[WIP] Fix database sync #20216

Workflow file for this run

	name: Tests

	on:
	push:
	branches:
	- main
	- main-release
	pull_request:
	merge_group:
	workflow_dispatch:

	env:
	SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
	AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
	IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
	BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey}}
	GRADLE_OPTS: -Xmx4g
	JAVA_OPTS: -Xmx4g

	concurrency:
	group: "${{ github.workflow }}-${{ github.head_ref \|\| github.ref }}"
	cancel-in-progress: true

	permissions:
	pull-requests: write

	jobs:
	checkstyle:
	name: Checkstyle
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v4
	with:
	java-version: 23.0.1
	distribution: 'temurin'
	- name: Run checkstyle reporter
	uses: dbelyaev/action-checkstyle@master
	with:
	reporter: github-pr-review
	github_token: ${{ secrets.GITHUB_TOKEN }}
	checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v4
	with:
	gradle-home-cache-cleanup: true
	- name: Run checkstyle using gradle
	run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh


	openrewrite:
	name: OpenRewrite
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v4
	with:
	java-version: 23.0.1
	distribution: 'temurin'
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v4
	with:
	gradle-home-cache-cleanup: true
	- name: Run OpenRewrite
	run: \|
	./gradlew rewriteDryRun

	modernizer:
	name: Modernizer
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v4
	with:
	java-version: 23.0.1
	distribution: 'temurin'
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v4
	with:
	gradle-home-cache-cleanup: true
	- name: Run modernizer
	run: \|
	# enable failing of this task if modernizer complains
	sed -i "s/failOnViolations = false/failOnViolations = true/" build.gradle
	./gradlew modernizer

	markdown:
	name: Markdown
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: 'false'
	show-progress: 'false'
	- name: markdownlint-cli2-action
	uses: DavidAnson/markdownlint-cli2-action@v17
	with:
	globs: \|
	*.md
	docs/*/.md

	changelog:
	name: CHANGELOG.md
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: 'false'
	show-progress: 'false'
	- name: Lint CHANGELOG.md
	run: \|
	# Install jbang
	curl -Ls https://sh.jbang.dev \| bash -s - app setup
	export PATH=$PATH:$HOME/.jbang/bin

	# run heylogs verification
	jbang com.github.nbbrd.heylogs:heylogs-cli:0.9.2:bin check CHANGELOG.md > heylogs.txt \|\| true

	# improve output
	sed -i 's/all-h2-contain-a-version/all-h2-contain-a-version (ignored)/' heylogs.txt

	cat heylogs.txt

	# exit 1 in case of error
	# We have 1 "valid" issue in CHANGELOG.md
	grep -q "1 problem" heylogs.txt \|\| exit 1

	changelog-unreleased-only:
	name: CHANGELOG.md - only unreleased touched
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: 'false'
	show-progress: 'false'
	fetch-depth: 0
	- name: Install clparse
	run: \|
	curl -LO https://github.com/marcaddeo/clparse/releases/download/0.9.1/clparse-0.9.1-x86_64-unknown-linux-musl.tar.gz
	tar xzvf clparse-0.9.1-x86_64-unknown-linux-musl.tar.gz
	sudo mv clparse /usr/local/bin/clparse
	- name: Check CHANGELOG.md diff
	run: \|
	diff \
	<(git show origin/main:CHANGELOG.md \| clparse --format=json --separator=– - \| jq '.releases[] \| select(.version != null)') \
	<(git show HEAD:CHANGELOG.md \| clparse --format=json --separator=– - \| jq '.releases[] \| select(.version != null)')

	tests:
	name: Unit tests
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v4
	with:
	java-version: 23.0.1
	distribution: 'temurin'
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v4
	with:
	gradle-home-cache-cleanup: true
	- name: Run tests
	run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
	env:
	CI: "true"
	- name: Prepare format failed test results
	if: failure()
	uses: awalsh128/cache-apt-pkgs-action@latest
	with:
	packages: xml-twig-tools xsltproc
	version: 1.0
	- name: Format failed test results
	if: failure()
	run: scripts/after-failure.sh

	databasetests:
	name: Database tests
	runs-on: ubuntu-latest
	steps:
	- name: Shutdown Ubuntu MySQL
	run: sudo service mysql stop # Shutdown the Default MySQL to save memory, "sudo" is necessary, please do not remove it
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v4
	with:
	java-version: 23.0.1
	distribution: 'temurin'
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v4
	with:
	gradle-home-cache-cleanup: true
	- name: Run tests on PostgreSQL
	run: ./gradlew databaseTest --rerun-tasks
	env:
	CI: "true"

	guitests:
	name: GUI tests
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v4
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v4
	with:
	java-version: 23.0.1
	distribution: 'temurin'
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v4
	with:
	gradle-home-cache-cleanup: true
	- name: Run GUI tests
	run: xvfb-run --auto-servernum ./gradlew guiTest
	env:
	CI: "true"

	codecoverage:
	name: Code coverage
	runs-on: ubuntu-latest
	services:
	postgres:
	image: postgres:10.8
	env:
	POSTGRES_USER: postgres
	POSTGRES_PASSWORD: postgres
	POSTGRES_DB: postgres
	ports:
	- 5432:5432
	# needed because the postgres container does not provide a healthcheck
	options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
	steps:
	- name: Check secrets presence
	id: checksecrets
	if: github.ref == 'refs/heads/main'
	shell: bash
	run: \|
	if [ "$CODECOV_TOKEN" == "" ]; then
	echo "secretspresent=NO" >> $GITHUB_OUTPUT
	echo "❌ Secret CODECOV_TOKEN not present"
	else
	echo "secretspresent=YES" >> $GITHUB_OUTPUT
	echo "✔️ Secret CODECOV_TOKEN present"
	fi
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	- name: Checkout source
	if: github.ref == 'refs/heads/main'
	uses: actions/checkout@v4
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	if: github.ref == 'refs/heads/main'
	uses: actions/setup-java@v4
	with:
	java-version: 23.0.1
	distribution: 'temurin'
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v4
	with:
	gradle-home-cache-cleanup: true
	- name: Update test coverage metrics
	if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
	run: xvfb-run --auto-servernum ./gradlew jacocoTestReport
	env:
	CI: "true"
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
	DBMS: "postgresql"
	- uses: codecov/codecov-action@v4
	if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	- name: Upload Codacy report
	if: (github.ref == 'refs/heads/main') && (steps.checksecrets.outputs.secretspresent == 'YES')
	run: bash <(curl -Ls https://coverage.codacy.com/get.sh)
	env:
	CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}

	requirements_coverage:
	name: "Validate requirement coverage"
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v4
	with:
	java-version: 23.0.1
	distribution: 'temurin'
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v4
	- run: ./gradlew traceRequirements
	- if: failure()
	run: cat build/reports/tracing.txt

	# This is https://github.com/marketplace/actions/gradle-wrapper-validation
	# It ensures that the jar file is from gradle and not by a strange third party.
	gradlevalidation:
	name: "Validate Gradle Wrapper"
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	show-progress: 'false'
	- uses: gradle/actions/wrapper-validation@v4

	# This ensures that no git merge conflict markers (<<<, ...) are contained
	merge_conflict_job:
	name: Find merge conflicts
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	show-progress: 'false'
	- name: Merge Conflict finder
	uses: olivernybroe/[email protected]

	other_than_main:
	name: Source branch is other than "main"
	runs-on: ubuntu-latest
	steps:
	- if: github.head_ref == 'main'
	uses: actions/github-script@v7
	with:
	script: \|
	core.setFailed('Pull requests should come from a branch other than "main"\n\n👉 Please read [the CONTRIBUTING guide](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md#contributing) carefully again. 👈')

	upload-pr-number:
	runs-on: ubuntu-latest
	steps:
	- name: Create pr_number.txt
	run: echo "${{ github.event.number }}" > pr_number.txt
	- uses: actions/upload-artifact@v4
	with:
	name: pr_number
	path: pr_number.txt

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[WIP] Fix database sync #20216

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[WIP] Fix database sync #20216

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Workflow file for this run