/*
Copyright (C) 2003 EBI, GRL
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package org.ensembl.mart.shell.test;
import junit.framework.Test;
import junit.framework.TestSuite;
import junit.textui.TestRunner;
import org.ensembl.mart.lib.FormatSpec;
import org.ensembl.mart.lib.Query;
import org.ensembl.mart.lib.test.Base;
import org.ensembl.mart.lib.test.StatOutputStream;
import org.ensembl.mart.shell.MartShellLib;
/**
* @author <a href="mailto:dlondon@ebi.ac.uk">Darin London</a>
* @author <a href="mailto:craig@ebi.ac.uk">Craig Melsopp</a>
*/
public class MartShellLibTest extends Base {
private MartShellLib msl;
public static void main(String[] args) {
if (args.length > 0)
TestRunner.run(TestClass(args[0]));
else
TestRunner.run(suite());
}
public static Test suite() {
return new TestSuite(MartShellLibTest.class);
}
public static Test TestClass(String testclass) {
TestSuite suite = new TestSuite();
suite.addTest(new MartShellLibTest(testclass));
return suite;
}
public MartShellLibTest(String name) {
super(name);
}
public void testMQLtoQuery() throws Exception {
String martSQL = "using hsapiens_gene_ensembl get gene_stable_id limit 100";
StatOutputStream stats = new StatOutputStream();
Query query = msl.MQLtoQuery(martSQL);
query.setDataSource(martJDataSource);
engine.execute(query, FormatSpec.TABSEPARATEDFORMAT, stats);
int charCount = stats.getCharCount();
int lineCount = stats.getLineCount();
assertTrue("No text returned from query\n", charCount > 0);
assertTrue("No lines returned from query\n", lineCount > 0);
assertEquals("Wrong number of genes returned from Query\n", 100, lineCount);
stats.close();
}
//TODO: when QueryToMQL works, uncomment this
// public void testQueryToMQL() throws Exception {
// msl.setEnvDataset("ensembl_genes_homo_sapiens");
//
// String test = "get ensembl_gene_id";
// Query testQuery = msl.MQLtoQuery(test);
// String response = msl.QueryToMQL(testQuery);
// assertEquals("using ensembl_genes_homo_sapiens " + test, response);
//
// test = "get ensembl_gene_id limit 10";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals("using ensembl_genes_homo_sapiens " + test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id, ensembl_transcript_id, ensembl_translation_id";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id where disease_genes only";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id where disease_genes excluded";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id where chromosome_name = 2";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id where chromosome_name in (1, 2)";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id where chromosome_name in data/exampleChromosomeList";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id where chromosome_name in file:data/exampleChromosomeList";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// String subMQL = "using ensembl_genes_mus_musculus get human_homologue_ensembl_gene_id where transmembrane_domains only as MouseHumanTrans";
// String subMQLQ = "using ensembl_genes_mus_musculus get human_homologue_ensembl_gene_id where transmembrane_domains only";
// String subMQLK = "MouseHumanTrans";
//
// msl.addStoredMQLCommand(subMQLK, subMQLQ);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id where ensembl_gene_id in MouseHumanTrans";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(subMQL + ";" + test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_gene_id where ensembl_gene_id in MouseHumanTrans and disease_genes only and snp_ka_ks_ratio > 0.1";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(subMQL + ";" + test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence peptide where disease_genes only";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get ensembl_transcript_id sequence 1000+gene_exons+1000 where disease_genes only";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// //test all sequences
// test = "using ensembl_genes_homo_sapiens get sequence coding";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence peptide";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence cdna";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence transcript_exons";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence transcript_exon_intron";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence 1000+transcript_flanks";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence gene_exon_intron";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence gene_exons";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence gene_flanks+1000";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence downstream_utr+1000";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
//
// test = "using ensembl_genes_homo_sapiens get sequence 1000+upstream_utr";
// testQuery = msl.MQLtoQuery(test);
// response = msl.QueryToMQL(testQuery);
// assertEquals(test, response);
// }
/* (non-Javadoc)
* @see junit.framework.TestCase#setUp()
*/
public void setUp() throws Exception {
super.setUp();
msl = new MartShellLib();
msl.addMart(martJDataSource);
msl.setEnvMart(martJDataSource.getName());
}
}