Java tutorial
/* * Copyright 2015-2016 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 org.junit.*; import org.junit.runner.RunWith; import org.opencb.biodata.models.variant.VariantSource; import org.opencb.datastore.core.QueryOptions; import org.opencb.opencga.lib.common.Config; import org.opencb.opencga.storage.core.StorageManagerFactory; import org.opencb.opencga.storage.core.variant.VariantStorageManager; import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor; import org.opencb.opencga.storage.core.variant.adaptors.VariantDBIterator; import org.springframework.batch.core.*; import org.springframework.batch.core.launch.JobLauncher; import org.springframework.batch.core.repository.JobRepository; import org.springframework.batch.test.JobLauncherTestUtils; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Qualifier; 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.JobOptions; import uk.ac.ebi.eva.pipeline.configuration.VariantAggregatedConfig; import uk.ac.ebi.eva.test.utils.JobTestUtils; import java.io.FileInputStream; import java.net.UnknownHostException; import java.nio.file.Paths; import java.util.ArrayList; import java.util.List; import java.util.zip.GZIPInputStream; import static junit.framework.TestCase.assertEquals; import static org.junit.Assert.*; import static uk.ac.ebi.eva.test.utils.JobTestUtils.cleanDBs; import static uk.ac.ebi.eva.test.utils.JobTestUtils.getTransformedOutputPath; /** * @author Jose Miguel Mut Lopez <jmmut@ebi.ac.uk> * * Test for {@link AggregatedVcfJob} */ @IntegrationTest @RunWith(SpringJUnit4ClassRunner.class) @ContextConfiguration(classes = { JobOptions.class, AggregatedVcfJob.class, VariantAggregatedConfig.class }) public class AggregatedVcfJobTest { @Autowired @Qualifier("aggregatedJob") public Job job; @Autowired private JobOptions jobOptions; @Autowired private JobLauncher jobLauncher; @Autowired private JobRepository jobRepository; private JobLauncherTestUtils jobLauncherTestUtils; private String input; private String outputDir; private String compressExtension; private String dbName; private static String opencgaHome = System.getenv("OPENCGA_HOME") != null ? System.getenv("OPENCGA_HOME") : "/opt/opencga"; @Test public void aggregatedTransformAndLoadShouldBeExecuted() throws Exception { Config.setOpenCGAHome(opencgaHome); JobExecution jobExecution = jobLauncherTestUtils.launchJob(); assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus()); assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus()); // check execution flow Assert.assertEquals(2, jobExecution.getStepExecutions().size()); List<StepExecution> steps = new ArrayList<>(jobExecution.getStepExecutions()); StepExecution transformStep = steps.get(0); StepExecution loadStep = steps.get(1); Assert.assertEquals(AggregatedVcfJob.NORMALIZE_VARIANTS, transformStep.getStepName()); Assert.assertEquals(AggregatedVcfJob.LOAD_VARIANTS, loadStep.getStepName()); assertTrue(transformStep.getEndTime().before(loadStep.getStartTime())); // check transformed file String outputFilename = getTransformedOutputPath(Paths.get(input).getFileName(), compressExtension, outputDir); long lines = JobTestUtils.getLines(new GZIPInputStream(new FileInputStream(outputFilename))); assertEquals(156, lines); // check ((documents in DB) == (lines in transformed file)) VariantStorageManager variantStorageManager = StorageManagerFactory.getVariantStorageManager(); VariantDBAdaptor variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null); VariantDBIterator iterator = variantDBAdaptor.iterator(new QueryOptions()); Assert.assertEquals(JobTestUtils.count(iterator), lines); // check that stats are loaded properly assertFalse(variantDBAdaptor.iterator(new QueryOptions()).next().getSourceEntries().values().iterator() .next().getCohortStats().isEmpty()); } @Test public void aggregationNoneOptionShouldNotLoadStats() throws Exception { VariantSource source = (VariantSource) jobOptions.getVariantOptions() .get(VariantStorageManager.VARIANT_SOURCE); jobOptions.getVariantOptions().put(VariantStorageManager.VARIANT_SOURCE, new VariantSource(input, source.getFileId(), source.getStudyId(), source.getStudyName(), source.getType(), VariantSource.Aggregation.NONE)); Config.setOpenCGAHome(opencgaHome); JobExecution jobExecution = jobLauncherTestUtils.launchJob(); assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus()); assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus()); // check transformed file String outputFilename = getTransformedOutputPath(Paths.get(input).getFileName(), compressExtension, outputDir); long lines = JobTestUtils.getLines(new GZIPInputStream(new FileInputStream(outputFilename))); assertEquals(156, lines); // check ((documents in DB) == (lines in transformed file)) VariantStorageManager variantStorageManager = StorageManagerFactory.getVariantStorageManager(); VariantDBAdaptor variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null); VariantDBIterator iterator = variantDBAdaptor.iterator(new QueryOptions()); Assert.assertEquals(JobTestUtils.count(iterator), lines); // check that stats are NOT loaded assertTrue(variantDBAdaptor.iterator(new QueryOptions()).next().getSourceEntries().values().iterator() .next().getCohortStats().isEmpty()); } @BeforeClass public static void beforeTests() throws UnknownHostException { cleanDBs(); } @Before public void setUp() throws Exception { jobOptions.loadArgs(); jobLauncherTestUtils = new JobLauncherTestUtils(); jobLauncherTestUtils.setJob(job); jobLauncherTestUtils.setJobLauncher(jobLauncher); jobLauncherTestUtils.setJobRepository(jobRepository); input = jobOptions.getPipelineOptions().getString("input.vcf"); outputDir = jobOptions.getPipelineOptions().getString("output.dir"); compressExtension = jobOptions.getPipelineOptions().getString("compressExtension"); dbName = jobOptions.getPipelineOptions().getString("db.name"); String inputFile = AggregatedVcfJobTest.class.getResource(input).getFile(); jobOptions.getPipelineOptions().put("input.vcf", inputFile); } @After public void tearDown() throws Exception { cleanDBs(dbName); } }