89 lines
4.5 KiB
Java
89 lines
4.5 KiB
Java
/*
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* Copyright (c) 2010, 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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* 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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.pipeline;
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import org.broadinstitute.sting.pipeline.Pipeline;
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import org.broadinstitute.sting.pipeline.PipelineSample;
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import org.testng.Assert;
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import org.broadinstitute.sting.utils.yaml.YamlUtils;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.util.Map;
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public class PipelineUnitTest {
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@Test
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public void testDumpAndLoad() throws Exception {
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Pipeline pipeline = new Pipeline();
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pipeline.getProject().setName("PRJ_NAME");
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pipeline.getProject().setReferenceFile(new File("my.fasta"));
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pipeline.getProject().setGenotypeDbsnp(new File("my.vcf"));
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pipeline.getProject().setEvalDbsnp(new File("my.dbsnp"));
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pipeline.getProject().getTags().put("testProjectTag", "project value here");
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PipelineSample sample = new PipelineSample();
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sample.setId("SMP_ID");
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sample.getBamFiles().put("recalibrated", new File("recalibrated.bam"));
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sample.getBamFiles().put("cleaned", new File("/absolute/path/to/cleaned.bam"));
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sample.getTags().put("testSampleTag", "sample value here");
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pipeline.getSamples().add(sample);
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File file = File.createTempFile("testDumpAndLoad", ".yaml");
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YamlUtils.dump(pipeline, file);
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Pipeline pipelineLoad = YamlUtils.load(Pipeline.class, file);
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Assert.assertEquals(pipelineLoad.getProject().getName(), pipeline.getProject().getName());
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Assert.assertEquals(pipeline.getProject().getReferenceFile(), pipelineLoad.getProject().getReferenceFile());
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Assert.assertEquals(pipeline.getProject().getIntervalList(), pipelineLoad.getProject().getIntervalList());
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Assert.assertEquals(pipeline.getProject().getGenotypeDbsnp(), pipelineLoad.getProject().getGenotypeDbsnp());
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Assert.assertEquals(pipeline.getProject().getGenotypeDbsnpType(), pipelineLoad.getProject().getGenotypeDbsnpType());
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Assert.assertEquals(pipeline.getProject().getEvalDbsnp(), pipelineLoad.getProject().getEvalDbsnp());
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Assert.assertEquals(pipeline.getProject().getEvalDbsnpType(), pipelineLoad.getProject().getEvalDbsnpType());
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Assert.assertEquals(pipelineLoad.getProject().getTags().size(), pipeline.getProject().getTags().size());
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for (Map.Entry<String, String> entry : pipeline.getProject().getTags().entrySet())
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Assert.assertEquals(pipeline.getProject().getTags().get(entry.getKey()), entry.getValue());
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Assert.assertEquals(pipelineLoad.getSamples().size(), pipeline.getSamples().size());
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for (int i = 0; i < pipeline.getSamples().size(); i++) {
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PipelineSample pipelineSample = pipeline.getSamples().get(i);
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PipelineSample pipelineLoadSample = pipelineLoad.getSamples().get(i);
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Assert.assertEquals(pipelineLoadSample.getId(), pipelineSample.getId());
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Assert.assertEquals(pipelineLoadSample.getBamFiles().size(), pipelineSample.getBamFiles().size());
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for (Map.Entry<String, File> entry : pipelineSample.getBamFiles().entrySet())
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Assert.assertEquals(entry.getValue(), pipelineSample.getBamFiles().get(entry.getKey()));
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Assert.assertEquals(pipelineLoadSample.getTags().size(), pipelineSample.getTags().size());
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for (Map.Entry<String, String> entry : pipelineSample.getTags().entrySet())
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Assert.assertEquals(pipelineSample.getTags().get(entry.getKey()), entry.getValue());
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}
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}
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}
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