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...va/uk/ac/ebi/eva/pipeline/configuration/jobs/steps/variantstats/VariantStatsStepTest.java
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| /* | ||
| * Copyright 2024 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.configuration.jobs.steps.variantstats; | ||
|
|
||
| import org.bson.Document; | ||
| import org.junit.After; | ||
| import org.junit.Assert; | ||
| import org.junit.Before; | ||
| import org.junit.Rule; | ||
| import org.junit.Test; | ||
| import org.junit.runner.RunWith; | ||
| import org.springframework.batch.core.JobExecution; | ||
| import org.springframework.batch.core.JobParameters; | ||
| import org.springframework.batch.test.JobLauncherTestUtils; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.test.context.ContextConfiguration; | ||
| import org.springframework.test.context.TestPropertySource; | ||
| import org.springframework.test.context.junit4.SpringRunner; | ||
| import uk.ac.ebi.eva.pipeline.configuration.BeanNames; | ||
| import uk.ac.ebi.eva.pipeline.configuration.MongoConfiguration; | ||
| import uk.ac.ebi.eva.pipeline.configuration.jobs.VariantStatsJobConfiguration; | ||
| import uk.ac.ebi.eva.pipeline.configuration.jobs.steps.VariantStatsStepConfiguration; | ||
| import uk.ac.ebi.eva.test.configuration.BatchTestConfiguration; | ||
| import uk.ac.ebi.eva.test.configuration.TemporaryRuleConfiguration; | ||
| import uk.ac.ebi.eva.test.rules.PipelineTemporaryFolderRule; | ||
| import uk.ac.ebi.eva.test.rules.TemporaryMongoRule; | ||
| import uk.ac.ebi.eva.utils.EvaJobParameterBuilder; | ||
|
|
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
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| import static org.junit.Assert.assertEquals; | ||
| import static uk.ac.ebi.eva.test.utils.JobTestUtils.assertCompleted; | ||
| import static uk.ac.ebi.eva.test.utils.TestFileUtils.getResourceUrl; | ||
|
|
||
| /** | ||
| * Test for {@link VariantStatsStepConfiguration} | ||
| */ | ||
| @RunWith(SpringRunner.class) | ||
| @TestPropertySource({"classpath:test-stats.properties"}) | ||
| @ContextConfiguration(classes = {VariantStatsJobConfiguration.class, BatchTestConfiguration.class, | ||
| TemporaryRuleConfiguration.class, MongoConfiguration.class}) | ||
| public class VariantStatsStepTest { | ||
| private static final String MONGO_DUMP = "/dump/VariantStatsConfigurationTest_vl"; | ||
|
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| private static final String COLLECTION_VARIANTS_NAME = "variants"; | ||
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| private static final String COLLECTION_FILES_NAME = "files"; | ||
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| private static final String DATABASE_NAME = "variant_stats_test_db"; | ||
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| private static final String STUDY_ID = "1"; | ||
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| @Autowired | ||
| @Rule | ||
| public TemporaryMongoRule mongoRule; | ||
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| @Rule | ||
| public PipelineTemporaryFolderRule temporaryFolderRule = new PipelineTemporaryFolderRule(); | ||
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| @Autowired | ||
| private JobLauncherTestUtils jobLauncherTestUtils; | ||
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| @Before | ||
| public void setUp() throws Exception { | ||
| mongoRule.getTemporaryDatabase(DATABASE_NAME).drop(); | ||
| } | ||
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| @After | ||
| public void cleanUp() { | ||
| mongoRule.getTemporaryDatabase(DATABASE_NAME).drop(); | ||
| } | ||
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| @Test | ||
| public void variantStatsStepShouldCalculateAndLoadStats() throws Exception { | ||
| mongoRule.restoreDump(getResourceUrl(MONGO_DUMP), DATABASE_NAME); | ||
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| JobParameters jobParameters = new EvaJobParameterBuilder() | ||
| .collectionFilesName(COLLECTION_FILES_NAME) | ||
| .collectionVariantsName(COLLECTION_VARIANTS_NAME) | ||
| .databaseName(DATABASE_NAME) | ||
| .inputStudyId(STUDY_ID) | ||
| .chunkSize("100") | ||
| .toJobParameters(); | ||
|
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| JobExecution jobExecution = jobLauncherTestUtils.launchStep(BeanNames.VARIANT_STATS_STEP, jobParameters); | ||
|
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| // check job completed successfully | ||
| assertCompleted(jobExecution); | ||
| List<Document> documents = mongoRule.getTemporaryDatabase(DATABASE_NAME).getCollection(COLLECTION_VARIANTS_NAME) | ||
| .find().into(new ArrayList<>()); | ||
| Assert.assertTrue(documents.size() == 300); | ||
| // assert all statistics are calculated for all documents | ||
| Assert.assertTrue(documents.stream().allMatch(doc -> doc.containsKey("st"))); | ||
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| // assert statistics for the variant with 20_61098_C_T | ||
| ArrayList<Document> variantStatsList = documents.stream().filter(doc -> doc.get("_id").equals("20_61098_C_T")) | ||
| .findFirst().get().get("st", ArrayList.class); | ||
| assertEquals(1, variantStatsList.size()); | ||
| Document variantStats = variantStatsList.get(0); | ||
| Document numOfGT = (Document) variantStats.get("numGt"); | ||
| assertEquals(1290, numOfGT.get("0|0")); | ||
| assertEquals(417, numOfGT.get("1|0")); | ||
| assertEquals(573, numOfGT.get("0|1")); | ||
| assertEquals(224, numOfGT.get("1|1")); | ||
| assertEquals(0.2871405780315399, variantStats.get("maf")); | ||
| assertEquals(0.228833869099617, variantStats.get("mgf")); | ||
| assertEquals("T", variantStats.get("mafAl")); | ||
| assertEquals("0|1", variantStats.get("mgfGt")); | ||
| assertEquals(0, variantStats.get("missAl")); | ||
| assertEquals(0, variantStats.get("missGt")); | ||
| } | ||
|
|
||
| } |
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