remove tests needing network

Last-Updated: 2016-12-09
Forwarded: no


Gbp-Pq: Name skip_network_related_tests

3 files changed, 0 insertions, 108 deletions

diff --git 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
index b74e8fe..21590d3 100644
--- 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
@@ -67,21 +67,6 @@ public class GenbankCookbookTest {
 	@Test
 	public void testProcess() throws Throwable {
 		/*
-		 * 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
 		 */
 		//Try with the GenbankReaderHelper
diff --git 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
index 78b6c16..c4d832f 100644
--- 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
@@ -75,90 +75,11 @@ public class GenbankProxySequenceReaderTest {
 
 	@Test
 	public void testFeatures() 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);
-
-		Assert.assertNotNull("protein sequence is null", seq);
-
-		/*
-		 parse description from header. There is no separate interface/abstract class for method getHeader()
-		 so it should be done here (manualy).
-		 */
-		genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);
-
-		// test description
-		Assert.assertTrue(seq.getDescription() != null);
-
-		// test accession Id
-		logger.info("accession id: {}", seq.getAccession().getID());
-		Assert.assertNotNull(seq.getAccession().getID());
-		// test GID number
-		if( seq.getAccession().getIdentifier() != null) { // GI: in header now optional. See #596
-			Assert.assertEquals(gi, seq.getAccession().getIdentifier());
-			logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
-		}
-		// test taxonomy id
-		logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
-		Assert.assertNotNull(seq.getTaxonomy().getID());
-		Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1]));
-
-		// test taxonomy name
-		String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").get(0).getValue();
-		logger.info("taxonomy name '{}'", taxonName);
-		Assert.assertNotNull(taxonName);
-
-		if (seq.getFeaturesByType("CDS").size() > 0) {
-			FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
-			logger.info("CDS: {}", CDS);
-			String codedBy = CDS.getQualifiers().get("coded_by").get(0).getValue();
-			Assert.assertNotNull(codedBy);
-			Assert.assertTrue(!codedBy.isEmpty());
-			logger.info("\t\tcoded_by: {}", codedBy);
-		}
 	}
 
 	@Test
 	public void testProteinSequenceFactoring() throws Exception {
-		logger.info("create protein sequence test for target {}", gi);
-
-		GenbankProxySequenceReader<AminoAcidCompound> genbankReader
-				= new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
-						this.gi,
-						AminoAcidCompoundSet.getAminoAcidCompoundSet());
-
-		ProteinSequence seq = new ProteinSequence(genbankReader);
-
-		// if target protein contain CDS/coded_by than it should contain parent nucleotide seq
-		ArrayList<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");
-
-		if (CDSs != null) {
-			if (CDSs.size() == 1) {
-				ArrayList<Qualifier> qualifiers = (ArrayList)CDSs.get(0).getQualifiers().get("coded_by");
-				Qualifier codedBy = qualifiers.get(0);
-				if (codedBy != null) {
-
-					AbstractSequence<?> parentSeq = seq.getParentSequence();
-					Assert.assertNotNull(parentSeq);
-
-					/*
-					 Sometimes protein might have many 'parents' with different accessions
-					 so accession is not set.
-
-					 That test is always failed
-					 */
-					//Assert.assertTrue(parentSeq.getAccession());
-					Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty());
-				}
-			}
-		} else {
-			logger.info("target {} has no CDS", gi);
-		}
 
 	}
 }
diff --git 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
index c6ade3d..dc415c0 100644
--- 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 class NonstandardProteinCompoundTest  {
 
 	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);
-
 
 	}