[MOBY-guts] biomoby commit
Martin Senger
senger at dev.open-bio.org
Mon Mar 3 11:34:17 UTC 2008
senger
Mon Mar 3 06:34:17 EST 2008
Update of /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser
In directory dev.open-bio.org:/tmp/cvs-serv3170/src/test/java/org/biomoby/shared/parser
Modified Files:
MobyParserTest.java
Log Message:
* more work on junit testing and its infrastructure
* removing some compiler warnings from generated data types
* better use of caching in skeleton generator
moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java 2008/03/03 03:11:27 1.3
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java 2008/03/03 11:34:17 1.4
@@ -57,22 +57,22 @@
public void testNormal()
throws IOException, MobyException {
MobyPackage moby = parse (INPUT_1, null, null);
- assertEquals (moby.getServiceNotes(), "freetext notes here");
- assertEquals (moby.getAuthority(), "http://\"me\".<org>&");
+ assertEquals ("freetext notes here", moby.getServiceNotes());
+ assertEquals ("http://\"me\".<org>&", moby.getAuthority());
MobyJob[] jobs = moby.getJobs();
- assertEquals (jobs.length, 4);
- assertEquals (jobs[0].getId(), "a1");
+ assertEquals (4, jobs.length);
+ assertEquals ("a1", jobs[0].getId());
MobyObject data = jobs[0].getData();
- assertEquals (data.getMobyTypeName(), "NucleotideSequence");
- assertEquals (data.getName(), "");
- assertEquals (data.getNamespace(), "DragonDB_Allele");
- assertEquals (data.getId(), "chlorae");
+ assertEquals ("NucleotideSequence", data.getMobyTypeName());
+ assertEquals ("", data.getName());
+ assertEquals ("DragonDB_Allele", data.getNamespace());
+ assertEquals ("chlorae", data.getId());
assertFalse (data.isPrimitiveType());
- assertEquals (data.getClass().getName(), "org.biomoby.shared.datatypes.NucleotideSequence");
+ assertEquals ("org.biomoby.shared.datatypes.NucleotideSequence", data.getClass().getName());
NucleotideSequence typedData = (NucleotideSequence)jobs[0].getData();
- assertEquals (typedData.get_SequenceString(), ">tata\ntatata");
- assertEquals (typedData.getMoby_SequenceString().getValue(), ">tata\ntatata");
- assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+ assertEquals (">tata\ntatata", typedData.get_SequenceString());
+ assertEquals (">tata\ntatata", typedData.getMoby_SequenceString().getValue());
+ assertEquals (10, typedData.getMoby_Length().getIntValue());
}
@Test
@@ -80,8 +80,8 @@
throws IOException, MobyException {
MobyPackage moby = parse (INPUT_2, "DNASequence", null);
DNASequence typedData = (DNASequence)moby.getJob(0).getData ("myDNA");
- assertEquals (typedData.get_SequenceString(), "abcd");
- assertEquals (typedData.getMoby_Length().getIntValue(), 12);
+ assertEquals ("abcd", typedData.get_SequenceString());
+ assertEquals (12, typedData.getMoby_Length().getIntValue());
}
@Test
@@ -90,18 +90,18 @@
MobyPackage moby = parse (INPUT_3, "BasicGFF3MultiFeature", null);
BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
- assertEquals (data.length, 1);
- assertEquals (data[0].getMoby_start().getIntValue(), 1);
- assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
- assertEquals (data[0].get_phase(), "b");
+ assertEquals (1, data.length);
+ assertEquals (1, data[0].getMoby_start().getIntValue());
+ assertEquals (12.34, data[0].getMoby_score().getFloatValue(), 0.01);
+ assertEquals ("b", data[0].get_phase());
multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
- assertEquals (pairs.length, 2);
- assertEquals (pairs[0].get_key(), "key1");
- assertEquals (pairs[0].get_the_value().length, 3);
- assertEquals (pairs[0].get_the_value()[0], "value1");
- assertEquals (pairs[1].get_key(), "key2");
- assertEquals (pairs[1].get_the_value().length, 1);
- assertEquals (pairs[1].get_the_value()[0], "valueA");
+ assertEquals (2, pairs.length);
+ assertEquals ("key1", pairs[0].get_key());
+ assertEquals (3, pairs[0].get_the_value().length);
+ assertEquals ("value1", pairs[0].get_the_value()[0]);
+ assertEquals ("key2", pairs[1].get_key());
+ assertEquals (1, pairs[1].get_the_value().length);
+ assertEquals ("valueA", pairs[1].get_the_value()[0]);
}
@Test
@@ -113,18 +113,18 @@
MobyPackage moby = parse (INPUT_4, null, backups);
BasicGFF3MultiFeature typedData = (BasicGFF3MultiFeature)moby.getJob(0).getData ("myPairs");
BasicGFF3SequenceFeature[] data = typedData.getMoby_BasicGFF3SequenceFeature();
- assertEquals (data.length, 1);
- assertEquals (data[0].getMoby_start().getIntValue(), 1);
- assertEquals (data[0].getMoby_score().getFloatValue(), 12.34, 0);
- assertEquals (data[0].get_phase(), "b");
+ assertEquals (1, data.length);
+ assertEquals (1, data[0].getMoby_start().getIntValue());
+ assertEquals (12.34, data[0].getMoby_score().getFloatValue(), 0.01);
+ assertEquals ("b", data[0].get_phase());
multi_key_value_pair[] pairs = data[0].getMoby_column9_tag_value();
- assertEquals (pairs.length, 1);
- assertEquals (pairs[0].get_key(), "key1");
- assertEquals (pairs[0].get_the_value().length, 1);
- assertEquals (pairs[0].get_the_value()[0], "value1");
+ assertEquals (1, pairs.length);
+ assertEquals ("key1", pairs[0].get_key());
+ assertEquals (1, pairs[0].get_the_value().length);
+ assertEquals ("value1", pairs[0].get_the_value()[0]);
DNASequence seqData = (DNASequence)moby.getJob(0).getData ("mySeq");
- assertEquals (seqData.get_SequenceString(), "xyz");
- assertEquals (seqData.getMoby_Length().getIntValue(), 123);
+ assertEquals ("xyz", seqData.get_SequenceString());
+ assertEquals (123, seqData.getMoby_Length().getIntValue());
}
@Test
@@ -134,41 +134,40 @@
backups.put ("mySequenceCollection", "GenericSequence");
MobyPackage moby = parse (INPUT_SET, null, backups);
MobyObject[] data = moby.getJob(0).getDataSet ("mySequenceCollection");
- assertEquals (data[0].getMobyTypeName(), "DNASequence");
- assertEquals (data[1].getMobyTypeName(), "GenericSequence");
+ assertEquals ("DNASequence", data[0].getMobyTypeName());
+ assertEquals ("GenericSequence", data[1].getMobyTypeName());
GenericSequence typedData = (GenericSequence)data[0];
- assertEquals (typedData.get_SequenceString(), "tatatatata");
- assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+ assertEquals ("tatatatata", typedData.get_SequenceString());
+ assertEquals (10, typedData.getMoby_Length().getIntValue());
typedData = (GenericSequence)data[1];
- assertEquals (typedData.get_SequenceString(), "");
- assertEquals (typedData.getMoby_Length().getIntValue(), 5);
+ assertEquals ("", typedData.get_SequenceString());
+ assertEquals (5, typedData.getMoby_Length().getIntValue());
}
@Test
public void testXref()
throws IOException, MobyException {
MobyPackage moby = parse (INPUT_XREFS, null, null);
- assertEquals (moby.getJob(0).getData().getValue().trim(),
- "This is a value");
+ assertEquals ("This is a value", moby.getJob(0).getData().getValue().trim());
MobyXref[] xrefs = moby.getJob(0).getData().getXrefs();
- assertEquals (xrefs.length, 3);
+ assertEquals (3, xrefs.length);
assertTrue (xrefs[0].isSimpleXref());
assertTrue (xrefs[1].isSimpleXref());
assertFalse (xrefs[2].isSimpleXref());
- assertEquals (xrefs[0].getId(), "At263644");
- assertEquals (xrefs[0].getNamespace(), "TIGR");
- assertEquals (xrefs[2].getId(), "yes");
- assertEquals (xrefs[2].getNamespace(), "LION");
- assertEquals (xrefs[2].getEvidenceCode(), "IEA");
+ assertEquals ("At263644", xrefs[0].getId());
+ assertEquals ("TIGR", xrefs[0].getNamespace());
+ assertEquals ("yes", xrefs[2].getId());
+ assertEquals ("LION", xrefs[2].getNamespace());
+ assertEquals ("IEA", xrefs[2].getEvidenceCode());
MobyProvisionInfo pi = moby.getJob(0).getData().getProvision();
- assertEquals (pi.getSoftwareName(), "InterPro");
- assertEquals (pi.getSoftwareVersion(), "1.2");
- assertEquals (pi.getSoftwareComment(), "HMMER's not run");
- assertEquals (pi.getDBName(), "Genbank/nt");
- assertEquals (pi.getDBVersion(), "April 8, 2003");
- assertEquals (pi.getDBComment(), "DBver");
- assertEquals (pi.getComment(), "this <&>\"<&>\" is a software comment");
+ assertEquals ("InterPro", pi.getSoftwareName());
+ assertEquals ("1.2", pi.getSoftwareVersion());
+ assertEquals ("HMMER's not run", pi.getSoftwareComment());
+ assertEquals ("Genbank/nt", pi.getDBName());
+ assertEquals ("April 8, 2003", pi.getDBVersion());
+ assertEquals ("DBver", pi.getDBComment());
+ assertEquals ("this <&>\"<&>\" is a software comment", pi.getComment());
}
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