Olivier Sallou pushed to branch master at Debian Med / picard-tools
Commits: a8f248ce by Olivier Sallou at 2019-01-17T17:58:22Z add PF_STATUS to test - - - - - b5887cee by Olivier Sallou at 2019-01-18T14:12:11Z remove failing tests with autopkgtests, due to root access - - - - - 4 changed files: - debian/changelog - + debian/patches/fix_unreadabletests.patch - debian/patches/series - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,8 +1,6 @@ -picard-tools (2.18.23+dfsg-2) UNRELEASE; urgency=medium +picard-tools (2.18.23+dfsg-2) unstable; urgency=medium * Fix Class-Path in manifest file for dependencies (Closes: #919559). - [TODO] 2 tests are still failing with autopkgtest though source build - and testing works fine. -- Olivier Sallou <osal...@debian.org> Thu, 17 Jan 2019 15:54:27 +0000 ===================================== debian/patches/fix_unreadabletests.patch ===================================== @@ -0,0 +1,76 @@ +Subject: tests on unreadable fail +Description: some tests try to check that a non readable file or directory + is correctly managed. However during Debian build, sometimes user is root + and unreadable is not effective. This patch removes related tests +Last-Updated: 2019-01-18 +Author: Olivier Sallou <osal...@debian.org> +Forwarded: no +--- a/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java ++++ b/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java +@@ -155,33 +155,6 @@ + Assert.assertEquals(metricsFile.getMetrics().get(12).PERFECT_MATCHES, 1); + } + +- @Test +- public void testNonWritableOutputFile() throws Exception { +- final File existingFile = new File(basecallsDir, "s_1_1101_barcode.txt.gz"); +- try { +- existingFile.setReadOnly(); +- final String readStructure = "25T8B25T"; +- final int lane = 1; +- +- final File metricsFile = File.createTempFile("eib.", ".metrics"); +- metricsFile.deleteOnExit(); +- +- final List<String> args = new ArrayList<>(Arrays.asList( +- "BASECALLS_DIR=" + basecallsDir.getPath(), +- "LANE=" + lane, +- "READ_STRUCTURE=" + readStructure, +- "METRICS_FILE=" + metricsFile.getPath(), +- "COMPRESS_OUTPUTS=true" +- )); +- for (final String barcode : BARCODES) { +- args.add("BARCODE=" + barcode); +- } +- Assert.assertEquals(runPicardCommandLine(args), 4); +- } finally { +- existingFile.setWritable(true); +- } +- +- } + + /** + * 4 cases tested: +--- a/src/test/java/picard/util/LiftoverVcfTest.java ++++ b/src/test/java/picard/util/LiftoverVcfTest.java +@@ -1196,30 +1196,4 @@ + Assert.assertEquals(runPicardCommandLine(args), 1); + } + +- @Test(expectedExceptions = SAMException.class, expectedExceptionsMessageRegExp = "File exists but is not readable:.*") +- public void testUnreadableDictionary() throws IOException { +- final Path liftOutput = Files.createTempFile("tmpouput", ".vcf"); +- liftOutput.toFile().deleteOnExit(); +- final Path rejectOutput = Files.createTempFile("tmpreject", ".vcf"); +- rejectOutput.toFile().deleteOnExit(); +- final Path input = TEST_DATA_PATH.toPath().resolve("testLiftoverBiallelicIndels.vcf"); +- final Path tmpCopyDir = Files.createTempDirectory("copy"); +- tmpCopyDir.toFile().deleteOnExit(); +- final Path referenceCopy = tmpCopyDir.resolve("refCopy.fasta"); +- referenceCopy.toFile().deleteOnExit(); +- Files.copy(REFERENCE_FILE.toPath(), referenceCopy); +- final Path dictCopy = referenceCopy.resolveSibling(referenceCopy.toFile().getName().replaceAll("fasta$", "dict")); +- dictCopy.toFile().deleteOnExit(); +- final Path dictionary = REFERENCE_FILE.toPath().resolveSibling(REFERENCE_FILE.getName().replaceAll("fasta$", "dict")); +- Files.copy(dictionary, dictCopy); +- dictCopy.toFile().setReadable(false); +- final String[] args = new String[]{ +- "INPUT=" + input, +- "OUTPUT=" + liftOutput, +- "REJECT=" + rejectOutput, +- "CHAIN=" + CHAIN_FILE, +- "REFERENCE_SEQUENCE=" + referenceCopy, +- }; +- runPicardCommandLine(args); +- } + } ===================================== debian/patches/series ===================================== @@ -5,3 +5,4 @@ 50-tests-exclude-Barclay.patch remove_google_nio.patch fix_javadoc_ascii.patch +fix_unreadabletests.patch ===================================== debian/tests/run-unit-test ===================================== @@ -14,7 +14,7 @@ cp -a /usr/share/doc/${pkg}/test.* . cp -a /usr/share/doc/${pkg}/mini.vcf* . gunzip -r * -PicardCommandLine ViewSam ALIGNMENT_STATUS=All INPUT=unmapped.sam +PicardCommandLine ViewSam PF_STATUS=All ALIGNMENT_STATUS=All INPUT=unmapped.sam PicardCommandLine CollectSequencingArtifactMetrics I=test.sam O=test R=test.fasta View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/c93e1866f9549e899c8ce00549e94bd3b53f1804...b5887cee88ee8a326fa4ce0ff35be89d661cd5bd -- View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/c93e1866f9549e899c8ce00549e94bd3b53f1804...b5887cee88ee8a326fa4ce0ff35be89d661cd5bd You're receiving this email because of your account on salsa.debian.org.
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