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AJ-1094: Initial Project Setup and Hello World CLI (#1)
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‎.github/workflows/build-and-test.yml

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name: Build and Test
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on:
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push:
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branches: [ main ]
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paths-ignore: [ '*.md' ]
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pull_request:
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branches: [ '**' ]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up JDK
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uses: actions/setup-java@v3
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with:
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java-version: '17'
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distribution: 'temurin'
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cache: 'gradle'
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- name: Build all projects without running tests
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run: ./gradlew --build-cache build -x test
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source-clear:
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needs: [ build ]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Set up JDK
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uses: actions/setup-java@v3
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with:
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java-version: '17'
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distribution: 'temurin'
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cache: 'gradle'
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- name: SourceClear scan
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env:
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SRCCLR_API_TOKEN: ${{ secrets.SRCCLR_API_TOKEN }}
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run: ./gradlew --build-cache srcclr
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unit-tests-and-sonarqube:
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needs: [ build ]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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# Needed by sonar to get the git history for the branch the PR will be merged into.
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with:
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fetch-depth: 0
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- name: Set up JDK
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uses: actions/setup-java@v3
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with:
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java-version: '17'
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distribution: 'temurin'
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cache: 'gradle'
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- name: Test with coverage
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run: ./gradlew --build-cache test jacocoTestReport
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- name: SonarQube scan for library
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run: ./gradlew --build-cache :library:sonar --info
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env:
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SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: SonarQube scan for cli
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run: ./gradlew --build-cache :cli:sonar --info
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env:
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SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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notify-slack:
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needs: [ build, unit-tests-and-sonarqube, source-clear ]
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runs-on: ubuntu-latest
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if: failure() && github.ref == 'refs/heads/main'
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steps:
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- name: Notify slack on failure
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uses: broadinstitute/[email protected]
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env:
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SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
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with:
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channel: '#dsp-analysis-journeys-alerts'
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status: failure
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author_name: Build on dev
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fields: job,message
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text: 'Build failed :sadpanda:'
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username: 'Java-PFB GitHub Action'
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dispatch-tag:
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needs: [ build, unit-tests-and-sonarqube, source-clear ]
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runs-on: ubuntu-latest
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if: success() && github.ref == 'refs/heads/main'
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steps:
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- name: Fire off tag action
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uses: broadinstitute/workflow-dispatch@v1
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with:
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workflow: Tag
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token: ${{ secrets.BROADBOT_TOKEN }}

‎.github/workflows/publish.yml

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name: Publish and deploy
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on: create
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env:
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SERVICE_NAME: ${{ github.event.repository.name }}
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GOOGLE_PROJECT: broad-dsp-gcr-public
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jobs:
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publish-job:
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if: startsWith(github.ref, 'refs/tags/')
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permissions:
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contents: 'read'
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id-token: 'write'
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runs-on: ubuntu-latest
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outputs:
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tag: ${{ steps.tag.outputs.tag }}
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steps:
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- name: Enable publish with AJ-1095
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run: echo "TODO"
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# - uses: actions/checkout@v3
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# - name: Set up JDK
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# uses: actions/setup-java@v3
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# with:
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# java-version: '17'
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# distribution: 'temurin'
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# cache: 'gradle'
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# - name: Parse tag
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# id: tag
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# run: echo "tag=$(git describe --tags)" >> $GITHUB_OUTPUT
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#
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# - name: Publish to Artifactory
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# run: ./gradlew --build-cache :client:artifactoryPublish
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# env:
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# ARTIFACTORY_USERNAME: ${{ secrets.ARTIFACTORY_USERNAME }}
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# ARTIFACTORY_PASSWORD: ${{ secrets.ARTIFACTORY_PASSWORD }}
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# ARTIFACTORY_REPO_KEY: "libs-release-local"
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#
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# - name: Notify slack on failure
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# uses: broadinstitute/[email protected]
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# if: failure()
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# env:
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# SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
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# with:
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# channel: '#dsp-analysis-journeys-alerts'
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# status: failure
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# author_name: Publish to dev
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# fields: job
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# text: 'Publish failed :sadpanda:'
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# username: 'Java-PFB GitHub Action'

‎.github/workflows/tag.yml

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name: Tag
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on: workflow_dispatch
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jobs:
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tag-job:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout current code
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uses: actions/checkout@v3
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with:
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token: ${{ secrets.BROADBOT_TOKEN }} # this allows the push to succeed later
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- name: Bump the tag to a new version
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# https://github.com/DataBiosphere/github-actions/tree/master/actions/bumper
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uses: databiosphere/github-actions/actions/[email protected]
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id: tag
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env:
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GITHUB_TOKEN: ${{ secrets.BROADBOT_TOKEN }}
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HOTFIX_BRANCHES: hotfix.*
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DEFAULT_BUMP: minor
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RELEASE_BRANCHES: main
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VERSION_FILE_PATH: settings.gradle
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VERSION_LINE_MATCH: "^\\s*gradle.ext.releaseVersion\\s*=\\s*'.*'"

‎.gitignore

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HELP.md
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.gradle
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build/
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!gradle/wrapper/gradle-wrapper.jar
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!**/src/main/**/build/
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!**/src/test/**/build/
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bootrun.log
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### STS ###
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.apt_generated
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.classpath
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.factorypath
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.project
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.settings
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.springBeans
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.sts4-cache
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bin/
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!**/src/main/**/bin/
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!**/src/test/**/bin/
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# Emacs backup files #
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*.*~
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### IntelliJ IDEA ###
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.idea/
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*.iml
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### VS Code ###
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.vscode/
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# Mac directory metadata
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.DS_Store
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# PyEnv environment files
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.env/
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# Ignore generated credentials from google-github-actions/auth
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gha-creds-*.json

‎LICENSE

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BSD 3-Clause License
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Copyright (c) 2023, Broad Institute
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README.md

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# java-pfb
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# Java-PFB
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A java implementation of the [pyPFB](https://github.com/uc-cdis/pypfb) library that includes a CLI and a java library.
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The CLI is a wrapper around the library. See the [CLI README](cli/README.md) for more information.
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## Running SourceClear locally
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[SourceClear](https://srcclr.github.io) is a static analysis tool that scans a project's Java
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dependencies for known vulnerabilities. If you get a build failure due a SourceClear error and want
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to debug the problem locally, you need to get the API token from vault before running the gradle
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task.
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```shell
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export SRCCLR_API_TOKEN=$(vault read -field=api_token secret/secops/ci/srcclr/gradle-agent)
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./gradlew srcclr
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```
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Results of the scan are uploaded to [Defect DOJO](https://defectdojo.dsp-appsec.broadinstitute.org/dashboard).
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## Running SonarQube locally
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[SonarQube](https://www.sonarqube.org) is a static analysis code that scans code for a wide
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range of issues, including maintainability and possible bugs. If you get a build failure due to
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SonarQube and want to debug the problem locally, you need to get the the sonar token from vault
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before runing the gradle task.
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```shell
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export SONAR_TOKEN=$(vault read -field=sonar_token secret/secops/ci/sonarcloud/java-pfb)
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./gradlew sonar
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```
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Unlike SourceClear, running this task produces no output unless your project has errors. To always
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generate a report, run using `--info`:
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```shell
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./gradlew sonar --info
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```
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We run the scans for two projects: [java-pfb](https://sonarcloud.io/project/overview?id=DataBiosphere_java-pfb) and [java-pfb-cli](https://sonarcloud.io/project/overview?id=DataBiosphere_java-pfb-cli). The results are uploaded to the sonarcloud dashbaord.

‎buildSrc/build.gradle

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plugins {
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id 'groovy-gradle-plugin'
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}
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repositories {
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gradlePluginPortal()
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}
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dependencies {
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implementation 'com.diffplug.spotless:spotless-plugin-gradle:6.11.0'
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implementation 'com.srcclr.gradle:com.srcclr.gradle.gradle.plugin:3.1.12'
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implementation 'org.sonarqube:org.sonarqube.gradle.plugin:4.2.1.3168'
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implementation 'info.picocli:picocli:4.7.4'
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}

‎buildSrc/src/main/groovy/bio.terra.pfb.java-common-conventions.gradle

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plugins {
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id 'idea'
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id 'jacoco'
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id 'java'
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id 'org.sonarqube'
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id 'com.diffplug.spotless'
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}
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boolean isCiServer = System.getenv().containsKey("CI")
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java {
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toolchain {
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languageVersion = JavaLanguageVersion.of(17)
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}
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}
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repositories {
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maven {
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// Terra proxy for maven central
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url 'https://broadinstitute.jfrog.io/broadinstitute/maven-central/'
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}
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mavenCentral()
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maven {
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url 'https://broadinstitute.jfrog.io/broadinstitute/libs-release/'
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}
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maven {
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url 'https://broadinstitute.jfrog.io/broadinstitute/libs-snapshot-local/'
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}
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}
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dependencies {
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testImplementation 'org.hamcrest:hamcrest:2.2'
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testImplementation 'org.junit.jupiter:junit-jupiter-api:5.8.1'
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testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.8.1'
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}
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version = gradle.releaseVersion
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group = 'bio.terra'
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spotless {
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java {
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targetExclude "${buildDir}/**"
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googleJavaFormat()
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}
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}
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// Run spotless check when running in github actions, otherwise run spotless apply.
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compileJava {
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if (isCiServer) {
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dependsOn(spotlessCheck)
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} else {
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dependsOn(spotlessApply)
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}
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}
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test {
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useJUnitPlatform()
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}
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jacocoTestReport {
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reports {
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// sonarqube requires XML coverage output to upload coverage data
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xml.required = true
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}
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}
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sonar {
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properties {
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property "sonar.projectKey", "DataBiosphere_java-pfb"
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property "sonar.projectName", "java-pfb"
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property "sonar.organization", "broad-databiosphere"
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property "sonar.host.url", "https://sonarcloud.io"
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}
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}

‎buildSrc/src/main/groovy/bio.terra.pfb.java-library-conventions.gradle

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plugins {
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id 'bio.terra.pfb.java-common-conventions'
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id 'java-library'
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}

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