + 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 diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..18797fc --- /dev/null +++ b/Dockerfile @@ -0,0 +1,39 @@ +ARG REPO_DIR=/opt/release-orthoinference + + +# ===== 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 compile assembly:single + + +# ===== stage 3 ===== +FROM eclipse-temurin:11-jre-focal + +ARG REPO_DIR + +ARG JAR_FILE=target/orthoinference-*-jar-with-dependencies.jar + +WORKDIR ${REPO_DIR} + +COPY --from=build-jar ${REPO_DIR}/${JAR_FILE} ./target/ diff --git a/checkstyle.xml b/checkstyle.xml new file mode 100644 index 0000000..8506a80 --- /dev/null +++ b/checkstyle.xml @@ -0,0 +1,9 @@ + + + + + + + diff --git a/pom.xml b/pom.xml index 56c8f42..679d958 100644 --- a/pom.xml +++ b/pom.xml @@ -103,8 +103,8 @@ maven-compiler-plugin 3.8.1 - 1.8 - 1.8 + 11 + 11 @@ -173,6 +173,33 @@ + + + org.apache.maven.plugins + maven-checkstyle-plugin + 3.1.1 + + + + com.puppycrawl.tools + checkstyle + 8.44 + + + + + checkstyle-check + + check + + + + + checkstyle.xml + + UTF-8 + + From b45e89761360a22aeab2f0167ac05e502f1aa060 Mon Sep 17 00:00:00 2001 From: Derek Tang Date: Wed, 20 Mar 2024 15:04:19 -0400 Subject: [PATCH 2/3] update release-common-lib --- .github/workflows/ci.yml | 9 ++---- pom.xml | 61 ++++++++++++++++++++++------------------ 2 files changed, 36 insertions(+), 34 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f4e50ef..50bdccf 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,24 +1,19 @@ name: release-orthoinference ci - on: - workflow_dispatch: - + workflow_dispatch: pull_request: types: - opened - - synchronize - + - synchronize push: branches: - main - permissions: id-token: write contents: read - jobs: lint: if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }} diff --git a/pom.xml b/pom.xml index 679d958..ed43993 100644 --- a/pom.xml +++ b/pom.xml @@ -65,7 +65,7 @@ org.reactome.release release-common-lib - 1.2.0 + 2.0.0-SNAPSHOT @@ -95,6 +95,13 @@ + + + ossrh + https://oss.sonatype.org/content/repositories/snapshots + + + @@ -174,32 +181,32 @@ - - org.apache.maven.plugins - maven-checkstyle-plugin - 3.1.1 - - - - com.puppycrawl.tools - checkstyle - 8.44 - - - - - checkstyle-check - - check - - - - - checkstyle.xml - - UTF-8 - - + + org.apache.maven.plugins + maven-checkstyle-plugin + 3.1.1 + + + + com.puppycrawl.tools + checkstyle + 8.44 + + + + + checkstyle-check + + check + + + + + checkstyle.xml + + UTF-8 + + From a124ebcd2c3032359c94630cd16be1367d41a6da Mon Sep 17 00:00:00 2001 From: Derek Tang Date: Wed, 20 Mar 2024 15:08:07 -0400 Subject: [PATCH 3/3] use public repo --- .github/workflows/ci.yml | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 50bdccf..f3f959b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -59,6 +59,14 @@ jobs: needs: docker-build runs-on: ubuntu-latest steps: + - uses: actions/download-artifact@v4 + with: + name: image-artifact + path: /tmp + + - id: get-hash + run: echo "short_sha=$(git rev-parse --short HEAD)" >> $GITHUB_OUTPUT + - env: AWS_REGION : us-east-1 uses: aws-actions/configure-aws-credentials@v4 @@ -68,17 +76,13 @@ jobs: - id: login-ecr uses: aws-actions/amazon-ecr-login@v2 - - - uses: actions/download-artifact@v4 - with: - name: image-artifact - path: /tmp - env: - AWS_REGISTRY : ${{ steps.login-ecr.outputs.registry }} - AWS_REPO : release-orthoinference - IMG_TAG : latest + AWS_REGISTRY: ${{ steps.login-ecr.outputs.registry }} + AWS_REGISTRY_ALIAS: k2y5k6e2 + AWS_REPO: release-orthoinference + 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