uk.ac.ebi.eva.pipeline.jobs.steps.processor.GeneFilterProcessorTest.java Source code

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Here is the source code for uk.ac.ebi.eva.pipeline.jobs.steps.processor.GeneFilterProcessorTest.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.jobs.steps.processor;

import org.junit.Test;
import org.springframework.batch.item.ExecutionContext;
import org.springframework.batch.test.MetaDataInstanceFactory;
import uk.ac.ebi.eva.pipeline.io.readers.GeneReader;
import uk.ac.ebi.eva.pipeline.jobs.steps.processors.GeneFilterProcessor;
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 static junit.framework.TestCase.assertEquals;

/**
 * {@link GeneFilterProcessor}
 * input: FeatureCoordinates
 * output: FeatureCoordinates that are "transcript" or "gene"
 */
public class GeneFilterProcessorTest {

    @Test
    public void shouldKeepGenesAndTranscripts() throws Exception {
        ExecutionContext executionContext = MetaDataInstanceFactory.createStepExecution().getExecutionContext();
        GeneFilterProcessor geneFilterProcessor = new GeneFilterProcessor();

        //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 count = 0;
        int keptGenes = 0;
        while ((gene = geneReader.read()) != null) {
            count++;
            FeatureCoordinates processedGene = geneFilterProcessor.process(gene);
            if (processedGene != null) {
                keptGenes++;
            }
        }

        assertEquals(7, count);
        assertEquals(4, keptGenes);
    }

}