Source Code Tests #5271

Workflow file for this run

.github/workflows/tests-code.yml at d5c3200

	name: Source Code Tests

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

	env:
	AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey_FOR_TESTS }}
	BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey_FOR_TESTS}}
	IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}
	SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
	MedlineAPiKey: ${{ secrets.MedlineApiKey_FOR_TESTS }}
	GRADLE_OPTS: -Xmx4g
	JAVA_OPTS: -Xmx4g

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

	permissions:
	# required for publish.yml
	actions: write
	contents: read
	pull-requests: write

	jobs:
	upload-pr-number:
	if: github.event_name == 'pull_request'
	runs-on: ubuntu-latest
	steps:
	- name: Create pr_number.txt
	run: echo "${{ github.event.number }}" > pr_number.txt
	- uses: actions/upload-artifact@v5
	with:
	name: pr_number
	path: pr_number.txt

	checkstyle:
	name: Checkstyle
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Run checkstyle reporter
	uses: dbelyaev/action-checkstyle@v3
	with:
	reporter: github-pr-review
	github_token: ${{ secrets.GITHUB_TOKEN }}
	checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v5
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	- name: Use cache
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- name: Run checkstyle using gradle
	run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh

	openrewrite:
	name: OpenRewrite
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 25
	distribution: 'corretto'
	check-latest: true
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v5
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	- name: Use cache
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- name: Run OpenRewrite
	run: \|
	./gradlew --no-configuration-cache :rewriteDryRun

	format:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v6
	- uses: leventeBajczi/intellij-idea-format@master
	with:
	file-mask: "*.java"
	settings-file: ".idea/codeStyles/Project.xml"
	# job should fail in case there are changes
	- name: Check if any files changed
	run: git diff --exit-code

	modernizer:
	name: Modernizer
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v5
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	- name: Use cache
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- name: Run modernizer
	run: \|
	# enable failing of this task if modernizer complains
	# sed -i "s/failOnViolations = false/failOnViolations = true/" build.gradle.kts
	./gradlew modernizer

	markdown:
	name: Markdown
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'false'
	show-progress: 'false'
	- name: markdownlint-cli2-action
	uses: DavidAnson/markdownlint-cli2-action@v21
	with:
	globs: \|
	*.md
	docs/*/.md

	changelog:
	name: CHANGELOG.md
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'false'
	show-progress: 'false'
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-heylogs-$(date +%F)" >> $GITHUB_OUTPUT
	- name: Use cache
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-heylogs-
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- name: Lint CHANGELOG.md
	run: \|
	# run heylogs verification
	jbang com.github.nbbrd.heylogs:heylogs-cli:0.14.1:bin check CHANGELOG.md > heylogs.txt \|\| true

	# ignore some errors
	grep -v no-empty-headings < heylogs.txt \| grep -v all-h2-contain-a-version \| tee heylogs.txt

	# exit 1 in case of an error
	remaining=$(
	grep -E " error " heylogs.txt \
	\| wc -l
	)

	echo "Remaining errors: $remaining"

	# We have two acceptable errors
	if [ "$remaining" -gt 2 ]; then
	echo "Failing because of $remaining remaining error(s)."
	exit 1
	fi

	changelog-unreleased-only:
	if: github.event_name == 'pull_request'
	name: CHANGELOG.md - only unreleased touched
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'false'
	show-progress: 'false'
	fetch-depth: 0
	- name: Cache clparse jar
	id: cache-clparse
	uses: actions/cache/restore@v4
	with:
	path: /tmp/clparse
	key: clparse-0.9.1
	- name: unzip
	if: steps.cache-clparse.outputs.cache-hit != 'true'
	run: \|
	cd /tmp
	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
	- name: Install clparse
	run: sudo mv /tmp/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)')

	javadoc:
	name: JavaDoc
	runs-on: ubuntu-latest
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v5
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	- name: Use cache
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- run: ./gradlew javadoc

	tests:
	name: "Unit tests – ${{ matrix.module }}"
	runs-on: ubuntu-latest
	strategy:
	matrix:
	module: [jablib, jabkit, jabsrv, jabgui]
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	# the only place in all workflows where the JBang cache is updated
	# placed here as this updates the cache for all operating systems - these are different according to https://github.com/actions/cache/tree/main?tab=readme-ov-file#cache-version
	- name: Update cache
	uses: actions/cache@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v5
	- name: Run ${{ matrix.module }} tests
	run: xvfb-run --auto-servernum ./gradlew :${{ matrix.module }}: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

	tests-windows:
	name: "Unit tests (Windows)"
	if: (github.event_name == 'push' \|\| github.event_name == 'workflow_dispatch') && (github.repository_owner == 'JabRef')
	runs-on: windows-latest
	strategy:
	matrix:
	module: [jablib]
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v5
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	- name: Use cache
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- name: Run ${{ matrix.module }} tests
	run: ./gradlew :${{ matrix.module }}:check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
	env:
	CI: "true"

	databasetests:
	if: (github.repository_owner == 'JabRef')
	name: Database tests
	runs-on: ubuntu-latest
	services:
	postgres:
	image: postgres:13-alpine
	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: 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@v6
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v5
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	- name: Use cache
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- name: Run tests on PostgreSQL
	run: ./gradlew :jablib:databaseTest --rerun-tasks
	env:
	CI: "true"
	DBMS: "postgresql"

	publish:
	if: github.ref == 'refs/heads/main'
	uses: ./.github/workflows/publish.yml
	secrets:
	KOPPOR_SIGNING_SECRETKEYRINGFILE_BASE64: ${{ secrets.KOPPOR_SIGNING_SECRETKEYRINGFILE_BASE64 }}
	KOPPOR_SIGNING_KEYID: ${{ secrets.KOPPOR_SIGNING_KEYID }}
	KOPPOR_SIGNING_PASSWORD: ${{ secrets.KOPPOR_SIGNING_PASSWORD }}
	KOPPOR_MAVENCENTRALUSERNAME: ${{ secrets.KOPPOR_MAVENCENTRALUSERNAME }}
	KOPPOR_MAVENCENTRALPASSWORD: ${{ secrets.KOPPOR_MAVENCENTRALPASSWORD }}

	jbang-main:
	name: JBang (main)
	runs-on: ubuntu-latest
	needs: publish
	if: github.ref == 'refs/heads/main'
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'false'
	show-progress: 'false'
	- name: Detect changed jablib classes
	id: changed-jablib-files
	uses: tj-actions/changed-files@v47
	with:
	files: \|
	.jbang/*.java
	jablib/src/main/java/*/.java
	jablib-examples/jbang/*/.java
	files_ignore: \|
	jablib/src/main/java/*/-*.java
	- name: Set up JDK
	if: steps.changed-jablib-files.outputs.any_changed != 'true'
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Generate JBang cache key
	if: steps.changed-jablib-files.outputs.any_changed != 'true'
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	- name: Use cache
	if: steps.changed-jablib-files.outputs.any_changed != 'true'
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-
	- name: Setup JBang
	if: steps.changed-jablib-files.outputs.any_changed != 'true'
	uses: jbangdev/setup-jbang@main

	# Build all JBang scripts
	- run: \|
	for f in .jbang/*.java; do
	echo "Building $f..."
	jbang build --fresh "$f"
	done
	if: steps.changed-jablib-files.outputs.any_changed != 'true'
	- run: \|
	for f in jablib-examples/jbang/*.java; do
	echo "Building $f..."
	jbang build --fresh "$f"
	done
	if: steps.changed-jablib-files.outputs.any_changed != 'true'

	# *Launcher.java should support "--help"
	- run: jbang run .jbang/JabKitLauncher.java --help
	if: steps.changed-jablib-files.outputs.any_changed != 'true'
	- run: jbang run .jbang/JabLsLauncher.java --help
	if: steps.changed-jablib-files.outputs.any_changed != 'true'
	- run: jbang run .jbang/JabSrvLauncher.java --help
	if: steps.changed-jablib-files.outputs.any_changed != 'true'

	jbang-pr:
	name: JBang (PR)
	runs-on: ubuntu-latest
	# does not need publish, because the JBang scripts are modified
	if: github.ref != 'refs/heads/main'
	strategy:
	fail-fast: false
	matrix:
	script: [.jbang/JabKitLauncher.java, .jbang/JabLsLauncher.java, .jbang/JabSrvLauncher.java, jablib-examples/jbang/doi_to_bibtex.java, jablib-examples/jbang/ieee_pdf_references_to_bibtex.java]
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'false'
	show-progress: 'false'
	- name: Detect changed jablib classes
	id: changed-jablib-files
	uses: tj-actions/changed-files@v47
	with:
	files: \|
	.jbang/*.java
	jabkit/src/main/java/*/.java
	jablib/src/main/java/*/.java
	jablib-examples/jbang/*/.java
	files_ignore: \|
	jablib/src/main/java/*/-*.java
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 25
	distribution: 'corretto'
	check-latest: true
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	- name: Use cache
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- name: Modify ${{ matrix.script }} to include changed classes
	shell: bash
	# We always run, because changes in jabls, jabsrv also could cause JBang to fail
	run: \|
	# We modify the JBang scripts directly to avoid issues with relative paths
	for f in ${{ steps.changed-jablib-files.outputs.all_changed_files }}; do
	case "$f" in
	.jbang/*)
	# skip scripts
	continue
	;;
	jablib-examples/*)
	# skip scripts
	continue
	;;
	jabkit/*)
	# only JabKit needs its modified sources if jabkit was modified
	if [ "${{ matrix.script }}" != ".jbang/JabKitLauncher.java" ]; then
	continue
	fi
	;;
	esac
	if [[ "${{ matrix.script }}" == .jbang/* ]]; then
	echo "//SOURCES ../$f" >> "${{ matrix.script }}"
	else
	echo "//SOURCES ../../$f" >> "${{ matrix.script }}"
	fi
	done
	- run: cat ${{ matrix.script }}
	- run: jbang build "${{ matrix.script }}"
	shell: bash
	- run: jbang "${{ matrix.script }}" --help
	if: ${{ contains(matrix.script, 'Launcher.java') }}
	shell: bash

	maven-examples:
	name: Maven examples (main)
	runs-on: ubuntu-latest
	needs: publish
	if: github.ref == 'refs/heads/main'
	strategy:
	fail-fast: false
	matrix:
	project: [jablib-examples/maven3/doi-to-bibtex]
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'false'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	cache: maven
	check-latest: true
	- run: \|
	cd ${{ matrix.project }}
	mvn --batch-mode --update-snapshots verify
	shell: bash

	maven-pr:
	name: Maven examples (PR)
	runs-on: ubuntu-latest
	# does not need publish, because there is no publishing on non-main
	if: github.ref != 'refs/heads/main'
	strategy:
	fail-fast: false
	matrix:
	project: [jablib-examples/maven3/doi-to-bibtex]
	steps:
	- name: Checkout source
	uses: actions/checkout@v6
	with:
	submodules: 'false'
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	cache: maven
	check-latest: true
	- run: \|
	cd ${{ matrix.project }}
	mvn --batch-mode --update-snapshots verify
	shell: bash

	codecoverage:
	if: false
	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: ${{ secrets.CODECOV_TOKEN }}
	- name: Checkout source
	if: github.ref == 'refs/heads/main'
	uses: actions/checkout@v6
	with:
	submodules: 'true'
	show-progress: 'false'
	- name: Set up JDK
	if: github.ref == 'refs/heads/main'
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v5
	- name: Generate JBang cache key
	id: cache-key
	shell: bash
	run: \|
	echo "cache_key=jbang-$(date +%Y-%m)" >> $GITHUB_OUTPUT
	- name: Use cache
	uses: actions/cache/restore@v4
	with:
	path: ~/.jbang
	key: ${{ steps.cache-key.outputs.cache_key }}
	restore-keys:
	jbang-
	- name: Setup JBang
	uses: jbangdev/setup-jbang@main
	- 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@v5
	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@v6
	with:
	show-progress: 'false'
	- name: Set up JDK
	uses: actions/setup-java@v5
	with:
	java-version: 24
	distribution: 'corretto'
	check-latest: true
	- name: Setup Gradle
	uses: gradle/actions/setup-gradle@v5
	- run: ./gradlew traceRequirements
	- if: always()
	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@v6
	with:
	show-progress: 'false'
	- uses: gradle/actions/wrapper-validation@v5

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Source Code Tests #5271

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Source Code Tests #5271

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