From 0ff7a35fd130fbe65f369fab105d11aed3bd274a Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Wed, 6 Mar 2024 13:24:16 -0500 Subject: [PATCH 1/4] Attempting to normalize the test results location between docker/ non docker --- .github/workflows/gatk-tests.yml | 4 ---- scripts/docker/dockertest.gradle | 3 +++ 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/gatk-tests.yml b/.github/workflows/gatk-tests.yml index 2f97d560b65..269fc4d4db2 100644 --- a/.github/workflows/gatk-tests.yml +++ b/.github/workflows/gatk-tests.yml @@ -230,10 +230,6 @@ jobs: bash --init-file /gatk/gatkenv.rc /root/run_unit_tests.sh; TEST_EXIT_VALUE=$?; $( exit ${TEST_EXIT_VALUE} ); - sudo chmod -R a+w build/reports/; - mkdir build/reports/tests/test \ - && cp -rp build/reports/tests/testOnPackagedReleaseJar/* build/reports/tests/test \ - && rm -r build/reports/tests/testOnPackagedReleaseJar; - uses: ./.github/actions/upload-gatk-test-results if: always() diff --git a/scripts/docker/dockertest.gradle b/scripts/docker/dockertest.gradle index bbbe4780d8e..692bc945db9 100644 --- a/scripts/docker/dockertest.gradle +++ b/scripts/docker/dockertest.gradle @@ -144,6 +144,9 @@ task testOnPackagedReleaseJar(type: Test){ jvmArgs = getJVMArgs(runtimeAddOpens, testAddOpens) + //Set this to match the name of the normal test output in order to simplify finding / uploading it + reports.html.outputLocation = file("$buildDir/reports/tests/test") + classpath = files( gatkJar, testDependencyJar, testClassesJar) testClassesDirs = files(testClassesUnpacked) } From ca97893b72d8a5728dbc676d499a2f09ba98b7a4 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Wed, 6 Mar 2024 13:28:06 -0500 Subject: [PATCH 2/4] add failing test --- .../hellbender/tools/PrintReadsIntegrationTest.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java index 028b5965efc..85f85f99935 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java @@ -27,6 +27,12 @@ public void testFileToFileWithMD5(String fileIn, String extOut, String reference doFileToFile(fileIn, extOut, reference, true); } + + @Test + public void failToTestReporting(){ + Assert.fail(); + } + @Test public void testNoConflictPG() throws IOException { final File inFile = new File(TEST_DATA_DIR, "print_reads_withPG.sam"); From e8670bb2baeff108540d5e89d9e50693636d5f90 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Wed, 6 Mar 2024 14:34:48 -0500 Subject: [PATCH 3/4] woopsy --- .github/actions/upload-gatk-test-results/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/upload-gatk-test-results/action.yml b/.github/actions/upload-gatk-test-results/action.yml index b210216d2f0..3353b727126 100644 --- a/.github/actions/upload-gatk-test-results/action.yml +++ b/.github/actions/upload-gatk-test-results/action.yml @@ -49,7 +49,7 @@ runs: id: uploadreports run: | gsutil -m cp -z html -z js -z xml -z css -r build/reports/tests gs:/${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/; - VIEW_URL=https://storage.googleapis.com${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/tests/testOnPackagedReleaseJar/index.html + VIEW_URL=https://storage.googleapis.com${{ env.HELLBENDER_TEST_LOGS }}${{ inputs.repo-path }}/tests/test/index.html echo "See the test report at ${VIEW_URL}"; echo view_url="${VIEW_URL}" >> $GITHUB_OUTPUT From 183f222d1c686079b3fff817b6b7c6705f9350dc Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Wed, 6 Mar 2024 17:52:03 -0500 Subject: [PATCH 4/4] remove deliberately failing test --- .../hellbender/tools/PrintReadsIntegrationTest.java | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java index 85f85f99935..028b5965efc 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/PrintReadsIntegrationTest.java @@ -27,12 +27,6 @@ public void testFileToFileWithMD5(String fileIn, String extOut, String reference doFileToFile(fileIn, extOut, reference, true); } - - @Test - public void failToTestReporting(){ - Assert.fail(); - } - @Test public void testNoConflictPG() throws IOException { final File inFile = new File(TEST_DATA_DIR, "print_reads_withPG.sam");