[med-svn] r15943 - in trunk/packages/biojava3/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2014-02-01 09:01:18 +0000 (Sat, 01 Feb 2014)
New Revision: 15943

Modified:
   trunk/packages/biojava3/trunk/debian/patches/series
   trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests
   trunk/packages/biojava3/trunk/debian/rules
Log:
new upstream release 3.0.7, fix tests and rules for new release

Modified: trunk/packages/biojava3/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/series	2014-02-01 08:37:58 UTC (rev 15942)
+++ trunk/packages/biojava3/trunk/debian/patches/series	2014-02-01 09:01:18 UTC (rev 15943)
@@ -1,5 +1,4 @@
 use_simple_json
-fix_code_to_support_latest_jmol
 fix_ascii_characters_mapping
 skip_network_related_tests
 fix_itext_class_updates

Modified: trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests	2014-02-01 08:37:58 UTC (rev 15942)
+++ trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests	2014-02-01 09:01:18 UTC (rev 15943)
@@ -29,3 +29,24 @@
  		
  	}
  	
+--- a/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
++++ b/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
+@@ -56,17 +56,7 @@
+ 	 * Method 1: With the GenbankProxySequenceReader
+ 	 */
+ 	//Try with the GenbankProxySequenceReader
+-	GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader 
+-	= new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+-	ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
+-	genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
+-	System.out.println("Sequence" + "(" + proteinSequence.getAccession() + "," + proteinSequence.getLength() + ")=" + proteinSequence.getSequenceAsString().substring(0, 10) + "...");
+-
+-	GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader 
+-	= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
+-	DNASequence dnaSequence = new DNASequence(genbankDNAReader);
+-	genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
+-	System.out.println("Sequence" + "(" + dnaSequence.getAccession() + "," + dnaSequence.getLength() + ")=" + dnaSequence.getSequenceAsString().substring(0, 10) + "...");
++	// Skipping it due to network requirements
+ 	/*
+ 	 * Method 2: With the GenbankReaderHelper
+ 	 */

Modified: trunk/packages/biojava3/trunk/debian/rules
===================================================================
--- trunk/packages/biojava3/trunk/debian/rules	2014-02-01 08:37:58 UTC (rev 15942)
+++ trunk/packages/biojava3/trunk/debian/rules	2014-02-01 09:01:18 UTC (rev 15943)
@@ -59,7 +59,8 @@
 	# Requires remote access and tmp directory write access
 	#cd biojava3-structure && ant test
 	cd biojava3-structure-gui && ant test
-	cd biojava3-ws && ant test
+	#No test in biojava-ws available
+	#cd biojava3-ws && ant test