Java tutorial
/* * 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; import com.mongodb.DBCollection; import com.mongodb.DBCursor; import com.mongodb.DBObject; import com.mongodb.MongoClient; import org.junit.After; import org.junit.Assert; import org.junit.Before; import org.junit.Test; import org.junit.runner.RunWith; import org.opencb.biodata.models.variant.annotation.VariantAnnotation; import org.opencb.opencga.storage.mongodb.variant.DBObjectToVariantAnnotationConverter; import org.springframework.batch.core.BatchStatus; import org.springframework.batch.core.ExitStatus; import org.springframework.batch.core.JobExecution; import org.springframework.batch.core.StepExecution; import org.springframework.batch.test.JobLauncherTestUtils; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.boot.test.IntegrationTest; import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; import uk.ac.ebi.eva.pipeline.configuration.AnnotationConfiguration; import uk.ac.ebi.eva.pipeline.configuration.JobOptions; import uk.ac.ebi.eva.test.utils.JobTestUtils; import java.io.*; import java.nio.file.Files; import java.nio.file.Paths; import java.util.*; import java.util.stream.Collectors; import static junit.framework.TestCase.assertEquals; import static org.junit.Assert.*; import static uk.ac.ebi.eva.pipeline.jobs.steps.VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION; import static uk.ac.ebi.eva.pipeline.jobs.steps.VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE; import static uk.ac.ebi.eva.pipeline.jobs.steps.AnnotationLoaderStep.LOAD_VEP_ANNOTATION; /** * @author Diego Poggioli * * Test for {@link AnnotationJob} */ @IntegrationTest @RunWith(SpringJUnit4ClassRunner.class) @ContextConfiguration(classes = { JobOptions.class, AnnotationJob.class, AnnotationConfiguration.class, JobLauncherTestUtils.class }) public class AnnotationJobTest { @Autowired private JobLauncherTestUtils jobLauncherTestUtils; @Autowired private JobOptions jobOptions; private File vepInputFile; private String dbName; private MongoClient mongoClient; private DBObjectToVariantAnnotationConverter converter; @Test public void allAnnotationStepsShouldBeExecuted() throws Exception { String dump = PopulationStatisticsJobTest.class.getResource("/dump/").getFile(); JobTestUtils.restoreMongoDbFromDump(dump); JobExecution jobExecution = jobLauncherTestUtils.launchJob(); assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus()); assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus()); Assert.assertEquals(3, jobExecution.getStepExecutions().size()); List<StepExecution> steps = new ArrayList<>(jobExecution.getStepExecutions()); StepExecution findVariantsToAnnotateStep = steps.get(0); StepExecution generateVepAnnotationsStep = steps.get(1); StepExecution loadVepAnnotationsStep = steps.get(2); Assert.assertEquals(FIND_VARIANTS_TO_ANNOTATE, findVariantsToAnnotateStep.getStepName()); Assert.assertEquals(GENERATE_VEP_ANNOTATION, generateVepAnnotationsStep.getStepName()); Assert.assertEquals(LOAD_VEP_ANNOTATION, loadVepAnnotationsStep.getStepName()); //check list of variants without annotation output file assertTrue(vepInputFile.exists()); assertEquals("20\t60343\t60343\tG/A\t+", JobTestUtils.readFirstLine(vepInputFile)); //check that documents have the annotation DBCursor cursor = collection(dbName, jobOptions.getDbCollectionsVariantsName()).find(); int cnt = 0; int consequenceTypeCount = 0; while (cursor.hasNext()) { cnt++; DBObject dbObject = (DBObject) cursor.next().get("annot"); if (dbObject != null) { VariantAnnotation annot = converter.convertToDataModelType(dbObject); assertNotNull(annot.getConsequenceTypes()); consequenceTypeCount += annot.getConsequenceTypes().size(); } } assertEquals(300, cnt); assertEquals(536, consequenceTypeCount); //check that one line is skipped because malformed List<StepExecution> variantAnnotationLoadStepExecution = jobExecution.getStepExecutions().stream() .filter(stepExecution -> stepExecution.getStepName().equals(LOAD_VEP_ANNOTATION)) .collect(Collectors.toList()); assertEquals(1, variantAnnotationLoadStepExecution.get(0).getReadSkipCount()); } @Test public void noVariantsToAnnotateOnlyFindVariantsToAnnotateStepShouldRun() throws Exception { JobExecution jobExecution = jobLauncherTestUtils.launchJob(); assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus()); assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus()); Assert.assertEquals(1, jobExecution.getStepExecutions().size()); StepExecution findVariantsToAnnotateStep = new ArrayList<>(jobExecution.getStepExecutions()).get(0); assertEquals(FIND_VARIANTS_TO_ANNOTATE, findVariantsToAnnotateStep.getStepName()); assertTrue(vepInputFile.exists()); assertTrue(Files.size(Paths.get(vepInputFile.toPath().toUri())) == 0); } @Before public void setUp() throws Exception { jobOptions.loadArgs(); vepInputFile = new File(jobOptions.getVepInput()); File vepPathFile = new File(AnnotationJobTest.class.getResource("/mockvep.pl").getFile()); jobOptions.setAppVepPath(vepPathFile); converter = new DBObjectToVariantAnnotationConverter(); mongoClient = new MongoClient(); dbName = jobOptions.getDbName(); } /** * Release resources and delete the temporary output file */ @After public void tearDown() throws Exception { mongoClient.close(); vepInputFile.delete(); new File(jobOptions.getVepOutput()).delete(); JobTestUtils.cleanDBs(dbName); } private DBCollection collection(String databaseName, String collectionName) { return mongoClient.getDB(databaseName).getCollection(collectionName); } }