// MobyParserTest.java // // Created: February 2008 // // Copyright 2008 Martin Senger // // Licensed under the Apache License, Version 2.0 (the "License"); // you may not use this file except in compliance with the License. // You may obtain a copy of the License at // // http://www.apache.org/licenses/LICENSE-2.0 // // Unless required by applicable law or agreed to in writing, software // distributed under the License is distributed on an "AS IS" BASIS, // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // See the License for the specific language governing permissions and // limitations under the License. // 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; import org.junit.Test; import static org.junit.Assert.*; import org.apache.commons.io.IOUtils; import org.apache.commons.io.FileUtils; import org.apache.commons.lang.StringUtils; import java.io.InputStream; import java.io.IOException; import java.util.Map; import java.util.HashMap; import java.util.Arrays; 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_XREFS = "parser-test-input-xrefs.xml"; private static final String INPUT_SET = "parser-test-input-set.xml"; /************************************************************************** * * Tests * **************************************************************************/ @Test public void testNormal() throws IOException, MobyException { MobyPackage moby = parse (INPUT_1, null, null); assertEquals ("freetext notes here", moby.getServiceNotes()); assertEquals ("http://\"me\".&", moby.getAuthority()); MobyJob[] jobs = moby.getJobs(); assertEquals (4, jobs.length); assertEquals ("a1", jobs[0].getId()); MobyObject data = jobs[0].getData(); assertEquals ("NucleotideSequence", data.getMobyTypeName()); assertEquals ("", data.getName()); assertEquals ("DragonDB_Allele", data.getNamespace()); assertEquals ("chlorae", data.getId()); assertFalse (data.isPrimitiveType()); assertEquals ("org.biomoby.shared.datatypes.NucleotideSequence", data.getClass().getName()); NucleotideSequence typedData = (NucleotideSequence)jobs[0].getData(); assertEquals (">tata\ntatata", typedData.get_SequenceString()); assertEquals (">tata\ntatata", typedData.getMoby_SequenceString().getValue()); assertEquals (10, typedData.getMoby_Length().getIntValue()); } @Test public void testUnknownTopLevel() throws IOException, MobyException { MobyPackage moby = parse (INPUT_2, "DNASequence", null); DNASequence typedData = (DNASequence)moby.getJob(0).getData ("myDNA"); assertEquals ("abcd", typedData.get_SequenceString()); assertEquals (12, typedData.getMoby_Length().getIntValue()); } @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 (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 (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 public void testMoreUnknownTopLevels() throws IOException, MobyException { Map backups = new HashMap(); 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 (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 (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 ("xyz", seqData.get_SequenceString()); assertEquals (123, seqData.getMoby_Length().getIntValue()); } @Test public void testSetWithSubstitution() throws IOException, MobyException { Map backups = new HashMap(); backups.put ("mySequenceCollection", "GenericSequence"); MobyPackage moby = parse (INPUT_SET, null, backups); MobyObject[] data = moby.getJob(0).getDataSet ("mySequenceCollection"); assertEquals ("DNASequence", data[0].getMobyTypeName()); assertEquals ("GenericSequence", data[1].getMobyTypeName()); GenericSequence typedData = (GenericSequence)data[0]; assertEquals ("tatatatata", typedData.get_SequenceString()); assertEquals (10, typedData.getMoby_Length().getIntValue()); typedData = (GenericSequence)data[1]; 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 ("This is a value", moby.getJob(0).getData().getValue().trim()); MobyXref[] xrefs = moby.getJob(0).getData().getXrefs(); assertEquals (3, xrefs.length); assertTrue (xrefs[0].isSimpleXref()); assertTrue (xrefs[1].isSimpleXref()); assertFalse (xrefs[2].isSimpleXref()); 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 ("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()); } /************************************************************************** * Create and return a MobyPackage form the XML 'infile'. Use * 'backup' (or 'backups') as the 'latest known data top-level(s)' * data type (any of them may be null). **************************************************************************/ protected MobyPackage parse (String infile, String backup, Map backups) throws IOException, MobyException { InputStream ins = null; try { // reading and parsing input ins = this.getClass().getClassLoader().getResourceAsStream (infile); if (ins == null) { fail ("Could not find test data resource '" + infile + "'."); throw new MobyException ("Test parsing failed."); } MobyPackage moby = null; if (backups != null) { moby = MobyPackage.createFromXML (IOUtils.toByteArray (ins), backups); } else { moby = MobyPackage.createFromXML (IOUtils.toByteArray (ins), backup); } assertFalse (moby == null); return moby; } finally { IOUtils.closeQuietly (ins); } } /************************************************************************** * * Optional parts * **************************************************************************/ /************************************************************************** * This is to be able to run this JUnit 4 tests with a JUnit 3.x runner. **************************************************************************/ public static junit.framework.Test suite() { return new junit.framework.JUnit4TestAdapter (getThisClass()); } /************************************************************************** * Run tests from the command line. **************************************************************************/ public static void main (String args[]) { org.junit.runner.JUnitCore.main (getThisClassName()); } /************************************************************************** * Get the class (name) of this class (note that this is a static * method). This madness is here just because I do not want to * change the class name in the optional methods above when I copy * and paste this into a new test file. **************************************************************************/ private static String getThisClassName() { Exception e = new Exception(); StackTraceElement[] sTrace = e.getStackTrace(); // sTrace[0] will be always there return sTrace[0].getClassName(); } private static Class getThisClass() { try { return org.apache.commons.lang.ClassUtils.getClass (getThisClassName()); } catch (ClassNotFoundException e) { System.err.println ("Cannot get class name."); return java.lang.Object.class; } } }