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ALS-6330: Fix test compile issues. Add variant list processor integra…
…tion test. Fix bug caused by bitmask paddings
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integration-test/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/test/Main.java
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service/src/main/resources/application-integration-test.properties
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...est/java/edu/harvard/hms/dbmi/avillach/hpds/test/VariantListProcessorIntegrationTest.java
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| package edu.harvard.hms.dbmi.avillach.hpds.test; | ||
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| import edu.harvard.hms.dbmi.avillach.hpds.data.query.Filter; | ||
| import edu.harvard.hms.dbmi.avillach.hpds.data.query.Query; | ||
| import edu.harvard.hms.dbmi.avillach.hpds.processing.VariantListProcessor; | ||
| import edu.harvard.hms.dbmi.avillach.hpds.test.util.BuildIntegrationTestEnvironment; | ||
| import org.junit.jupiter.api.BeforeAll; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.junit.jupiter.api.extension.ExtendWith; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.boot.autoconfigure.EnableAutoConfiguration; | ||
| import org.springframework.boot.test.context.SpringBootTest; | ||
| import org.springframework.test.context.ActiveProfiles; | ||
| import org.springframework.test.context.junit.jupiter.SpringExtension; | ||
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| import java.io.IOException; | ||
| import java.util.*; | ||
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| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
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| @ExtendWith(SpringExtension.class) | ||
| @EnableAutoConfiguration | ||
| @SpringBootTest(classes = edu.harvard.hms.dbmi.avillach.hpds.service.HpdsApplication.class) | ||
| @ActiveProfiles("integration-test") | ||
| public class VariantListProcessorIntegrationTest { | ||
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| private static Logger log = LoggerFactory.getLogger(VariantListProcessorIntegrationTest.class); | ||
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| @Autowired | ||
| private VariantListProcessor variantListProcessor; | ||
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| @BeforeAll | ||
| public static void beforeAll() { | ||
| BuildIntegrationTestEnvironment instance = BuildIntegrationTestEnvironment.INSTANCE; | ||
| } | ||
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| @Test | ||
| public void runVcfExcerptQuery_validGeneWithVariantQuery() throws IOException { | ||
| Query query = new Query(); | ||
| List<Query.VariantInfoFilter> variantInfoFilters = new ArrayList<>(); | ||
| Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); | ||
| variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[]{"LOC102723996"}); | ||
| variantInfoFilters.add(variantInfoFilter); | ||
| query.setVariantInfoFilters(variantInfoFilters); | ||
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| String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); | ||
| log.debug(vcfExerpt); | ||
| String[] vcfExcerptLines = vcfExerpt.split("\\n"); | ||
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| int totalExpectedPatients = 16; | ||
| int totalExpectedVariants = 4; | ||
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| // there should be a line per variant, plus one line for the header | ||
| assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); | ||
| List<String> header = Arrays.asList(vcfExcerptLines[0].split("\\t")); | ||
| String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); | ||
| Arrays.stream(variantLines).forEach(line -> { | ||
| String[] columns = line.split("\\t"); | ||
| assertEquals("chr21", columns[0]); | ||
| int patientCount = 0; | ||
| for (String column : columns) { | ||
| if ("1/1".equals(column) || "0/1".equals(column)) | ||
| patientCount++; | ||
| } | ||
| assertTrue(patientCount > 0); | ||
| assertEquals(patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset")); | ||
| assertEquals("LOC102723996", getValueAtColumn(columns, header, "Gene_with_variant")); | ||
| }); | ||
| } | ||
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| @Test | ||
| public void runVcfExcerptQuery_validGeneWithVariantAndPhenoQuery() throws IOException { | ||
| Query query = new Query(); | ||
| List<Query.VariantInfoFilter> variantInfoFilters = new ArrayList<>(); | ||
| Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); | ||
| variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[]{"LOC102723996"}); | ||
| variantInfoFilters.add(variantInfoFilter); | ||
| query.setVariantInfoFilters(variantInfoFilters); | ||
| query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(35.0, 45.0))); | ||
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| String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); | ||
| log.debug(vcfExerpt); | ||
| String[] vcfExcerptLines = vcfExerpt.split("\\n"); | ||
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| int totalExpectedPatients = 4; | ||
| int totalExpectedVariants = 2; | ||
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| // there should be a line per variant, plus one line for the header | ||
| assertEquals(totalExpectedVariants + 1, vcfExcerptLines.length); | ||
| List<String> header = Arrays.asList(vcfExcerptLines[0].split("\\t")); | ||
| String[] variantLines = Arrays.copyOfRange(vcfExcerptLines, 1, vcfExcerptLines.length); | ||
| Arrays.stream(variantLines).forEach(line -> { | ||
| String[] columns = line.split("\\t"); | ||
| assertEquals("chr21", columns[0]); | ||
| int patientCount = 0; | ||
| for (String column : columns) { | ||
| if ("1/1".equals(column) || "0/1".equals(column)) | ||
| patientCount++; | ||
| } | ||
| assertTrue(patientCount > 0); | ||
| assertEquals(patientCount + "/" + totalExpectedPatients, getValueAtColumn(columns, header, "Patients with this variant in subset")); | ||
| assertEquals("LOC102723996", getValueAtColumn(columns, header, "Gene_with_variant")); | ||
| }); | ||
| } | ||
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| @Test | ||
| public void runVcfExcerptQuery_validQueryNoResults() throws IOException { | ||
| Query query = new Query(); | ||
| List<Query.VariantInfoFilter> variantInfoFilters = new ArrayList<>(); | ||
| Query.VariantInfoFilter variantInfoFilter = new Query.VariantInfoFilter(); | ||
| variantInfoFilter.categoryVariantInfoFilters = Map.of("Gene_with_variant", new String[]{"LOC102723996"}); | ||
| variantInfoFilters.add(variantInfoFilter); | ||
| query.setVariantInfoFilters(variantInfoFilters); | ||
| query.setNumericFilters(Map.of("\\open_access-1000Genomes\\data\\SYNTHETIC_AGE\\", new Filter.DoubleFilter(0.0, 1.0))); | ||
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| String vcfExerpt = variantListProcessor.runVcfExcerptQuery(query, true); | ||
| assertEquals("No Variants Found", vcfExerpt); | ||
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| } | ||
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| private static String getValueAtColumn(String[] rowColumns, List<String> header, String key) { | ||
| return rowColumns[header.indexOf(key)]; | ||
| } | ||
| } |
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...test/src/test/resources/test_vcfIndex.tsv → service/src/test/resources/test_vcfIndex.tsv
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