build.gradle | 127 21 + 106 - 0 !
1 file changed, 21 insertions(+), 106 deletions(-)

 modifies the upstream build system.

src/test/java/htsjdk/beta/codecs/reads/htsget/HtsgetBAM/HtsgetBAMCodecTest.java | 10 5 + 5 - 0 !
src/test/java/htsjdk/samtools/BAMRemoteFileTest.java | 269 0 + 269 - 0 !
src/test/java/htsjdk/samtools/HtsgetBAMFileReaderTest.java | 24 12 + 12 - 0 !
src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java | 5 0 + 5 - 0 !
src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java | 66 0 + 66 - 0 !
src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java | 61 0 + 61 - 0 !
src/test/java/htsjdk/samtools/sra/SRAIndexTest.java | 81 0 + 81 - 0 !
src/test/java/htsjdk/samtools/sra/SRAQueryTest.java | 2 1 + 1 - 0 !
src/test/java/htsjdk/samtools/sra/SRATest.java | 373 0 + 373 - 0 !
src/test/java/htsjdk/samtools/util/HttpUtilsTest.java | 34 0 + 34 - 0 !
src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java | 47 0 + 47 - 0 !
src/test/java/htsjdk/tribble/readers/TabixReaderTest.java | 23 0 + 23 - 0 !
src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java | 61 0 + 61 - 0 !
src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java | 221 0 + 221 - 0 !
src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java | 14 0 + 14 - 0 !
src/test/java/htsjdk/variant/PrintVariantsExampleTest.java | 2 2 + 0 - 0 !
16 files changed, 20 insertions(+), 1273 deletions(-)

 remove network related tests
 fixing bug 808593
Bug-Debian: https://bugs.debian.org/923539
Last-Updated: 2023-06-13

build.gradle | 13 11 + 2 - 0 !
gradle.properties | 1 1 + 0 - 0 !
2 files changed, 12 insertions(+), 2 deletions(-)

 use debian/changelog as source for version instead of git
 Also force the name of the root project to avoid it to be copied from the directory name

build.gradle | 21 4 + 17 - 0 !
1 file changed, 4 insertions(+), 17 deletions(-)

 debian repo does not have scalatest dependency, so in the
 meanwhile, disable scala related tests

build.gradle | 11 6 + 5 - 0 !
1 file changed, 6 insertions(+), 5 deletions(-)

 enable tests using testng

src/test/java/htsjdk/samtools/SAMIntegerTagTest.java | 10 5 + 5 - 0 !
src/test/java/htsjdk/samtools/cram/BAIEntryTest.java | 1 0 + 1 - 0 !
src/test/java/htsjdk/samtools/cram/io/LTF8Test.java | 15 0 + 15 - 0 !
src/test/java/htsjdk/samtools/cram/structure/CRAMRecordTestHelper.java | 2 1 + 1 - 0 !
src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java | 8 4 + 4 - 0 !
src/test/java/htsjdk/samtools/seekablestream/SeekableStreamGZIPinputStreamIntegrationTest.java | 6 4 + 2 - 0 !
src/test/java/htsjdk/samtools/util/GZIIndexTest.java | 4 3 + 1 - 0 !
src/test/java/htsjdk/utils/SamtoolsTestUtilsTest.java | 3 3 + 0 - 0 !
8 files changed, 20 insertions(+), 29 deletions(-)

 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 and a few other testng errors

build.gradle | 8 0 + 8 - 0 !
src/test/java/htsjdk/samtools/SamStreamsTest.java | 42 0 + 42 - 0 !
src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java | 10 0 + 10 - 0 !
3 files changed, 60 deletions(-)

 remove unsupported *tags* and disable ftp tests as require network connection

build.gradle | 2 2 + 0 - 0 !
src/test/java/htsjdk/TestDataProviders.java | 5 5 + 0 - 0 !
src/test/java/htsjdk/samtools/SamReaderFactoryTest.java | 63 0 + 63 - 0 !
src/test/java/htsjdk/samtools/util/BlockCompressedInputStreamTest.java | 24 0 + 24 - 0 !
4 files changed, 7 insertions(+), 87 deletions(-)

 skip test requiring http connection
 Also skipping tests in HtsgetBAMFileReaderTest, which require the network,
 and adding a test in TestDataProviders as it may need to run methods from
 HtsgetBAMFileReaderTest.

build.gradle | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 xml.bind has been removed from openjdk 11,
 add jaxb-api jar file to compilation and classpath

src/test/java/htsjdk/samtools/fastq/BasicFastqWriterTest.java | 5 4 + 1 - 0 !
1 file changed, 4 insertions(+), 1 deletion(-)

 the test testflushnotspammed has been introduced by upstream as an
 answer to their issue 1497. Yet I am unsure it should be expected to pass in
 any situation as, in my understanding, it success may depend on when the
 garbage collector deletes the objects.
 Anyway, the test is failing with openjdk-17.

build.gradle | 1 1 + 0 - 0 !
src/main/java/htsjdk/samtools/filter/AbstractJavascriptFilter.java | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 1 deletion(-)

 using the rhino javascript engine, as nashorn has been removed
 between openjdk-11 and openjdk-17.

src/test/java/htsjdk/tribble/gff/Gff3WriterTest.java | 8 7 + 1 - 0 !
1 file changed, 7 insertions(+), 1 deletion(-)

 ensuring directories exist before creating temp files inside, as
 some tests seem to rely on other ones creating the directories for them

src/main/java/htsjdk/beta/io/bundle/BundleJSON.java | 29 15 + 14 - 0 !
src/main/java/htsjdk/samtools/util/htsget/HtsgetErrorResponse.java | 4 2 + 2 - 0 !
src/main/java/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.java | 12 6 + 6 - 0 !
src/main/java/htsjdk/samtools/util/htsget/HtsgetResponse.java | 15 9 + 6 - 0 !
src/test/java/htsjdk/beta/io/bundle/BundleJSONTest.java | 10 5 + 5 - 0 !
src/test/java/htsjdk/samtools/util/HtsgetRequestUnitTest.java | 26 13 + 13 - 0 !
6 files changed, 50 insertions(+), 46 deletions(-)

 adapting code to use debian package libjson-java instead of the
 non-free org.json.
 - Beware, in libjson-java, JSONObject.put returns the added object, not the
 JSONObject. Calls to put thus cannot be chained.
 - In JSONArray there is no put method, using add instead.
 - Error messages are not exactly the same in org.json and libjson-java.
 - Ignoring default excludes when parsing json string to avoid skipping a
 field named "class".

src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java | 3 2 + 1 - 0 !
src/test/java/htsjdk/variant/vcf/VCFFileReaderTest.java | 3 2 + 1 - 0 !
2 files changed, 4 insertions(+), 2 deletions(-)

 deactivating the tests that use newest vcf 4.4, as the comments in
 the code itself suggest version 4.4 is not handled by htsjdk. Certainly this
 patch can be removed when some later upstream version gets packaged.