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

Example 1 with PatientReader

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

the class LoadClinicalData method writeClinicalData.

private static void writeClinicalData(@NotNull final Options clinicalOptions, @NotNull final CommandLine cmd, @NotNull final List<RunContext> runContexts, @NotNull final DatabaseAccess dbAccess) throws IOException, XMLStreamException {
    final String ecrfFilePath = cmd.getOptionValue(ECRF_FILE);
    final String limsJson = cmd.getOptionValue(LIMS_JSON);
    final String preLIMSArrivalDatesCsv = cmd.getOptionValue(PRE_LIMS_ARRIVAL_DATES_CSV);
    final String formStatusCsv = cmd.getOptionValue(FORM_STATUS_CSV);
    final String csvOutputDir = cmd.getOptionValue(CSV_OUT_DIR);
    final Optional<String> cancerTypesLink = Optional.ofNullable(cmd.getOptionValue(CANCER_TYPES_LINK));
    final Optional<String> portalDataLink = Optional.ofNullable(cmd.getOptionValue(PORTAL_DATA_LINK));
    if (Utils.anyNull(ecrfFilePath, limsJson, preLIMSArrivalDatesCsv, formStatusCsv, csvOutputDir)) {
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("patient-db", clinicalOptions);
    } else {
        LOGGER.info("Clearing database...");
        dbAccess.clearClinicalTables();
        LOGGER.info("Cleared database, loading samples from LIMS...");
        Lims lims = LimsFactory.fromLimsJsonWithPreLIMSArrivalDates(limsJson, preLIMSArrivalDatesCsv);
        Map<String, List<SampleData>> samplesPerPatient = readSamplesPerPatient(lims, runContexts);
        LOGGER.info("Loaded samples for {} patients from LIMS, loading ecrf...", samplesPerPatient.size());
        FormStatusModel formStatusModel = FormStatusReader.buildModelFromCsv(formStatusCsv);
        CpctEcrfModel ecrfModel = CpctEcrfModel.loadFromXML(ecrfFilePath, formStatusModel);
        TreatmentCurator treatmentCurator = TreatmentCurator.fromProductionResource();
        TumorLocationCurator tumorLocationCurator = TumorLocationCurator.fromProductionResource();
        PatientReader patientReader = new PatientReader(ecrfModel, treatmentCurator, tumorLocationCurator);
        final Map<String, Patient> readPatients = readEcrfPatients(patientReader, ecrfModel.patients(), samplesPerPatient);
        LOGGER.info("Loaded {} patients from ecrf", readPatients.size());
        DumpClinicalData.writeClinicalDumps(csvOutputDir, readPatients.values(), cancerTypesLink, portalDataLink);
        LOGGER.info("Writing clinical data for {} sequenced patients.", readPatients.size());
        for (final String patientIdentifier : samplesPerPatient.keySet()) {
            final Patient patient = readPatients.get(patientIdentifier);
            if (patient == null) {
                if (patientIdentifier.startsWith("CPCT")) {
                    LOGGER.error("Could not find patient with id: " + patientIdentifier + " in ecrf file.");
                }
                dbAccess.writeSampleClinicalData(patientIdentifier, samplesPerPatient.get(patientIdentifier));
            } else {
                dbAccess.writeFullClinicalData(patient);
                final List<ValidationFinding> findings = PatientValidator.validatePatient(patient);
                dbAccess.writeValidationFindings(findings);
                dbAccess.writeValidationFindings(patient.matchFindings());
            }
        }
        dbAccess.writeValidationFindings(CurationValidator.validateTreatmentCurator(treatmentCurator));
        dbAccess.writeValidationFindings(CurationValidator.validateTumorLocationCurator(tumorLocationCurator));
        LOGGER.info("Done!");
    }
}