[med-svn] r18680 - trunk/packages/biojava4-live/trunk/debian/patches

[Olivier Sallou]

Author: osallou
Date: 2015-01-31 16:53:06 +0000 (Sat, 31 Jan 2015)
New Revision: 18680

Modified:
   trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
Log:
skip more network tests

Modified: trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests	2015-01-31 16:40:11 UTC (rev 18679)
+++ trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests	2015-01-31 16:53:06 UTC (rev 18680)
@@ -50,3 +50,39 @@
  		
  	}
  	
+--- 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 @@
+ 
+     @Test
+     public void biojava3() 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());
+ 
+-        // why only tests on protein sequences?
+-        ProteinSequence seq = new ProteinSequence(genbankReader, AminoAcidCompoundSet.getAminoAcidCompoundSet());
+-
+-        Assert.assertNotNull("protein sequence is null", seq);
+-        genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);
+-        
+-        Assert.assertTrue(seq.getDescription() != null);
+-
+-        Assert.assertFalse(seq.getFeaturesKeyWord().getKeyWords().isEmpty());
+-        Assert.assertFalse(seq.getFeaturesByType("source").get(0).getSource().isEmpty());
+-        
+-        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");
+-
+-        if (!codedBy.isEmpty()) {
+-            // get parent DNA
+-            Assert.assertNotNull(seq.getParentSequence().getSequenceAsString() != null);
+-        }
+     }
+ }