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 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 Clinical Data File.
*
* @throws DaoException Database Access Error.
* @throws IOException IO Error.
*/
@Test
@Ignore("To be fixed")
public void testImportClinicalDataSurvival() throws Exception {
// TBD: change this to use getResourceAsStream()
File clinicalFile = new File("target/test-classes/clinical_data.txt");
ImportClinicalData importClinicalData = new ImportClinicalData(study, clinicalFile);
importClinicalData.importData();
LinkedHashSet<String> caseSet = new LinkedHashSet<String>();
caseSet.add("TCGA-A1-A0SB");
caseSet.add("TCGA-A1-A0SI");
caseSet.add("TCGA-A1-A0SE");
List<Patient> clinicalCaseList =
DaoClinicalData.getSurvivalData(study.getInternalId(), caseSet);
assertEquals(3, clinicalCaseList.size());
Patient clinical0 = clinicalCaseList.get(0);
assertEquals(new Double(79.04), clinical0.getAgeAtDiagnosis());
assertEquals("DECEASED", clinical0.getOverallSurvivalStatus());
assertEquals("Recurred/Progressed", clinical0.getDiseaseFreeSurvivalStatus());
assertEquals(new Double(43.8), clinical0.getOverallSurvivalMonths());
assertEquals(new Double(15.05), clinical0.getDiseaseFreeSurvivalMonths());
Patient clinical1 = clinicalCaseList.get(1);
assertEquals(new Double(55.53), clinical1.getAgeAtDiagnosis());
assertEquals("LIVING", clinical1.getOverallSurvivalStatus());
assertEquals("DiseaseFree", clinical1.getDiseaseFreeSurvivalStatus());
assertEquals(new Double(49.02), clinical1.getOverallSurvivalMonths());
assertEquals(new Double(49.02), clinical1.getDiseaseFreeSurvivalMonths());
Patient clinical2 = clinicalCaseList.get(2);
assertEquals(null, clinical2.getDiseaseFreeSurvivalMonths());
}