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commit 8b45109a7eea9574435d3d86fdf92ed195d0f8fd Author: Olivier Sallou <[email protected]> Date: Wed Oct 18 08:49:25 2017 +0000 use simple test instead of scalatest as not packaged yet in debian --- debian/changelog | 2 + debian/control | 4 +- debian/patches/13-skip_network_tests | 44 ++++++++++++----- debian/patches/30-disable-scalatest.patch | 79 +++++++++++++++++++++++++++++++ debian/patches/series | 1 + 5 files changed, 116 insertions(+), 14 deletions(-) diff --git a/debian/changelog b/debian/changelog index 4c13b54..ce89b80 100644 --- a/debian/changelog +++ b/debian/changelog @@ -3,6 +3,8 @@ htsjdk (2.12.0+dfsg-1) UNRELEASED; urgency=medium * New upstream version * cme fix dpkg-control * Standards-Version: 4.1.1 + * d/patches/30-disable-scalatest.patch + Disable scala testing as scalatest is not available in Debian yet -- Andreas Tille <[email protected]> Wed, 11 Oct 2017 10:14:36 +0200 diff --git a/debian/control b/debian/control index 6ed56f7..a24112b 100644 --- a/debian/control +++ b/debian/control @@ -21,7 +21,9 @@ Build-Depends: default-jdk (>= 2:1.8), default-jdk-doc, # required for tests: testng (>= 6.9.9), - junit4 + junit4, + libjimfs-java, + scala-library Standards-Version: 4.1.1 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/htsjdk.git Vcs-Git: https://anonscm.debian.org/git/debian-med/htsjdk.git diff --git a/debian/patches/13-skip_network_tests b/debian/patches/13-skip_network_tests index 27a487e..70775fd 100644 --- a/debian/patches/13-skip_network_tests +++ b/debian/patches/13-skip_network_tests @@ -5,7 +5,7 @@ Description: remove network related tests Last-Updated: 2015-01-06 --- a/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java +++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java -@@ -41,58 +41,7 @@ public class SeekableBufferedStreamTest +@@ -41,58 +41,7 @@ private final String BAM_URL_STRING = "http://broadinstitute.github.io/picard/testdata/index_test.bam";; private static File TestFile = new File("src/test/resources/htsjdk/samtools/seekablestream/megabyteZeros.dat"); @@ -66,7 +66,7 @@ Last-Updated: 2015-01-06 public void testSkip() throws IOException { --- a/src/test/java/htsjdk/samtools/sra/SRAIndexTest.java +++ b/src/test/java/htsjdk/samtools/sra/SRAIndexTest.java -@@ -50,85 +50,4 @@ public class SRAIndexTest extends Abstra +@@ -50,85 +50,4 @@ private static final int LAST_BIN_LEVEL = GenomicIndexUtil.LEVEL_STARTS.length - 1; private static final int SRA_BIN_OFFSET = GenomicIndexUtil.LEVEL_STARTS[LAST_BIN_LEVEL]; @@ -154,7 +154,7 @@ Last-Updated: 2015-01-06 } --- a/src/test/java/htsjdk/samtools/sra/SRATest.java +++ b/src/test/java/htsjdk/samtools/sra/SRATest.java -@@ -57,378 +57,4 @@ import java.util.TreeSet; +@@ -57,378 +57,4 @@ */ public class SRATest extends AbstractSRATest { @@ -535,7 +535,7 @@ Last-Updated: 2015-01-06 } --- a/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java +++ b/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java -@@ -15,18 +15,4 @@ import static org.testng.Assert.assertTr +@@ -15,18 +15,4 @@ */ public class FTPUtilsTest extends HtsjdkTest { @@ -556,7 +556,7 @@ Last-Updated: 2015-01-06 } --- a/src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java +++ b/src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java -@@ -24,225 +24,4 @@ public class FTPClientTest extends Htsjd +@@ -24,225 +24,4 @@ static byte[] expectedBytes = "abcdefghijklmnopqrstuvwxyz\n".getBytes(); FTPClient client; @@ -784,7 +784,7 @@ Last-Updated: 2015-01-06 } --- a/src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java +++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java -@@ -39,68 +39,6 @@ import java.net.URL; +@@ -39,68 +39,6 @@ public class SeekableFTPStreamTest extends HtsjdkTest { @@ -855,7 +855,7 @@ Last-Updated: 2015-01-06 --- a/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java +++ b/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java -@@ -8,9 +8,4 @@ import java.io.IOException; +@@ -8,9 +8,4 @@ public class EnaRefServiceTest extends HtsjdkTest { @@ -867,7 +867,7 @@ Last-Updated: 2015-01-06 } --- a/src/test/java/htsjdk/samtools/BAMRemoteFileTest.java +++ b/src/test/java/htsjdk/samtools/BAMRemoteFileTest.java -@@ -44,285 +44,7 @@ import static org.testng.Assert.*; +@@ -44,285 +44,7 @@ public class BAMRemoteFileTest extends HtsjdkTest { private final File BAM_INDEX_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai"); private final File BAM_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam"); @@ -1155,7 +1155,7 @@ Last-Updated: 2015-01-06 } --- a/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java +++ b/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java -@@ -135,30 +135,6 @@ public class TabixReaderTest extends Hts +@@ -135,30 +135,6 @@ } /** @@ -1188,7 +1188,7 @@ Last-Updated: 2015-01-06 * @throws java.io.IOException --- a/src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java +++ b/src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java -@@ -153,26 +153,6 @@ public class ParsingUtilsTest extends Ht +@@ -153,67 +153,10 @@ tstExists(file.toUri().toString(), false); } @@ -1215,11 +1215,29 @@ Last-Updated: 2015-01-06 private void tstExists(String path, boolean expectExists) throws IOException{ boolean exists = ParsingUtils.resourceExists(path); Assert.assertEquals(exists, expectExists); -@@ -198,22 +178,5 @@ public class ParsingUtilsTest extends Ht - tstStream(file.toUri().toString()); } - @Test +- public void testFileOpenInputStream() throws IOException{ +- File tempFile = File.createTempFile(getClass().getSimpleName(), ".tmp"); +- tempFile.deleteOnExit(); +- OutputStream os = IOUtil.openFileForWriting(tempFile); +- BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(os)); +- writer.write("hello"); +- writer.close(); +- tstStream(tempFile.getAbsolutePath()); +- tstStream(tempFile.toURI().toString()); +- } +- +- @Test +- public void testInMemoryNioFileOpenInputStream() throws IOException{ +- FileSystem fs = Jimfs.newFileSystem(Configuration.unix()); +- Path file = fs.getPath("/file"); +- Files.write(file, "hello".getBytes("UTF-8")); +- tstStream(file.toUri().toString()); +- } +- +- @Test - public void testFTPOpenInputStream() throws IOException{ - tstStream(AVAILABLE_FTP_URL); - } @@ -1240,7 +1258,7 @@ Last-Updated: 2015-01-06 } --- a/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java +++ b/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java -@@ -50,89 +50,6 @@ public class AbstractFeatureReaderTest e +@@ -50,89 +50,6 @@ //wrapper which skips the first byte of a file and leaves the rest unchanged private static final Function<SeekableByteChannel, SeekableByteChannel> WRAPPER = SkippingByteChannel::new; diff --git a/debian/patches/30-disable-scalatest.patch b/debian/patches/30-disable-scalatest.patch new file mode 100644 index 0000000..a7be702 --- /dev/null +++ b/debian/patches/30-disable-scalatest.patch @@ -0,0 +1,79 @@ +Author: Olivier Sallou <[email protected]> +Subject: disable scala testing due to missing scalatest package +Description: Debian repo does not have scalatest dependency, so in the + meanwhile, disable scala related tests +Forwarded: not-needed +Last-Updated: 2017-10-18 +--- a/build.gradle ++++ b/build.gradle +@@ -6,7 +6,7 @@ + + plugins { + id 'java' +- id 'scala' ++ //id 'scala' + id 'maven' + id 'signing' + } +@@ -23,11 +23,11 @@ + compile "org.tukaani:xz:1.5" + compile "gov.nih.nlm.ncbi:ngs-java:1.2.4" + +- testCompile "org.scala-lang:scala-library:2.12.1" +- testCompile "org.scalatest:scalatest_2.12:3.0.1" +- testRuntime 'org.pegdown:pegdown:1.4.2' // Necessary for generating HTML reports with ScalaTest +- testCompile "org.testng:testng:6.9.9" +- testCompile "com.google.jimfs:jimfs:1.1" ++ testCompile "org.scala-lang:scala-library:2.11.x" ++ //testCompile "org.scalatest:scalatest_2.12:3.0.1" ++ //testRuntime 'org.pegdown:pegdown:1.4.2' // Necessary for generating HTML reports with ScalaTest ++ testCompile "org.testng:testng:debian" ++ testCompile "com.google.jimfs:jimfs:debian" + } + + sourceCompatibility = 1.8 +@@ -90,22 +90,20 @@ + jvmArgs += '-Dsamjdk.sra_libraries_download=true' + } + +- tags { +- exclude "slow" +- exclude "broken" +- if (System.env.CI == "false") exclude "sra" +- if (!OperatingSystem.current().isUnix()) exclude "unix" +- } ++ exclude 'htsjdk/samtools/sra/**' ++ exclude 'htsjdk/samtools/BAMFileIndexTest.java' ++ exclude 'htsjdk/samtools/util/BlockCompressedOutputStreamTest.java' ++ + } dependsOn findScalaAndJavaTypes + + task testSRA(type: Test) { + description = "Run the SRA tests" + jvmArgs += '-Dsamjdk.sra_libraries_download=true' + +- tags { +- exclude "slow" +- exclude "broken" +- } ++ exclude 'htsjdk/samtools/sra/**' ++ exclude 'htsjdk/samtools/BAMFileIndexTest.java' ++ exclude 'htsjdk/samtools/util/BlockCompressedOutputStreamTest.java' ++ + } + + task wrapper(type: Wrapper) { +--- a/src/test/java/htsjdk/HtsjdkTest.java ++++ b/src/test/java/htsjdk/HtsjdkTest.java +@@ -1,10 +1,9 @@ + package htsjdk; + +-import org.scalatest.testng.TestNGSuite; + + /** + * Base class for all Java tests in HTSJDK. + */ +-public class HtsjdkTest extends TestNGSuite { ++public class HtsjdkTest { + + } diff --git a/debian/patches/series b/debian/patches/series index aaaa071..461fe49 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ 10-build.xml.patch 13-skip_network_tests 20-fix-version.patch +30-disable-scalatest.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htsjdk.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
