uk.ac.ebi.eva.pipeline.io.readers.GeneReaderTest.java Source code

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Here is the source code for uk.ac.ebi.eva.pipeline.io.readers.GeneReaderTest.java

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/*
 * Copyright 2016 EMBL - European Bioinformatics Institute
 *
 * 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 uk.ac.ebi.eva.pipeline.io.readers;

import org.junit.Test;
import org.springframework.batch.item.ExecutionContext;
import org.springframework.batch.test.MetaDataInstanceFactory;
import uk.ac.ebi.eva.pipeline.model.FeatureCoordinates;
import uk.ac.ebi.eva.test.data.GtfStaticTestData;
import uk.ac.ebi.eva.test.utils.JobTestUtils;
import java.io.File;
import java.io.FileInputStream;
import java.util.zip.GZIPInputStream;
import static junit.framework.TestCase.assertEquals;

/**
 * {@link GeneReader}
 * input: a GTF File
 * output: a FeatureCoordinates each time `.read()` is called
 */
public class GeneReaderTest {

    @Test
    public void shouldReadAllLinesInGtf() throws Exception {
        ExecutionContext executionContext = MetaDataInstanceFactory.createStepExecution().getExecutionContext();

        //simulate VEP output file
        File file = JobTestUtils.makeGzipFile(GtfStaticTestData.GTF_CONTENT);

        GeneReader geneReader = new GeneReader(file);
        geneReader.setSaveState(false);
        geneReader.open(executionContext);

        FeatureCoordinates gene;
        int chromosomeCount = 0;
        int count = 0;
        while ((gene = geneReader.read()) != null) {
            count++;
            if (gene.getChromosome() != null && !gene.getChromosome().isEmpty()) {
                chromosomeCount++;
            }
        }
        // all should have at least the chromosome field
        assertEquals(count, chromosomeCount);

        // GeneReader should get all the lines from the file
        long actualCount = JobTestUtils.getLines(new GZIPInputStream(new FileInputStream(file)));
        assertEquals(actualCount, count);
    }

}