Author: Olivier Sallou <osallou@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-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
 	 */
--- 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 @@
 	
 	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);
-		
-		
-		
-		@SuppressWarnings("unused")
-		float[] values = Jronn.getDisorderScores(seq);
-		
 		
 	}
 	
