Author: Olivier Sallou <osallou@debian/org>
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/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>(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet());
-	DNASequence dnaSequence = new DNASequence(genbankDNAReader);
-	genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
-	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 @@
 	
 	private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException {
 		
-		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());
-		} 
-		*/
-		assertTrue(compoundSet.isValidSequence(seq));
-		
-		
-		
-		Jronn.getDisorderScores(seq);
-		
 		
 	}
 	
--- 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);
-        }
     }
 }
