[med-svn] [htsjdk] 01/01: use simple test instead of scalatest as not packaged yet in debian
Olivier Sallou
osallou at debian.org
Wed Oct 18 11:05:39 UTC 2017
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository htsjdk.
commit 8b45109a7eea9574435d3d86fdf92ed195d0f8fd
Author: Olivier Sallou <osallou at debian.org>
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 <tille at debian.org> 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 <osallou at debian.org>
+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
--
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