| Patch |
File delta |
Description |
| gradle_dependencies.patch | (download) |
build.gradle |
31 0 + 31 - 0 !
src/main/java/module-info.java |
41 0 + 41 - 0 !
2 files changed, 72 deletions(-) |
adapting gradle build files to debian environment
Coordinates of Debian libraries are indicated.
Also omitting all the modules stuff.
|
| skip_tests_network.patch | (download) |
build.gradle |
69 69 + 0 - 0 !
src/test/java/org/broad/igv/bbfile/BBDataSourceTest.java |
5 5 + 0 - 0 !
src/test/java/org/broad/igv/feature/ExonTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/feature/FeatureDBTest.java |
6 6 + 0 - 0 !
src/test/java/org/broad/igv/feature/genome/GenomeTest.java |
3 3 + 0 - 0 !
src/test/java/org/broad/igv/feature/genome/SequenceWrapperTest.java |
7 6 + 1 - 0 !
src/test/java/org/broad/igv/feature/genome/fasta/FastaBlockCompressedSequenceTest.java |
3 3 + 0 - 0 !
src/test/java/org/broad/igv/htsget/HtsgetBAMReaderTest.java |
3 2 + 1 - 0 !
src/test/java/org/broad/igv/htsget/HtsgetReaderTest.java |
4 3 + 1 - 0 !
src/test/java/org/broad/igv/htsget/HtsgetVariantSourceTest.java |
4 3 + 1 - 0 !
src/test/java/org/broad/igv/sam/AlignmentDataManagerTest.java |
1 1 + 0 - 0 !
src/test/java/org/broad/igv/sam/cram/CRAMReaderTest.java |
8 7 + 1 - 0 !
src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java |
4 4 + 0 - 0 !
src/test/java/org/broad/igv/sam/reader/BAMHttpReaderTest.java |
4 4 + 0 - 0 !
src/test/java/org/broad/igv/sam/reader/CGIAlignmentReaderTest.java |
3 3 + 0 - 0 !
src/test/java/org/broad/igv/tdf/TDFReaderTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/tdf/TDFRegressionTests.java |
4 4 + 0 - 0 !
src/test/java/org/broad/igv/tools/CoverageCounterTest.java |
1 1 + 0 - 0 !
src/test/java/org/broad/igv/tools/IGVToolsTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/tools/converters/ExpressionFormatterTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/tools/motiffinder/MotifFinderSourceTest.java |
4 4 + 0 - 0 !
src/test/java/org/broad/igv/tools/parsers/GCTtoIGVConverterTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/tools/parsers/TestBEDCodecs.java |
3 3 + 0 - 0 !
src/test/java/org/broad/igv/track/TrackLoaderTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/util/HttpUtilsTest.java |
1 1 + 0 - 0 !
src/test/java/org/broad/igv/util/IGVHttpClientUtilsTest.java |
3 3 + 0 - 0 !
src/test/java/org/broad/igv/util/ParsingUtilsTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/util/blat/BlatClientTest.java |
4 3 + 1 - 0 !
src/test/java/org/broad/igv/util/stream/IGVSeekableBufferedStreamTest.java |
3 3 + 0 - 0 !
29 files changed, 155 insertions(+), 6 deletions(-) |
ignoring build-time tests that require network access
Also excluding all test classes extending AbstractHeadlessTest, as this class
systematically looks for data on the Internet.
|
| using_home_made_icons.patch | (download) |
build.gradle |
2 1 + 1 - 0 !
src/main/java/org/broad/igv/ui/commandbar/IGVCommandBar.java |
4 2 + 2 - 0 !
src/main/java/org/broad/igv/ui/util/ApplicationStatusBar.java |
2 1 + 1 - 0 !
src/main/java/org/broad/igv/ui/util/IconFactory.java |
8 4 + 4 - 0 !
4 files changed, 8 insertions(+), 8 deletions(-) |
using free icons to replace the non-free ones
|
| old_gradle_name.patch | (download) |
build.gradle |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
in debian-packaged gradle, archivefilename does not exist,
using archiveName instead.
|
| jide_dependency.patch | (download) |
build.gradle |
1 1 + 0 - 0 !
1 file changed, 1 insertion(+) |
jide dependency has been omitted from build.gradle by upstream
because it is not in Maven Central anymore.
We provide Debian coordinated instead.
|
| omit_aws_stuff.patch | (download) |
build.gradle |
3 3 + 0 - 0 !
src/main/java/org/broad/igv/aws/S3LoadDialog.java |
4 2 + 2 - 0 !
src/main/java/org/broad/igv/oauth/OAuthProvider.java |
16 9 + 7 - 0 !
src/main/java/org/broad/igv/oauth/OAuthUtils.java |
4 2 + 2 - 0 !
src/main/java/org/broad/igv/track/TrackLoader.java |
4 2 + 2 - 0 !
src/main/java/org/broad/igv/ui/IGVMenuBar.java |
23 13 + 10 - 0 !
src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java |
8 4 + 4 - 0 !
src/main/java/org/broad/igv/util/HttpUtils.java |
9 5 + 4 - 0 !
src/main/java/org/broad/igv/util/ParsingUtils.java |
2 1 + 1 - 0 !
9 files changed, 41 insertions(+), 32 deletions(-) |
patching to build without aws support
Because the Amazon SDK is not packaged, we get rid of the classes that need
it. We also cannot use JWTParser, which has a non DFSG-free license.
|
| omit_spark_in_tests.patch | (download) |
src/test/java/org/broad/igv/util/HttpUtilsTest.java |
7 4 + 3 - 0 !
1 file changed, 4 insertions(+), 3 deletions(-) |
omitting spark in the tests, as the needed libraries are not
packaged in Debian.
|
| dont_parse_glat_output_in_tests.patch | (download) |
src/test/java/org/broad/igv/util/blat/LegacyBlatClientTest.java |
6 5 + 1 - 0 !
1 file changed, 5 insertions(+), 1 deletion(-) |
ignoring tests that cannot run anymore, as we have removed files
they used from the source tarball. Yet the tests were passing when the files
were present.
|
| wrong_override.patch | (download) |
src/main/java/org/broad/igv/sam/cram/IGVReferenceSource.java |
1 0 + 1 - 0 !
1 file changed, 1 deletion(-) |
the @override annotation is wrong because the debian-packaged
htsjdk is (at the moment) older than the one upstream relies on.
|
