[med-svn] r19916 - in trunk/packages/biojava4-live/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2015-08-12 07:39:10 +0000 (Wed, 12 Aug 2015)
New Revision: 19916

Modified:
   trunk/packages/biojava4-live/trunk/debian/changelog
   trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
Log:
new upstream release 4.1.0

Modified: trunk/packages/biojava4-live/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/changelog	2015-08-11 13:05:05 UTC (rev 19915)
+++ trunk/packages/biojava4-live/trunk/debian/changelog	2015-08-12 07:39:10 UTC (rev 19916)
@@ -1,3 +1,9 @@
+biojava4-live (4.1.0+dfsg-1) unstable; urgency=medium
+
+  * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org>  Wed, 12 Aug 2015 09:32:50 +0200
+
 biojava4-live (4.0.0+dfsg-1) unstable; urgency=medium
 
   * BioJava4 packaging  (Closes: #776704).

Modified: trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests	2015-08-11 13:05:05 UTC (rev 19915)
+++ trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests	2015-08-12 07:39:10 UTC (rev 19916)
@@ -52,37 +52,55 @@
  	
 --- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
 +++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
-@@ -75,33 +75,6 @@
+@@ -75,51 +75,6 @@
  
      @Test
-     public void biojava3() throws IOException, InterruptedException, CompoundNotFoundException  { 
+     public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
 -        logger.info("run test for protein: {}", gi);
 -        GenbankProxySequenceReader<AminoAcidCompound> genbankReader
--                = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"), 
--                                                                    this.gi, 
--                                                                    AminoAcidCompoundSet.getAminoAcidCompoundSet());
- 
+-                = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
+-                        this.gi,
+-                        AminoAcidCompoundSet.getAminoAcidCompoundSet());
+-
 -        // why only tests on protein sequences?
--        ProteinSequence seq = new ProteinSequence(genbankReader, AminoAcidCompoundSet.getAminoAcidCompoundSet());
+-        ProteinSequence seq = new ProteinSequence(genbankReader);
 -
 -        Assert.assertNotNull("protein sequence is null", seq);
+-
+-        /*
+-         parse description from header. There is no separate interface/abstract class for method getHeader()
+-         so it should be done here (manualy).
+-         */
 -        genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);
--        
+-
+-        // test description
 -        Assert.assertTrue(seq.getDescription() != null);
 -
--        Assert.assertFalse(seq.getFeaturesKeyWord().getKeyWords().isEmpty());
--        Assert.assertFalse(seq.getFeaturesByType("source").get(0).getSource().isEmpty());
--        
+-        // test accession Id
+-        logger.info("accession id: {}", seq.getAccession().getID());
+-        Assert.assertNotNull(seq.getAccession().getID());
+-        // test GID number
+-        Assert.assertEquals(gi, seq.getAccession().getIdentifier());
+-        logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
+-
+-        // test taxonomy id
 -        logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
 -        Assert.assertNotNull(seq.getTaxonomy().getID());
--        Assert.assertNotNull(seq.getSequenceAsString());
--        
--        
--        List<FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound>> codedBy = seq.getFeaturesByType("coded_by");
+-        Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1]));
 -
--        if (!codedBy.isEmpty()) {
--            // get parent DNA
--            Assert.assertNotNull(seq.getParentSequence().getSequenceAsString() != null);
+-        // test taxonomy name
+-        String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").getValue();
+-        logger.info("taxonomy name '{}'", taxonName);
+-        Assert.assertNotNull(taxonName);
+-
+-        if (seq.getFeaturesByType("CDS").size() > 0) {
+-            FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
+-            logger.info("CDS: {}", CDS);
+-            String codedBy = CDS.getQualifiers().get("coded_by").getValue();
+-            Assert.assertNotNull(codedBy);
+-            Assert.assertTrue(!codedBy.isEmpty());
+-            logger.info("\t\tcoded_by: {}", codedBy);
 -        }
      }
- }
+ 
+     @Test