reintroduce tests

  [TODO - O. Sallou in progress]

  * Reintroduce unit tests now that gradle 3.4 is available in sid

    - new patch is needed for latest upstream, referencing junit classes

    - add testng() call in build.gradle with a patch and set test call in d/rules back

    - testng fails now with jcommander classnotfound exception (was working before),

      may need to add dependency in testCompile of build.gradle, don't understand the reason (testng depends on it, but gradle does not find it)

    - [done] new patch added for latest upstream, referencing junit classes

    - [done] added testng() call in build.gradle with a patch and set test call in d/rules back

    - testng fails now with jcommander classnotfound exception, this is a testng bug

      (#895886: testng: jcommander classes not found), wait to be fixed to enable tests in d/rules

 -- Andreas Tille <tille@debian.org>  Wed, 28 Mar 2018 14:19:04 +0200

--- a/build.gradle

+++ b/build.gradle

@@ -86,9 +86,14 @@

         events "failed", "skipped"

     }

+    useTestNG()

+    minHeapSize = "1G"

+    maxHeapSize = "2G"

+

     if (System.env.CI == "true") {

         jvmArgs += '-Dsamjdk.sra_libraries_download=true'

     }

+    jvmArgs += ["--add-modules", "java.xml.bind"]

     exclude 'htsjdk/samtools/sra/**'

     exclude 'htsjdk/samtools/BAMFileIndexTest.java'

--- a/src/test/java/htsjdk/utils/ClassFinderTest.java

+++ b/src/test/java/htsjdk/utils/ClassFinderTest.java

@@ -1,7 +1,7 @@

 package htsjdk.utils;

 import htsjdk.HtsjdkTest;

-import org.junit.Assert;

+import org.testng.Assert;

 import org.testng.annotations.Test;

 /**

@@ -28,4 +28,4 @@

         Assert.assertEquals(finder.getClasses().stream()

                 .filter(c -> c.getName().equals("htsjdk.utils.ClassFinder")).count(), 1);

     }

-}

\ No newline at end of file

+}

Subject: testng issue with auto parameter mapping

Description: testng below or equal to 6.9.13.4 does nto correctly map

 long and Integers. This leads to test issues when provider [0,9] values

 and methods expects a long (testng sends an Integer).

 This patch disable some tests around this

Author: Olivier Sallou <osallou@debian.org>

Forwarded: Not-Needed

Last-Updated: 2018-02-19

--- a/src/test/java/htsjdk/samtools/SAMIntegerTagTest.java

+++ b/src/test/java/htsjdk/samtools/SAMIntegerTagTest.java

@@ -296,11 +296,11 @@

         List<Object[]> params = new ArrayList<Object[]>();

         for (FORMAT format:FORMAT.values()) {

             for (ValidationStringency stringency:ValidationStringency.values()) {

-                params.add(new Object[]{0, format, stringency});

-                params.add(new Object[]{1, format, stringency});

-                params.add(new Object[]{-1, format, stringency});

-                params.add(new Object[]{Integer.MIN_VALUE, format, stringency});

-                params.add(new Object[]{Integer.MAX_VALUE, format, stringency});

+                //params.add(new Object[]{0, format, stringency});

+                //params.add(new Object[]{1, format, stringency});

+                //params.add(new Object[]{-1, format, stringency});

+                //params.add(new Object[]{Integer.MIN_VALUE, format, stringency});

+                //params.add(new Object[]{Integer.MAX_VALUE, format, stringency});

                 params.add(new Object[]{1L, format, stringency});

                 params.add(new Object[]{-1L, format, stringency});

--- a/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java

+++ b/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java

@@ -115,10 +115,10 @@

         intervalList_unmapped.add(interval);

         return new Object[][]{

-                {intervalList_twoPair, 4},

-                {intervalList_noMatch, 0},

-                {intervalList_onePair, 2},

-                {intervalList_unmapped, 4}

+                {intervalList_twoPair, 4L},

+                {intervalList_noMatch, 0L},

+                {intervalList_onePair, 2L},

+                {intervalList_unmapped, 4L}

         };

     }

 }

--- a/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamGZIPinputStreamIntegrationTest.java

+++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamGZIPinputStreamIntegrationTest.java

@@ -118,6 +118,7 @@

         return data.iterator();

     }

+    /*

     @Test(dataProvider = "compressedVcfsToTest")

     public void testWrappedSeekableStreamInGZIPinputStream(final File input, final long nLines) throws Exception {

         try (final LineReader reader = new BufferedLineReader(new GZIPInputStream(new SeekableFileStream(input)))) {

@@ -126,9 +127,10 @@

             }

             Assert.assertNull(reader.readLine());

             Assert.assertEquals(reader.getLineNumber(), nLines);

-        }

     }

+    */

+    /*

     @Test(dataProvider = "compressedVcfsToTest")

     public void testConsistencyWithBgzip(final File input, final long nLines) throws Exception {

         try (final InputStream gzIs = new GZIPInputStream(new SeekableFileStream(input));

@@ -139,7 +141,7 @@

                 bgz = bgzIs.read();

             }

             Assert.assertEquals(gzIs.read(), bgz);

-        }

     }

+    */

 }

--- a/src/test/java/htsjdk/samtools/util/GZIIndexTest.java

+++ b/src/test/java/htsjdk/samtools/util/GZIIndexTest.java

@@ -110,6 +110,7 @@

         return data.iterator();

     }

+    /*

     @Test(dataProvider = "virtualOffsetForSeekData")

     public void testGetVirtualOffsetForSeek(final long uncompressedOffset,

             final long expectedBlockAddress, final long expectedBlockOffset,

@@ -118,5 +119,6 @@

         Assert.assertEquals(BlockCompressedFilePointerUtil.getBlockAddress(virtualOffset), expectedBlockAddress);

         Assert.assertEquals(BlockCompressedFilePointerUtil.getBlockOffset(virtualOffset), expectedBlockOffset);

     }

+    */

-}

\ No newline at end of file

+}

30-disable-scalatest.patch

40-fix-java9

50-fix-javadoc

60-enable-tests

70-removesometests-testng.patch

	dh_auto_build -- jar javadoc

override_dh_auto_test:

	# Bug 877590: gradle 3.2 fails to execute tests, disable unit testing

	# waiting for gradle 3.4 availability

	# testng bug 895886: testng: jcommander classes not found

	# dh_auto_build -- test

override_jh_installlibs: