| Patch |
File delta |
Description |
| gradle_dependencies.patch | (download) |
build.gradle |
228 4 + 224 - 0 !
src/main/java/module-info.java |
47 0 + 47 - 0 !
2 files changed, 4 insertions(+), 271 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 |
73 73 + 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 |
1 1 + 0 - 0 !
src/test/java/org/broad/igv/feature/genome/fasta/FastaBlockCompressedSequenceTest.java |
3 3 + 0 - 0 !
src/test/java/org/broad/igv/feature/genome/load/JsonGenomeLoaderTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/htsget/HtsgetBAMReaderTest.java |
1 1 + 0 - 0 !
src/test/java/org/broad/igv/htsget/HtsgetReaderTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/htsget/HtsgetVariantSourceTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/sam/AlignmentDataManagerTest.java |
1 1 + 0 - 0 !
src/test/java/org/broad/igv/sam/cram/CRAMReaderTest.java |
6 6 + 0 - 0 !
src/test/java/org/broad/igv/sam/cram/IGVReferenceSourceTest.java |
4 4 + 0 - 0 !
src/test/java/org/broad/igv/sam/mods/BaseModificationCountsTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/sam/reader/BAMHttpReaderTest.java |
4 4 + 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/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/ucsc/bb/BBDataSourceTest.java |
4 4 + 0 - 0 !
src/test/java/org/broad/igv/ucsc/bb/BBFeatureSourceTest.java |
9 5 + 4 - 0 !
src/test/java/org/broad/igv/ucsc/bb/BBFileTest.java |
4 3 + 1 - 0 !
src/test/java/org/broad/igv/ucsc/twobit/TwoBitSequenceTest.java |
2 2 + 0 - 0 !
src/test/java/org/broad/igv/util/IGVHttpClientUtilsTest.java |
3 3 + 0 - 0 !
src/test/java/org/broad/igv/util/blat/BlatClientTest.java |
4 4 + 0 - 0 !
src/test/java/org/broad/igv/util/stream/IGVSeekableBufferedStreamTest.java |
3 3 + 0 - 0 !
29 files changed, 154 insertions(+), 5 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
|
| 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 |
20 11 + 9 - 0 !
src/main/java/org/broad/igv/ui/action/LoadFromURLMenuAction.java |
7 4 + 3 - 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, 39 insertions(+), 30 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.
|
| 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.
|
| source_target_level.patch | (download) |
build.gradle |
6 6 + 0 - 0 !
1 file changed, 6 insertions(+) |
raising the source/target java level so that the package can be
built in a Debian environment
|
| opening_sealed_interface.patch | (download) |
src/main/java/org/broad/igv/event/IGVEvent.java |
20 1 + 19 - 0 !
1 file changed, 1 insertion(+), 19 deletions(-) |
avoid using sealed interfaces as we are not using modules to allow
large inheritance relationships
|
| no_spark.patch | (download) |
src/test/java/org/broad/igv/util/HttpUtilsTest.java |
49 0 + 49 - 0 !
1 file changed, 49 deletions(-) |
spark is not packaged in debian, omitting related tests
|
| omit_blat_tests.patch | (download) |
src/test/java/org/broad/igv/util/blat/LegacyBlatClientTest.java |
6 5 + 1 - 0 !
1 file changed, 5 insertions(+), 1 deletion(-) |
skipping blat tests as their data have been removed when repacking
|
