/** * 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); }