public static Matcher<Variant> withStudy(final String study) { return withStudy(study, notNullValue()); }
@Test public void testIncludeStudies() throws Exception { query = new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1"); this.queryResult = query(query, options); assertEquals(dbAdaptor.count(null).first().intValue(), this.queryResult.getNumResults()); assertThat(this.queryResult, everyResult(allOf(withStudy("S_2", nullValue()), withStudy("S_3", nullValue()), withStudy("S_4", nullValue())))); }
@Test public void testGetByStudiesNegated() throws Exception { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1" + AND + NOT + "S_2"); queryResult = query(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1,S_2"), options); assertThat(queryResult, everyResult(allVariants, allOf(withStudy("S_1"), not(withStudy("S_2"))))); }
@Test public void testGetAllVariants_samples_gt() { Query query = new Query(SAMPLE.key(), "NA19600").append(GENOTYPE.key(), "NA19685" + IS + homRef).append(INCLUDE_SAMPLE.key(), ALL); thrown.expect(VariantQueryException.class); thrown.expectMessage("Can not be used along with filter \"genotype\""); queryResult = query(query, new QueryOptions()); assertThat(queryResult, everyResult(allVariants, withStudy(STUDY_NAME, allOf( withSampleData("NA19600", "GT", containsString("1")), withSampleData("NA19685", "GT", is(homRef)))))); }
@Test public void testGetAllVariants_filterStudies2_not_3() { String studyIds = studyConfiguration2.getStudyName() + ";!" + studyConfiguration3.getStudyName(); query = new Query(STUDY.key(), studyIds) .append(INCLUDE_STUDY.key(), ALL); queryResult = dbAdaptor.get(query, options); assertThat(queryResult, everyResult(allVariants, allOf(withStudy(studyConfiguration2.getStudyName()), withStudy(studyConfiguration3.getStudyName(), nullValue())))); query = new Query(STUDY.key(), studyIds).append(FILE.key(), Arrays.asList(file3, file4)) .append(INCLUDE_STUDY.key(), ALL) .append(INCLUDE_FILE.key(), ALL) .append(INCLUDE_SAMPLE.key(), ALL); queryResult = dbAdaptor.get(query, options); assertThat(queryResult, everyResult(allVariants, allOf(withStudy(studyConfiguration2.getStudyName()), withStudy(studyConfiguration3.getStudyName(), nullValue())))); }
@Test public void testGetByFileNamesMultiStudiesImplicitAnd() { query = new Query() .append(VariantQueryParam.FILE.key(), file12877 + AND + file12882); queryResult = query(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12882") .append(VariantQueryParam.INCLUDE_FILE.key(), asList(file12877 , file12882)), options); assertThat(queryResult, everyResult(allVariants, allOf(withStudy("S_1", withFileId(file12877)), withStudy("S_2", withFileId(file12882))))); }
@Test public void testGetAllVariants_mgf() throws Exception { queryResult = query(new Query(STATS_MGF.key(), STUDY_NAME + ":ALL>0.2"), null); System.out.println(queryResult.getNumResults()); assertThat(queryResult, everyResult(allVariants, withStudy(STUDY_NAME, withStats("ALL", withMgf(gt(0.2)))))); queryResult = query(new Query(STATS_MGF.key(), STUDY_NAME + ":ALL<0.2"), null); System.out.println(queryResult.getNumResults()); assertThat(queryResult, everyResult(allVariants, withStudy(STUDY_NAME, withStats("ALL", withMgf(lt(0.2)))))); }
@Test public void testGetByFileNamesMultiStudiesImplicitOr() { query = new Query() .append(VariantQueryParam.FILE.key(), file12877 + OR + file12882); queryResult = query(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12882") .append(VariantQueryParam.INCLUDE_FILE.key(), asList(file12877 , file12882)), options); assertThat(queryResult, everyResult(allVariants, anyOf(withStudy("S_1", withFileId(file12877)), withStudy("S_2", withFileId(file12882))))); }
@Test public void testGetAllVariants_filterStudies2_AND_3() { String studyIds = studyConfiguration2.getStudyName() + ';' + studyConfiguration3.getStudyName(); Query query = new Query(STUDY.key(), studyIds) .append(INCLUDE_STUDY.key(), ALL); QueryResult<Variant> queryResult = dbAdaptor.get(query, options); assertThat(queryResult, everyResult(allVariants, allOf(withStudy(studyConfiguration2.getStudyName()), withStudy(studyConfiguration3.getStudyName())))); query = new Query(STUDY.key(), studyIds).append(FILE.key(), Arrays.asList(file3, file4, file5)) .append(INCLUDE_STUDY.key(), ALL) .append(INCLUDE_FILE.key(), ALL) .append(INCLUDE_SAMPLE.key(), ALL); queryResult = dbAdaptor.get(query, options); assertThat(queryResult, everyResult(allVariants, allOf(withStudy(studyConfiguration2.getStudyName()), withStudy(studyConfiguration3.getStudyName())))); }
@Test public void testGetByFileNamesMultiStudiesAnd() { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1,S_2") .append(VariantQueryParam.FILE.key(), file12877 + AND + file12882); queryResult = query(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1,S_2") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12882") .append(VariantQueryParam.INCLUDE_FILE.key(), asList(file12877 , file12882)), options); assertThat(queryResult, everyResult(allVariants, allOf(withStudy("S_1", withFileId(file12877)), withStudy("S_2", withFileId(file12882))))); }
@Test public void testGetByFilterByIncludeSample() { VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), sampleNA12877) .append(VariantQueryParam.INCLUDE_FILE.key(), asList(file12877)), options); query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.FILTER.key(), "LowGQX;LowMQ") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), sampleNA12877); queryResult = query(query, options); assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877, withAttribute(FILTER, allOf(containsString("LowGQX"), containsString("LowMQ"))))))); }
@Test public void testGetByStudies() throws Exception { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1"); queryResult = query(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1"), options); assertThat(queryResult, everyResult(allVariants, withStudy("S_1"))); }
private void checkQueryGenotypes(VariantHadoopDBAdaptor dbAdaptor) { StudyConfiguration sc = dbAdaptor.getStudyConfigurationManager().getStudyConfiguration(STUDY_ID, null).first(); List<Variant> allVariants = dbAdaptor.get(new Query(), new QueryOptions()).getResult(); for (String sample : StudyConfiguration.getIndexedSamples(sc).keySet()) { VariantQueryResult<Variant> queryResult = dbAdaptor.get(new Query(VariantQueryParam.SAMPLE.key(), sample) .append(VariantQueryParam.INCLUDE_SAMPLE.key(), VariantQueryUtils.ALL) .append(VariantQueryParam.INCLUDE_FILE.key(), VariantQueryUtils.ALL), new QueryOptions("explain", true)); assertThat(queryResult, everyResult(allVariants, withStudy(STUDY_NAME, withSampleData(sample, "GT", containsString("1"))))); } }
@Test public void testGetBySampleName() throws Exception { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.SAMPLE.key(), "NA12877"); queryResult = query(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877") .append(VariantQueryParam.INCLUDE_FILE.key(), file12877), options); assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(withFileId(file12877), withSampleData("NA12877", "GT", containsString("1")))))); }
public void testGetBySampleName(String expectedSource, QueryOptions options) throws Exception { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.SAMPLE.key(), "NA12877"); // queryResult = dbAdaptor.get(query, options); queryResult = variantStorageEngine.get(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877") .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options); assertEquals(expectedSource, queryResult.getSource()); assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), withSampleData("NA12877", "GT", containsString("1")))))); }
@Test public void testGetByFileNamesAnd() { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.FILE.key(), file12877 + AND + file12878); queryResult = query(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878") .append(VariantQueryParam.INCLUDE_FILE.key(), asList(file12877 , file12878)), options); assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(withFileId(file12877), withFileId(file12878))))); }
public void testGetByFileName(String expectedSource, QueryOptions options) throws Exception { query = new Query() // .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"); // queryResult = dbAdaptor.get(query, options); queryResult = variantStorageEngine.get(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "all") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877") .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options); assertEquals(expectedSource, queryResult.getSource()); assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz")))); }
@Test public void testGetByFileName() throws Exception { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.FILE.key(), file12877); queryResult = query(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "all") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877") .append(VariantQueryParam.INCLUDE_FILE.key(), file12877), options); assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877)))); }
public void testGetBySampleNameMultiRegion(String expectedSource, QueryOptions options) throws Exception { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.SAMPLE.key(), "NA12877") .append(VariantQueryParam.REGION.key(), "1:1-12783,M"); // queryResult = dbAdaptor.get(query, options); queryResult = variantStorageEngine.get(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877") .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options); assertEquals(expectedSource, queryResult.getSource()); assertThat(queryResult, everyResult(allVariants, allOf(anyOf(overlaps(new Region("1:1-12783")), overlaps(new Region("M"))), withStudy("S_1", allOf(withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), withSampleData("NA12877", "GT", containsString("1"))))))); }
public void testGetByGenotypeMultiRegion(String expectedSource, QueryOptions options) throws Exception { query = new Query() .append(VariantQueryParam.STUDY.key(), "S_1") .append(VariantQueryParam.GENOTYPE.key(), "NA12877:1/1") .append(VariantQueryParam.REGION.key(), "1:1-12783,M"); // queryResult = dbAdaptor.get(query, options); queryResult = variantStorageEngine.get(query, options); VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query() .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1") .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877") .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options); assertEquals(expectedSource, queryResult.getSource()); assertThat(queryResult, everyResult(allVariants, allOf(anyOf(overlaps(new Region("1:1-12783")), overlaps(new Region("M"))), withStudy("S_1", allOf(withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), withSampleData("NA12877", "GT", is("1/1"))))))); }