[med-svn] r19962 - in trunk/packages/biojava4-live/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2015-08-16 14:59:53 +0000 (Sun, 16 Aug 2015)
New Revision: 19962

Modified:
   trunk/packages/biojava4-live/trunk/debian/changelog
   trunk/packages/biojava4-live/trunk/debian/copyright
   trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
Log:
remove neetwork related tests, closes 795685

Modified: trunk/packages/biojava4-live/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/changelog	2015-08-16 13:51:07 UTC (rev 19961)
+++ trunk/packages/biojava4-live/trunk/debian/changelog	2015-08-16 14:59:53 UTC (rev 19962)
@@ -1,8 +1,8 @@
-biojava4-live (4.1.0+dfsg-2) UNRELEASED; urgency=medium
+biojava4-live (4.1.0+dfsg-2) unstable; urgency=medium
 
-  * NOT RELEASED YET
+  * Remove some network related tests (Closes: #795685). 
 
- -- Olivier Sallou <osallou at debian.org>  Wed, 12 Aug 2015 11:10:20 +0200
+ -- Olivier Sallou <osallou at debian.org>  Sun, 16 Aug 2015 16:33:47 +0200
 
 biojava4-live (4.1.0+dfsg-1) unstable; urgency=medium
 

Modified: trunk/packages/biojava4-live/trunk/debian/copyright
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/copyright	2015-08-16 13:51:07 UTC (rev 19961)
+++ trunk/packages/biojava4-live/trunk/debian/copyright	2015-08-16 14:59:53 UTC (rev 19962)
@@ -10,26 +10,13 @@
            2011 Qing Zhang
            2011 P.E. Bourne
 License: LGPL-2.1+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation; either version 2 .1 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU Lesser General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU Lesser General
- Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
 
 Files: biojava-forester
 Copyright: 2008-2009 Christian M. Zmasek
            2008-2009 Burnham Institute for Medical Research
 License: LGPL-2.1+
+
+License: LGPL-2.1+
  This package is free software; you can redistribute it and/or modify
  it under the terms of the GNU Lesser General Public License as published by
  the Free Software Foundation; either version 2 .1 of the License, or
@@ -46,7 +33,6 @@
  On Debian systems, the complete text of the GNU Lesser General
  Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
 
-
 Files: *
 Copyright: 2008-2012 the Individual authors who contributed the code,
     as identified by the @authors tag of the respective source file.

Modified: trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests	2015-08-16 13:51:07 UTC (rev 19961)
+++ trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests	2015-08-16 14:59:53 UTC (rev 19962)
@@ -52,7 +52,7 @@
  	
 --- 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
-@@ -75,51 +75,6 @@
+@@ -75,88 +75,10 @@
  
      @Test
      public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
@@ -104,3 +104,40 @@
      }
  
      @Test
+     public void testProteinSequenceFactoring() throws Exception {
+         logger.info("create protein sequence test for target {}", gi);
+-
+-        GenbankProxySequenceReader<AminoAcidCompound> genbankReader
+-                = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
+-                        this.gi,
+-                        AminoAcidCompoundSet.getAminoAcidCompoundSet());
+-
+-        ProteinSequence seq = new ProteinSequence(genbankReader);
+-
+-        // if target protein contain CDS/coded_by than it should contain parent nucleotide seq
+-        ArrayList<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");
+-
+-        if (CDSs != null) {
+-            if (CDSs.size() == 1) {
+-                Qualifier codedBy = (Qualifier) CDSs.get(0).getQualifiers().get("coded_by");
+-                if (codedBy != null) {
+-
+-                    AbstractSequence<?> parentSeq = seq.getParentSequence();
+-                    Assert.assertNotNull(parentSeq);
+-
+-                    /* 
+-                     Sometimes protein might have many 'parents' with different accessions
+-                     so accession is not set.
+-                
+-                     That test is always failed
+-                     */
+-                    //Assert.assertTrue(parentSeq.getAccession()); 
+-                    Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty());
+-                }
+-            }
+-        } else {
+-            logger.info("target {} has no CDS", gi);
+-        }
+-
+     }
+ }