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Fix IOUtil.unrollPaths for http paths with query parameters #251

Fix IOUtil.unrollPaths for http paths with query parameters

Fix IOUtil.unrollPaths for http paths with query parameters #251

Workflow file for this run

# This is a github actions workflow which runs htsjdk tests and spotbugs.
name: Build and Test
on:
push:
branches: [master]
pull_request:
workflow_dispatch:
jobs:
test:
env:
HTSJDK_SAMTOOLS_BIN: /usr/bin/samtools
runs-on: ubuntu-latest
strategy:
matrix:
java: [ 17 ]
experimental: [false]
fail-fast: false
continue-on-error: ${{ matrix.experimental }}
name: Java ${{ matrix.Java }} build and test
steps:
- uses: actions/checkout@v3
- name: Set up java ${{ matrix.Java }}
uses: actions/setup-java@v3
with:
java-version: ${{ matrix.Java }}
distribution: 'adopt'
cache: gradle
- name: Grant execute permission for gradlew
run: chmod +x gradlew
- name: Compile with Gradle
run: ./gradlew compileJava
- name: Install Samtools
run: scripts/install-samtools.sh
- name: Start the htsget server
run: scripts/htsget-scripts/start-htsget-test-server.sh
- name: Run tests
run: ./gradlew test jacocoTestReport
- name: Upload test results
if: always()
uses: actions/upload-artifact@v3
with:
name: test-results-${{ matrix.Java }}
path: build/reports/tests
testExternalApis:
continue-on-error: true
runs-on: ubuntu-latest
name: Tests that require external APIs
steps:
- uses: actions/checkout@v3
- name: Set up java 17
uses: actions/setup-java@v3
with:
java-version: '17'
distribution: 'adopt'
cache: gradle
- name: Grant execute permission for gradlew
run: chmod +x gradlew
- name: Compile with Gradle
run: ./gradlew compileJava
- name: Run tests
run: ./gradlew testFTP jacocoTestReport
# - name: Upload to codecov
# run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash)
- name: Upload test results
if: always()
uses: actions/upload-artifact@v3
with:
name: test-results-external-apis
path: build/reports/tests
testFTP:
continue-on-error: true
runs-on: ubuntu-latest
name: FTP tests
steps:
- uses: actions/checkout@v3
- name: Set up java 17
uses: actions/setup-java@v3
with:
java-version: '17'
distribution: 'adopt'
cache: gradle
- name: Grant execute permission for gradlew
run: chmod +x gradlew
- name: Compile with Gradle
run: ./gradlew compileJava
- name: Run tests
run: ./gradlew testFTP jacocoTestReport
# - name: Upload to codecov
# run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash)
- name: Upload test results
if: always()
uses: actions/upload-artifact@v3
with:
name: test-results-ftp
path: build/reports/tests
spotBugs:
runs-on: ubuntu-latest
name: SpotBugs
steps:
- uses: actions/checkout@v3
- name: Set up java 17
uses: actions/setup-java@v3
with:
java-version: '17'
distribution: 'adopt'
cache: gradle
- name: Grant execute permission for gradlew
run: chmod +x gradlew
- name: Compile with Gradle
run: ./gradlew spotBugsMain spotBugsTest
- name: Upload spotBugs Report
if: failure()
uses: actions/upload-artifact@v3
with:
name: spotBugs-Report
path: build/reports/spotbugs