[med-svn] r12731 - in trunk/packages/biojava3/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2013-01-03 10:11:25 +0000 (Thu, 03 Jan 2013)
New Revision: 12731

Added:
   trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests
Modified:
   trunk/packages/biojava3/trunk/debian/changelog
   trunk/packages/biojava3/trunk/debian/patches/series
Log:
skip network tests

Modified: trunk/packages/biojava3/trunk/debian/changelog
===================================================================
--- trunk/packages/biojava3/trunk/debian/changelog	2013-01-01 21:26:01 UTC (rev 12730)
+++ trunk/packages/biojava3/trunk/debian/changelog	2013-01-03 10:11:25 UTC (rev 12731)
@@ -1,3 +1,9 @@
+biojava3-live (3.0.5-2) unstable; urgency=low
+
+  * Remove tests needing network access (Closes: #696947)
+
+ -- Olivier Sallou <osallou at debian.org>  Thu, 03 Jan 2013 11:08:51 +0100
+
 biojava3-live (3.0.5-1) unstable; urgency=low
 
   * New upstream release

Modified: trunk/packages/biojava3/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/series	2013-01-01 21:26:01 UTC (rev 12730)
+++ trunk/packages/biojava3/trunk/debian/patches/series	2013-01-03 10:11:25 UTC (rev 12731)
@@ -1,3 +1,4 @@
 use_simple_json
 fix_code_to_support_latest_jmol
 fix_ascii_characters_mapping
+skip_network_related_tests

Added: trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests	                        (rev 0)
+++ trunk/packages/biojava3/trunk/debian/patches/skip_network_related_tests	2013-01-03 10:11:25 UTC (rev 12731)
@@ -0,0 +1,31 @@
+Author: Olivier Sallou <osallou at debian/org>
+Last-Updated: 2013-01-03
+Subject: Some tests use network access
+Description: Remove tests requiring external
+ network access
+Forwarded: yes
+Bug: https://redmine.open-bio.org/issues/3402
+--- a/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
++++ b/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
+@@ -40,20 +40,7 @@
+ 	
+ 	public void testUniprot(String uniprotID) throws Exception{
+ 		
+-		ProteinSequence seq = getUniprot(uniprotID);
+-		
+-		AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+-		
+-/*		for (AminoAcidCompound compound : seq) {
+-			System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
+-		} 
+-		*/
+-		compoundSet.verifySequence(seq);
+-		
+-		
+-		
+-		float[] values = Jronn.getDisorderScores(seq);
+-		
++	// Skip network related tests
+ 		
+ 	}
+