private void runImportCnaData() throws DaoException, IOException { DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance(); DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance(); // the largest current true Entrez gene ID counts 8 digits daoGene.addGene(new CanonicalGene(999999207, "TESTAKT1")); daoGene.addGene(new CanonicalGene(999999208, "TESTAKT2")); daoGene.addGene(new CanonicalGene(999910000, "TESTAKT3")); daoGene.addGene(new CanonicalGene(999999369, "TESTARAF")); daoGene.addGene(new CanonicalGene(999999472, "TESTATM")); daoGene.addGene(new CanonicalGene(999999673, "TESTBRAF")); daoGene.addGene(new CanonicalGene(999999672, "TESTBRCA1")); daoGene.addGene(new CanonicalGene(999999675, "TESTBRCA2")); ProgressMonitor.setConsoleMode(false); // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/cna_test.txt"); ImportTabDelimData parser = new ImportTabDelimData(file, "Barry", geneticProfileId, null); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); String value = dao.getGeneticAlteration(geneticProfileId, sample1, 999999207); assertEquals("0", value); value = dao.getGeneticAlteration(geneticProfileId, sample4, 999999207); assertEquals("-1", value); value = dao.getGeneticAlteration(geneticProfileId, sample2, 999999207); assertEquals("0", value); value = dao.getGeneticAlteration(geneticProfileId, sample2, 999910000); assertEquals("2", value); value = dao.getGeneticAlteration(geneticProfileId, sample3, 999910000); assertEquals("2", value); int cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample3, 999910000)); assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus); cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample2, 999910000)); assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus); cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample4, 999999207)); assertEquals(CopyNumberStatus.HEMIZYGOUS_DELETION, cnaStatus); Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SB"); Sample sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SB-01"); assertTrue( DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId)); patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SJ"); sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SJ-01"); assertTrue( DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId)); ArrayList caseIds = DaoSampleProfile.getAllSampleIdsInProfile(geneticProfileId); assertEquals(14, caseIds.size()); }
private void runImportRnaData1() throws DaoException, IOException { DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance(); DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance(); daoGene.addGene(new CanonicalGene(999999780, "A")); daoGene.addGene(new CanonicalGene(999995982, "B")); daoGene.addGene(new CanonicalGene(999993310, "C")); daoGene.addGene(new CanonicalGene(999997849, "D")); daoGene.addGene(new CanonicalGene(999992978, "E")); daoGene.addGene(new CanonicalGene(999997067, "F")); daoGene.addGene(new CanonicalGene(999911099, "G")); daoGene.addGene(new CanonicalGene(999999675, "6352")); GeneticProfile geneticProfile = new GeneticProfile(); geneticProfile.setCancerStudyId(studyId); geneticProfile.setStableId("gbm_mrna"); geneticProfile.setGeneticAlterationType(GeneticAlterationType.MRNA_EXPRESSION); geneticProfile.setDatatype("CONTINUOUS"); geneticProfile.setProfileName("MRNA Data"); geneticProfile.setProfileDescription("mRNA Data"); DaoGeneticProfile.addGeneticProfile(geneticProfile); int newGeneticProfileId = DaoGeneticProfile.getGeneticProfileByStableId("gbm_mrna").getGeneticProfileId(); ProgressMonitor.setConsoleMode(true); // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/mrna_test.txt"); ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); ConsoleUtil.showMessages(); int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "DD639").getInternalId(); String value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999992978); assertEquals("2.01", value); sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "DD638").getInternalId(); value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997849); assertEquals("0.55", value); }
private void runImportCnaData2() throws DaoException, IOException { DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance(); ProgressMonitor.setConsoleMode(false); // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/cna_test2.txt"); ImportTabDelimData parser = new ImportTabDelimData(file, geneticProfileId, null); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); String value = dao.getGeneticAlteration(geneticProfileId, sample1, 207); assertEquals(value, "0"); value = dao.getGeneticAlteration(geneticProfileId, sample4, 207); assertEquals(value, "-1"); value = dao.getGeneticAlteration(geneticProfileId, sample2, 207); assertEquals(value, "0"); value = dao.getGeneticAlteration(geneticProfileId, sample2, 10000); assertEquals(value, "2"); value = dao.getGeneticAlteration(geneticProfileId, sample3, 10000); assertEquals(value, "2"); int cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample3, 10000)); assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus); cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample2, 10000)); assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus); cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample4, 207)); assertEquals(CopyNumberStatus.HEMIZYGOUS_DELETION, cnaStatus); Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SB"); Sample sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SB-01"); assertTrue( DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId)); patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SJ"); sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SJ-01"); assertTrue( DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId)); ArrayList sampleIds = DaoSampleProfile.getAllSampleIdsInProfile(geneticProfileId); assertEquals(14, sampleIds.size()); }
/** * Test importing of data_rppa file. * * @throws Exception All Errors. */ @Test public void testImportRppaData() throws Exception { MySQLbulkLoader.bulkLoadOn(); DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance(); DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance(); // Genes with alias: daoGene.addGene(makeGeneWithAlias(999999931, "TESTACACA", "TESTACC1")); daoGene.addGene(makeGeneWithAlias(999999207, "TESTAKT1", "TESTAKT")); daoGene.addGene(makeGeneWithAlias(999999597, "TESTSANDER", "TESTACC1")); daoGene.addGene(makeGeneWithAlias(999997158, "TESTTP53BP1", "TEST53BP1")); // test for NA being a special case in RPPA, and not the usual alias daoGene.addGene(makeGeneWithAlias(999997504, "XK", "NA")); // Other genes: daoGene.addGene(new CanonicalGene(999999932, "TESTACACB")); daoGene.addGene(new CanonicalGene(999999208, "TESTAKT2")); daoGene.addGene(new CanonicalGene(999999369, "TESTARAF")); daoGene.addGene(new CanonicalGene(999991978, "TESTEIF4EBP1")); daoGene.addGene(new CanonicalGene(999995562, "TESTPRKAA1")); daoGene.addGene(new CanonicalGene(999997531, "TESTYWHAE")); daoGene.addGene(new CanonicalGene(999910000, "TESTAKT3")); daoGene.addGene(new CanonicalGene(999995578, "TESTPRKCA")); GeneticProfile geneticProfile = new GeneticProfile(); geneticProfile.setCancerStudyId(studyId); geneticProfile.setStableId("gbm_rppa"); geneticProfile.setGeneticAlterationType(GeneticAlterationType.PROTEIN_LEVEL); geneticProfile.setDatatype("LOG2-VALUE"); geneticProfile.setProfileName("RPPA Data"); geneticProfile.setProfileDescription("RPPA Data"); DaoGeneticProfile.addGeneticProfile(geneticProfile); int newGeneticProfileId = DaoGeneticProfile.getGeneticProfileByStableId("gbm_rppa").getGeneticProfileId(); ProgressMonitor.setConsoleMode(true); // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/tabDelimitedData/data_rppa.txt"); ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); ConsoleUtil.showMessages(); int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE1").getInternalId(); String value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997531); assertEquals("1.5", value); sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE4").getInternalId(); value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997531); assertEquals("2", value); sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE4").getInternalId(); value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997504); assertEquals( "NaN", value); // "NA" is not expected to be stored because of workaround for bug in firehose. See // also https://github.com/cBioPortal/cbioportal/issues/839#issuecomment-203523078 sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE1").getInternalId(); value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999995578); assertEquals("1.5", value); }
/** * Test importing of data_expression file. * * @throws Exception All Errors. */ @Test public void testImportmRnaData2() throws Exception { MySQLbulkLoader.bulkLoadOn(); DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance(); DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance(); // Gene with alias: daoGene.addGene(makeGeneWithAlias(999997504, "TESTXK", "NA")); // Other genes: daoGene.addGene(new CanonicalGene(999999999, "TESTNAT1")); daoGene.addGene(new CanonicalGene(999997124, "TESTTNF")); daoGene.addGene(new CanonicalGene(999991111, "TESTCHEK1")); daoGene.addGene(new CanonicalGene(999999919, "TESTABCA1")); // will get generated negative id: daoGene.addGene(new CanonicalGene(-1, "TESTphosphoprotein")); GeneticProfile geneticProfile = new GeneticProfile(); geneticProfile.setCancerStudyId(studyId); geneticProfile.setStableId("gbm_mrna"); geneticProfile.setGeneticAlterationType(GeneticAlterationType.MRNA_EXPRESSION); geneticProfile.setDatatype("CONTINUOUS"); geneticProfile.setProfileName("MRNA Data"); geneticProfile.setProfileDescription("mRNA Data"); DaoGeneticProfile.addGeneticProfile(geneticProfile); int newGeneticProfileId = DaoGeneticProfile.getGeneticProfileByStableId("gbm_mrna").getGeneticProfileId(); ProgressMonitor.setConsoleMode(true); // TBD: change this to use getResourceAsStream() File file = new File("src/test/resources/tabDelimitedData/data_expression2.txt"); ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null); int numLines = FileUtil.getNumLines(file); parser.importData(numLines); // check if expected warnings are given: ArrayList<String> warnings = ProgressMonitor.getWarnings(); int countDuplicatedRowWarnings = 0; int countInvalidEntrez = 0; int countSkippedWarnings = 0; for (String warning : warnings) { if (warning.contains("Duplicated row")) { countDuplicatedRowWarnings++; } if (warning.contains("invalid Entrez_Id")) { // invalid Entrez countInvalidEntrez++; } if (warning.contains("Record will be skipped")) { // Entrez is a valid number, but not found countSkippedWarnings++; } } // check that we have 11 warning messages: assertEquals(2, countDuplicatedRowWarnings); assertEquals(3, countInvalidEntrez); assertEquals(6, countSkippedWarnings); Set<Long> entrezGeneIds = DaoGeneticAlteration.getGenesIdInProfile(newGeneticProfileId); // data will be loaded for 5 of the genes assertEquals(5, entrezGeneIds.size()); HashMap<Long, HashMap<Integer, String>> dataMap = dao.getGeneticAlterationMap(newGeneticProfileId, entrezGeneIds); assertEquals(5, dataMap.entrySet().size()); int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE1").getInternalId(); String value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997124); assertEquals("770", value); sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE3").getInternalId(); value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997124); assertEquals("220", value); // gene should also be loaded via its alias "NA" as defined above: sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE3").getInternalId(); value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997504); assertEquals("9940", value); }