[MOBY-guts] biomoby commit
Martin Senger
senger at dev.open-bio.org
Mon Mar 3 03:11:28 UTC 2008
senger
Sun Mar 2 22:11:27 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-serv2132/src/test/java/org/biomoby/shared/parser
Modified Files:
MobyParserTest.java
Log Message:
More junit tests for XML parser
moby-live/Java/src/test/java/org/biomoby/shared/parser MobyParserTest.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java 2008/03/02 12:45:27 1.2
+++ /home/repository/moby/moby-live/Java/src/test/java/org/biomoby/shared/parser/MobyParserTest.java 2008/03/03 03:11:27 1.3
@@ -20,6 +20,7 @@
package org.biomoby.shared.parser;
import org.biomoby.shared.MobyException;
+import org.biomoby.shared.data.MobyProvisionInfo;
import org.biomoby.shared.datatypes.*;
import org.junit.Before;
@@ -39,10 +40,12 @@
public class MobyParserTest {
- private static final String INPUT_1 = "parser-test-input-1.xml";
- private static final String INPUT_2 = "parser-test-input-2.xml";
- private static final String INPUT_3 = "parser-test-input-3.xml";
- private static final String INPUT_4 = "parser-test-input-4.xml";
+ private static final String INPUT_1 = "parser-test-input-1.xml";
+ private static final String INPUT_2 = "parser-test-input-2.xml";
+ private static final String INPUT_3 = "parser-test-input-3.xml";
+ private static final String INPUT_4 = "parser-test-input-4.xml";
+ private static final String INPUT_XREFS = "parser-test-input-xrefs.xml";
+ private static final String INPUT_SET = "parser-test-input-set.xml";
/**************************************************************************
*
@@ -72,26 +75,101 @@
assertEquals (typedData.getMoby_Length().getIntValue(), 10);
}
-// @Test
-// public void testUnknownTopLevel()
-// throws IOException, MobyException {
-// parse (INPUT_2, "DNASequence", null);
-// }
-
-// @Test
-// public void testUnknownTopLevelAndMember()
-// throws IOException, MobyException {
-// parse (INPUT_3, "BasicGFF3MultiFeature", null);
-// }
-
-// @Test
-// public void testMoreUnknownTopLevels()
-// throws IOException, MobyException {
-// Map<String,String> backups = new HashMap<String,String>();
-// backups.put ("mySeq", "DNASequence");
-// backups.put ("myPairs", "BasicGFF3MultiFeature");
-// parse (INPUT_4, null, backups);
-// }
+ @Test
+ public void testUnknownTopLevel()
+ 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);
+ }
+
+ @Test
+ public void testUnknownTopLevelAndMember()
+ throws IOException, MobyException {
+ 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");
+ 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");
+ }
+
+ @Test
+ public void testMoreUnknownTopLevels()
+ throws IOException, MobyException {
+ Map<String,String> backups = new HashMap<String,String>();
+ backups.put ("mySeq", "DNASequence");
+ backups.put ("myPairs", "BasicGFF3MultiFeature");
+ 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");
+ 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");
+ DNASequence seqData = (DNASequence)moby.getJob(0).getData ("mySeq");
+ assertEquals (seqData.get_SequenceString(), "xyz");
+ assertEquals (seqData.getMoby_Length().getIntValue(), 123);
+ }
+
+ @Test
+ public void testSetWithSubstitution()
+ throws IOException, MobyException {
+ Map<String,String> backups = new HashMap<String,String>();
+ 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");
+ GenericSequence typedData = (GenericSequence)data[0];
+ assertEquals (typedData.get_SequenceString(), "tatatatata");
+ assertEquals (typedData.getMoby_Length().getIntValue(), 10);
+ typedData = (GenericSequence)data[1];
+ assertEquals (typedData.get_SequenceString(), "");
+ assertEquals (typedData.getMoby_Length().getIntValue(), 5);
+ }
+
+ @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");
+ MobyXref[] xrefs = moby.getJob(0).getData().getXrefs();
+ assertEquals (xrefs.length, 3);
+ 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");
+
+ 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");
+ }
/**************************************************************************
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