Examples with LimsSampleReader com.hartwig.hmftools.patientdb.readers.LimsSampleReader used on opensource projects

Example 1 with LimsSampleReader

use of com.hartwig.hmftools.patientdb.readers.LimsSampleReader in project hmftools by hartwigmedical.

the class LoadClinicalData method readSamplesPerPatient.

@NotNull
private static Map<String, List<SampleData>> readSamplesPerPatient(@NotNull Lims lims, @NotNull List<RunContext> runContexts) {
    LimsSampleReader sampleReader = new LimsSampleReader(lims);
    final Set<String> sequencedPatientIdentifiers = Utils.sequencedPatientIds(runContexts).stream().filter(identifier -> identifier.startsWith("CPCT") || identifier.startsWith("DRUP")).collect(Collectors.toSet());
    Map<String, List<SampleData>> samplesPerPatient = Maps.newHashMap();
    for (String patientIdentifier : sequencedPatientIdentifiers) {
        List<String> sampleIds = getTumorSamplesForPatient(patientIdentifier, runContexts);
        samplesPerPatient.put(patientIdentifier, sampleReader.read(sampleIds));
    }
    return samplesPerPatient;
}