| Patch |
File delta |
Description |
| fix_itext_class_updates.patch | (download) |
forester/org/forester/archaeopteryx/PdfExporter.java |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
one of the class from itext moved to another package.
Upstream code needs to refer to this new package and depends on
newer release if iText5
|
| use_simple_json.patch | (download) |
biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java |
20 10 + 10 - 0 !
1 file changed, 10 insertions(+), 10 deletions(-) |
json.org library is not "free", use simple_json
library and update according to API
.
[ Gilles Filippini <pini@debian.org> ]
Patche updated to migrate away from deprecated json-simple 1.x classes
See json-simple 2.0.0 changelog:
> * Deprecated JSONParse and JSONValue in favor of Jsoner.
> * Deprecated JSONStreamAware and JSONAware in favor of Jsonable.
> * Deprecated JSONObject in favor of JsonObject.
> * Deprecated JSONArray in favor of JsonArray.
.
This patch now uses the new json-simple Json* classes. It is compatible
with both 2.x and 3.x json-simple releases, with a few ajustments
regarding backward incompatible changes in json-simple 3.x:
- The package name, changed to com.github.cliftonlabs.json_simple
This change is handled using place-holders @JSON_SIMPLE_PACKAGE@ which
are substituted at build time by debian/rules.
.
With this trick the package is compatible with json-simple 2.x and 3.x.
Last-Updated: 2020-05-15
|
| fix_import.patch | (download) |
biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java |
7 7 + 0 - 0 !
1 file changed, 7 insertions(+) |
some classes are not imported
|
| faketest.patch | (download) |
biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/ProfeatPropertiesImplTest.java |
7 7 + 0 - 0 !
1 file changed, 7 insertions(+) |
empty test creates failure at compilate, add fake test
to allow compilation and global test success
|
| fix_ascii_characters_mapping.patch | (download) |
forester/org/forester/test/Test.java |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
unmappable character for encoding ascii
|
| skip_network_related_tests.patch | (download) |
biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java |
3 3 + 0 - 0 !
biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java |
1 1 + 0 - 0 !
biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java |
15 0 + 15 - 0 !
biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java |
89 0 + 89 - 0 !
biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java |
10 10 + 0 - 0 !
biojava-modfinder/src/test/java/org/biojava/nbio/protmod/phosphosite/TestAcetylation.java |
2 2 + 0 - 0 !
biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ModifiedCompoundSerializationTest.java |
6 6 + 0 - 0 !
biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java |
3 3 + 0 - 0 !
biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java |
14 0 + 14 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/AtomPositionMapTest.java |
6 6 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/ChemCompTest.java |
4 4 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java |
6 6 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueRangeTest.java |
9 9 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java |
12 12 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java |
4 4 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomIterator.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestBioAssemblyIdentifier.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java |
16 16 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestChargeAdder.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestCloning.java |
8 8 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestDNAAlignment.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestDownloadChemCompProvider.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestEntityResIndexMapping.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestExperimentalTechniques.java |
5 5 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestLoadStructureFromURL.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestNucleotides.java |
4 4 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureCrossReferences.java |
5 5 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/align/TestAlignmentConsistency.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/CeCPMainTest.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/align/ce/TestSmallAlignment.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentWriter.java |
7 7 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/util/TestMultipleAlignmentXMLParser.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java |
9 9 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java |
4 4 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/basepairs/TestBasePairParameters.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitCluster.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/cluster/TestSubunitExtractor.java |
4 4 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java |
7 7 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/geometry/TestUnitQuaternions.java |
4 4 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/FastaAFPChainConverterTest.java |
6 6 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/StructureSequenceMatcherTest.java |
5 5 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestDifficultMmCIFFiles.java |
6 6 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHardBioUnits.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java |
4 4 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMcifOrganismParsing.java |
4 4 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestNonDepositedFiles.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFFeatures.java |
5 5 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseMmCIFLigands.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestParseOnAsymId.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestQuaternaryStructureProviders.java |
8 8 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestSiftsParsing.java |
4 4 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestTitleParsing.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestWriteLargeCoordinatePDB.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestChemCompProvider.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestEntityNameAndType.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseInternalChainId.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmcif/TestParseMmcifHeader.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestBondFinding.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfUtils.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/rcsb/RCSBLigandsFactoryTest.java |
5 5 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/redmine/Test1DARSeqAlign.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestSecStrucCalc.java |
3 3 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestCeSymm.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSequenceFunctionOrderDetector.java |
2 2 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestCrystalInfo.java |
5 5 + 0 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/xtal/TestInterfaceClustering.java |
3 3 + 0 - 0 !
73 files changed, 277 insertions(+), 118 deletions(-) |
debian builds expects to run with no network
|
| remove_openchart_use.patch | (download) |
forester/org/forester/application/msa_compactor.java |
3 1 + 2 - 0 !
forester/org/forester/msa_compactor/Chart.java |
179 4 + 175 - 0 !
2 files changed, 5 insertions(+), 177 deletions(-) |
biojava makes use of a limited set of forester
As openchart is not available in Debian, remove openchart related calls
to make forester compilation OK in biojava context
|
| ignore_fake_tests.patch | (download) |
biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java |
5 4 + 1 - 0 !
biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java |
5 4 + 1 - 0 !
2 files changed, 8 insertions(+), 2 deletions(-) |
some class tests do not have tests inside, but junit tries to execute them.
Simple skip those classes with no real test to avoid errors during build.
|
| poms.patch | (download) |
biojava-alignment/pom.xml |
5 3 + 2 - 0 !
biojava-structure-gui/pom.xml |
4 2 + 2 - 0 !
pom.xml |
7 2 + 5 - 0 !
3 files changed, 7 insertions(+), 9 deletions(-) |
including forester and jcolorbrewer into the maven build
|
| wrong_version_in_dependency.patch | (download) |
biojava-protein-comparison-tool/pom.xml |
10 5 + 5 - 0 !
1 file changed, 5 insertions(+), 5 deletions(-) |
many version numbers in one sub-pom file are wrong
|
| jmol_path_in_pom.patch | (download) |
biojava-structure-gui/pom.xml |
2 2 + 0 - 0 !
1 file changed, 2 insertions(+) |
currently jmol does not ship maven artifacts
|
| adapting_to_ciftools java3.patch | (download) |
biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumer.java |
95 44 + 51 - 0 !
biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java |
94 44 + 50 - 0 !
biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConverter.java |
6 3 + 3 - 0 !
biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImpl.java |
58 29 + 29 - 0 !
biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImplTest.java |
7 4 + 3 - 0 !
5 files changed, 124 insertions(+), 136 deletions(-) |
some packages and classes have changed in ciftools-java 3.0.0
|
| adapting_to_jgrapht1.5.1.patch | (download) |
biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java |
2 1 + 1 - 0 !
biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentOrderDetector.java |
2 1 + 1 - 0 !
biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/GraphComponentRefiner.java |
2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 3 deletions(-) |
some packages have changed in jgrapht 1.5.1
|
| remove_tests_needing_junitx.patch | (download) |
biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java |
40 0 + 40 - 0 !
1 file changed, 40 deletions(-) |
omitting tests needing junitx.framework.fileassert as junitx is
not packaged in Debian
|
| fix_ambiguous_method_call.patch | (download) |
biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ZipChemCompProvider.java |
2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-) |
add explicit cast to fix ambiguous method call error
Taken from upstream to match expected method call
https://github.com/biojava/biojava/blob/master/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
|
