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());
}
@Before
public void setUp() throws DaoException {
study = DaoCancerStudy.getCancerStudyByStableId("study_tcga_pub");
DaoGeneticProfile.reCache();
DaoPatient.reCache();
DaoSample.reCache();
}
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());
}