Author: osallou
Date: 2015-01-31 16:53:06 +0000 (Sat, 31 Jan 2015)
New Revision: 18680
Modified:
trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
Log:
skip more network 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 16:40:11 UTC (rev 18679)
+++
trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests
2015-01-31 16:53:06 UTC (rev 18680)
@@ -50,3 +50,39 @@
}
+---
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);
+- }
+ }
+ }
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