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base repository: alliance-genome/agr_curation
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base: v0.32.0
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head repository: alliance-genome/agr_curation
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compare: alpha
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Showing 1,985 changed files with 76,958 additions and 34,388 deletions.
6 changes: 3 additions & 3 deletions .github/workflows/alpha-build-and-deploy.yml
Original file line number Diff line number Diff line change
@@ -9,7 +9,7 @@ jobs:
if: github.event.pull_request.merged == true && !contains(github.event.pull_request.labels.*.name, 'no-deploy')
permissions:
id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
steps:
- name: Check out repository code
uses: actions/checkout@v3
@@ -41,7 +41,7 @@ jobs:
docker push $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG
docker push $ECR_REGISTRY/$ECR_REPOSITORY:${GITHUB_REF#refs/heads/}
build-deploy-maven-central-package:
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
steps:
- name: Check out repository code
uses: actions/checkout@v3
@@ -70,7 +70,7 @@ jobs:
permissions:
id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
needs: [build-and-push-docker-image]
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
steps:
- name: Slack Notification
uses: tokorom/action-slack-incoming-webhook@main
19 changes: 19 additions & 0 deletions .github/workflows/checkstyle.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
name: Checkstyle Action
on: pull_request

jobs:
checkstyle_job:
runs-on: ubuntu-latest
name: Checkstyle Job
steps:
- name: Checkout
uses: actions/checkout@v2
- name: Run check style
uses: dbelyaev/action-checkstyle@master
with:
level: 'error'
fail_on_error: 'true'
github_token: ${{ secrets.GH_DEVOPS_PAT }}
reporter: github-pr-review
checkstyle_config: checkstyle.xml
checkstyle_version: "10.17.0"
138 changes: 129 additions & 9 deletions .github/workflows/github-actions-PR-validation.yml
Original file line number Diff line number Diff line change
@@ -8,7 +8,8 @@ on:
- production
jobs:
check-branching-rules:
runs-on: ubuntu-20.04
name: Check Branching Rules
runs-on: ubuntu-24.04
steps:
- name: Check out repository code
uses: actions/checkout@v3
@@ -17,8 +18,41 @@ jobs:
- name: Check branching rules
run: |
bash ci-scripts/check-branching.sh ${{ github.base_ref }} ${{ github.head_ref }}
verify-test-api:
runs-on: ubuntu-20.04
checkstyle-api:
name: Checkstyle API
runs-on: ubuntu-24.04
steps:
- name: Report workflow details
run: |
echo "Repository ${{ github.repository }}."
echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
- name: Check out repository code
uses: actions/checkout@v3
- run: cp src/main/resources/application.properties.defaults src/main/resources/application.properties
- name: Report files updated in PR
run: |
git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
- name: Set up JDK 17
uses: actions/setup-java@v4
with:
java-version: '17'
distribution: 'temurin'
- name: Report runtime details
run: |
echo "Github runner OS: ${{ runner.os }}"
- name: Report Maven version
run: |
mvn --version
- name: Run Check Styles
run: |
mvn -ntp checkstyle:check
verify-api:
name: Verify API
runs-on: ubuntu-24.04
steps:
- name: Report workflow details
run: |
@@ -36,11 +70,42 @@ jobs:
with:
java-version: '17'
distribution: 'temurin'
- name: Report runtime details
run: |
echo "Github runner OS: ${{ runner.os }}"
- id: install-secret-key
name: Install gpg secret key
run: |
cat <(echo -e "${{ secrets.OSSRH_GPG_SECRET_KEY }}") | gpg --batch --import
gpg --list-secret-keys --keyid-format LONG
- name: Report Maven version
run: |
mvn --version
- name: Run Maven verify
run: |
mvn -ntp --batch-mode --update-snapshots verify
test-api:
name: Test API
runs-on: ubuntu-24.04
steps:
- name: Report workflow details
run: |
echo "Repository ${{ github.repository }}."
echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
- name: Check out repository code
uses: actions/checkout@v3
- run: cp src/main/resources/application.properties.defaults src/main/resources/application.properties
- name: Report files updated in PR
run: |
git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
- name: Set up JDK 17
uses: actions/setup-java@v4
with:
java-version: '17'
distribution: 'temurin'
- name: Report runtime details
run: |
echo "Github runner OS: ${{ runner.os }}"
@@ -49,13 +114,65 @@ jobs:
mvn --version
- name: Run Maven test
run: |
mvn --no-transfer-progress test
- name: Run Maven verify
mvn -ntp test
package-api:
name: Package API
runs-on: ubuntu-24.04
steps:
- name: Report workflow details
run: |
echo "Repository ${{ github.repository }}."
echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
- name: Check out repository code
uses: actions/checkout@v3
- run: cp src/main/resources/application.properties.defaults src/main/resources/application.properties
- name: Report files updated in PR
run: |
mvn --no-transfer-progress --batch-mode --update-snapshots verify
git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
- name: Set up JDK 17
uses: actions/setup-java@v4
with:
java-version: '17'
distribution: 'temurin'
- name: Report runtime details
run: |
echo "Github runner OS: ${{ runner.os }}"
- name: Report Maven version
run: |
mvn --version
- name: Package API
run: |
mvn clean package -Dquarkus.package.type=uber-jar -ntp
mvn -ntp clean package -Dquarkus.package.type=uber-jar -ntp
integration-test-api:
name: Integration Test API
runs-on: ubuntu-24.04
steps:
- name: Report workflow details
run: |
echo "Repository ${{ github.repository }}."
echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
- name: Check out repository code
uses: actions/checkout@v3
- run: cp src/main/resources/application.properties.defaults src/main/resources/application.properties
- name: Report files updated in PR
run: |
git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
- name: Set up JDK 17
uses: actions/setup-java@v4
with:
java-version: '17'
distribution: 'temurin'
- name: Report runtime details
run: |
echo "Github runner OS: ${{ runner.os }}"
- name: Report Maven version
run: |
mvn --version
- name: Create test containers properties file
run: |
touch ~/.testcontainers.properties
@@ -64,7 +181,8 @@ jobs:
make integration-test
verify-test-ui:
runs-on: ubuntu-20.04
name: Verify Test UI
runs-on: ubuntu-24.04
steps:
- name: Report workflow details
run: |
@@ -87,10 +205,12 @@ jobs:
working-directory: src/main/cliapp
run: |
npm ci
npx prettier --check .
npm test -- --watchAll=false
npm run build
test-build-docker-image:
runs-on: ubuntu-20.04
name: Test Build Docker Image
runs-on: ubuntu-24.04
steps:
- name: Check out repository code
uses: actions/checkout@v3
10 changes: 5 additions & 5 deletions .github/workflows/github-release-build-and-deploy.yml
Original file line number Diff line number Diff line change
@@ -6,7 +6,7 @@ jobs:
build-release-image:
permissions:
id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
steps:
- name: Check out repository code
uses: actions/checkout@v3
@@ -31,7 +31,7 @@ jobs:
docker push $ECR_REGISTRY/$ECR_REPOSITORY:$ENV_TAG
build-deploy-maven-central-package:
needs: [build-release-image]
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
steps:
- name: Check out repository code
uses: actions/checkout@v3
@@ -57,7 +57,7 @@ jobs:
MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}
generate-deployment-package:
needs: [build-release-image]
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
steps:
- name: Check out repository code
uses: actions/checkout@v3
@@ -78,7 +78,7 @@ jobs:
permissions:
id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
needs: [generate-deployment-package]
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
steps:
- name: Fetch deployment package from cache
uses: actions/cache@v4
@@ -114,7 +114,7 @@ jobs:
needs: [generate-deployment-package]
permissions:
id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
steps:
- name: Fetch deployment package from cache
uses: actions/cache@v4
6 changes: 3 additions & 3 deletions .github/workflows/release-PR-merge-actions.yml
Original file line number Diff line number Diff line change
@@ -8,7 +8,7 @@ on:
jobs:
shared-variables:
if: github.event.pull_request.merged == true && !contains(github.event.pull_request.labels.*.name, 'no-deploy')
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
outputs:
tagname: ${{ steps.tagname.outputs.tagname }}
prerelease: ${{ steps.releaseflags.outputs.prerelease }}
@@ -43,7 +43,7 @@ jobs:
run: |
echo "Variable prerelease is empty. Failing step." && false
tag-and-release:
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
needs: [shared-variables]
permissions:
contents: write
@@ -76,7 +76,7 @@ jobs:
skipIfReleaseExists: true
token: ${{ secrets.GH_PAT }}
open-mergeback-PR-to-alpha:
runs-on: ubuntu-20.04
runs-on: ubuntu-24.04
needs: [shared-variables, tag-and-release]
permissions:
contents: write
16 changes: 14 additions & 2 deletions Makefile
Original file line number Diff line number Diff line change
@@ -31,6 +31,9 @@ uirun:
make -B -C src/main/cliapp
make -B -C src/main/cliapp run

pretty:
make -B -C src/main/cliapp pretty

uirunalpha:
export API_URL=https://alpha-curation.alliancegenome.org; make -B -C src/main/cliapp run; unset API_URL

@@ -58,13 +61,22 @@ docker-run:
debug:
java -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=5045 -jar target/agr_curation_api-bootable.jar

checkstyle:
mvn checkstyle:check

prettier-check:
npx prettier 'src/main/cliapp/**/*.js' --check

prettier-write:
npx prettier 'src/main/cliapp/**/*.js' --write

test:
mvn test

integration-test:
mvn clean package
mvn -ntp clean package
mvn -ntp failsafe:integration-test -Dokta.authentication=false
mvn failsafe:verify
mvn -ntp failsafe:verify

verify:
mvn verify
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