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@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);
-
}
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