[med-svn] r18679 - trunk/packages/biojava4-live/trunk/debian/patches

[Olivier Sallou]

Author: osallou
Date: 2015-01-31 16:40:11 +0000 (Sat, 31 Jan 2015)
New Revision: 18679

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

Modified: trunk/packages/biojava4-live/trunk/debian/patches/series
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/series	2015-01-31 16:14:36 UTC (rev 18678)
+++ trunk/packages/biojava4-live/trunk/debian/patches/series	2015-01-31 16:40:11 UTC (rev 18679)
@@ -3,3 +3,4 @@
 fix_import
 faketest
 fix_ascii_characters_mapping
+skip_network_related_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 16:14:36 UTC (rev 18678)
+++ trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests	2015-01-31 16:40:11 UTC (rev 18679)
@@ -1,36 +1,37 @@
 Author: Olivier Sallou <osallou at debian/org>
-Last-Updated: 2013-01-03
+Last-Updated: 2015-01-31
 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-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) + "...");
+--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
++++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
+@@ -75,18 +75,7 @@
+         /*
+          * Method 1: With the GenbankProxySequenceReader
+          */
+-        //Try with the GenbankProxySequenceReader
+-        GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
+-                = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+-        ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
+-        genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
+-        logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
 -
 -	GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader 
--	= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
+-	= new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("java.io.tmpdir"), "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
- 	 */
---- a/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
-+++ b/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
-@@ -43,21 +43,6 @@
+-	logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
++
+         /*
+          * Method 2: With the GenbankReaderHelper
+          */
+--- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
++++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
+@@ -67,20 +67,6 @@
  	
- 	public void testUniprot(String uniprotID) throws Exception{
+ 	private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException {
  		
 -		ProteinSequence seq = getUniprot(uniprotID);
 -		
@@ -40,12 +41,11 @@
 -			System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
 -		} 
 -		*/
--		compoundSet.verifySequence(seq);
+-		assertTrue(compoundSet.isValidSequence(seq));
 -		
 -		
 -		
--		@SuppressWarnings("unused")
--		float[] values = Jronn.getDisorderScores(seq);
+-		Jronn.getDisorderScores(seq);
 -		
  		
  	}