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Subject: remove tests needing network
Description: debian builds expects to run with no network
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2016-12-09
Forwarded: no
--- 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 @@
@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
--- 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
@@ -75,90 +75,11 @@
@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);
- }
}
}
--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java
@@ -27,6 +27,7 @@
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
+import org.junit.Ignore;
import org.junit.Test;
import static org.junit.Assert.*;
@@ -78,6 +79,7 @@
/**
* Constructor test specifying Factory
*/
+ @Ignore("Attemps to use the network")
@Test
public void testConstructorWithoutFactoryGuess() {
String resource = "/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml";
@@ -95,6 +97,7 @@
/**
* Constructor test specifying Factory and using a evalue threshold filter
*/
+ @Ignore("Attemps to use the network")
@Test
public void testConstructorWithEvalueHspFilter() {
//
--- a/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/search/io/blast/BlastXMLParserTest.java
@@ -31,6 +31,7 @@
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
+import org.junit.Ignore;
import org.junit.Test;
import static org.junit.Assert.*;
import org.junit.Ignore;
@@ -84,6 +85,7 @@
/**
* Test of createObjects method, of class BlastXMLParser.
*/
+ @Ignore("Attempts to use the network")
@Test
public void testCreateObjects() throws Exception {
System.out.println("createObjects");
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