127 lines
5.0 KiB
Java
127 lines
5.0 KiB
Java
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.commandline;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.variant.variantcontext.VariantContext;
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import org.testng.Assert;
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import org.testng.annotations.BeforeMethod;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.util.Collection;
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public class RodBindingCollectionUnitTest extends BaseTest {
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private ParsingEngine parsingEngine;
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private Tags mytags;
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private static final String defaultTagString = "VCF";
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private static final String testVCFFileName = privateTestDir + "empty.vcf";
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private static final String testListFileName = privateTestDir + "oneVCF.list";
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@BeforeMethod
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public void setUp() {
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parsingEngine = new ParsingEngine(null);
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RodBinding.resetNameCounter();
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mytags = new Tags();
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mytags.addPositionalTag(defaultTagString);
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}
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private class RodBindingCollectionArgProvider {
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@Argument(fullName="input",doc="input",shortName="V")
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public RodBindingCollection<VariantContext> input;
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}
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@Test
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public void testStandardVCF() {
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final String[] commandLine = new String[] {"-V", testVCFFileName};
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parsingEngine.addArgumentSource( RodBindingCollectionArgProvider.class );
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parsingEngine.parse( commandLine );
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parsingEngine.validate();
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final RodBindingCollectionArgProvider argProvider = new RodBindingCollectionArgProvider();
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parsingEngine.loadArgumentsIntoObject( argProvider );
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Assert.assertEquals(argProvider.input.getRodBindings().iterator().next().getSource(), testVCFFileName, "Argument is not correctly initialized");
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}
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@Test
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public void testList() {
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final String[] commandLine = new String[] {"-V", testListFileName};
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parsingEngine.addArgumentSource(RodBindingCollectionArgProvider.class);
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parsingEngine.parse( commandLine );
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parsingEngine.validate();
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final RodBindingCollectionArgProvider argProvider = new RodBindingCollectionArgProvider();
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parsingEngine.loadArgumentsIntoObject( argProvider );
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Assert.assertEquals(argProvider.input.getRodBindings().iterator().next().getSource(), "private/testdata/empty.vcf", "Argument is not correctly initialized");
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}
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@Test
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public void testDefaultTagsInFile() throws IOException {
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final File testFile = File.createTempFile("RodBindingCollectionUnitTest.defaultTags", ".list");
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testFile.deleteOnExit();
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final FileWriter writer = new FileWriter(testFile);
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writer.write(testVCFFileName, 0, testVCFFileName.length());
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writer.close();
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ArgumentTypeDescriptor.getRodBindingsCollection(testFile, parsingEngine, VariantContext.class, "foo", mytags, "input");
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final Collection<RodBinding> bindings = parsingEngine.getRodBindings();
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Assert.assertNotNull(bindings);
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Assert.assertEquals(bindings.size(), 1);
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final RodBinding binding = bindings.iterator().next();
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Assert.assertEquals(parsingEngine.getTags(binding), mytags);
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}
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@Test
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public void testOverrideTagsInFile() throws IOException {
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final File testFile = File.createTempFile("RodBindingCollectionUnitTest.overrideTags", ".list");
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testFile.deleteOnExit();
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final FileWriter writer = new FileWriter(testFile);
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final String textToWrite = "foo " + testVCFFileName;
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writer.write(textToWrite, 0, textToWrite.length());
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writer.close();
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ArgumentTypeDescriptor.getRodBindingsCollection(testFile, parsingEngine, VariantContext.class, "foo", mytags, "input");
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final Collection<RodBinding> bindings = parsingEngine.getRodBindings();
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Assert.assertNotNull(bindings);
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Assert.assertEquals(bindings.size(), 1);
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final RodBinding binding = bindings.iterator().next();
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Assert.assertNotEquals(parsingEngine.getTags(binding), mytags);
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}
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}
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