Examples with ResourceType org.hl7.fhir.dstu3.model.ResourceType used on opensource projects

Example 56 with ResourceType

use of org.hl7.fhir.dstu3.model.ResourceType in project CRD by HL7-DaVinci.

the class CdsConnectFileStore method processFhirFiles.

private void processFhirFiles(List<CdsConnectFile> files, String topic) {
    // process the fhir resource files
    // setup the proper FHIR Context for the version of FHIR we are dealing with
    FhirContext r4ctx = new org.hl7.davinci.r4.FhirComponents().getFhirContext();
    IParser r4parser = r4ctx.newJsonParser();
    // suppress the unknown element warnings
    r4parser.setParserErrorHandler(new SuppressParserErrorHandler());
    // process all of the files found within the topic/artifact
    for (CdsConnectFile file : files) {
        String path = file.getPath();
        String filename = file.getFilename();
        if (filename.endsWith(".json")) {
            logger.info("        process: FHIR Resource: " + filename);
            String[] parts = filename.split("-");
            if (parts.length > 2) {
                // String resourceType = parts[0];
                String fhirVersion = parts[1];
                String name = parts[2];
                IBaseResource baseResource = null;
                byte[] fileContents = file.getCqlBundle();
                if (fhirVersion.equalsIgnoreCase("R4")) {
                    baseResource = r4parser.parseResource(new ByteArrayInputStream(fileContents));
                }
                processFhirResource(baseResource, path, filename, fhirVersion, topic);
            }
        }
    }
}

Example 57 with ResourceType

use of org.hl7.fhir.dstu3.model.ResourceType in project CRD by HL7-DaVinci.

the class GitHubFileStore method processFhirFolder.

private void processFhirFolder(String topic, String fhirVersion, String fhirPath) {
    fhirVersion = fhirVersion.toUpperCase();
    logger.info("      GitHubFileStore::processFhirFolder(): " + fhirVersion + ": " + fhirPath);
    // setup the proper FHIR Context for the version of FHIR we are dealing with
    FhirContext ctx = null;
    if (fhirVersion.equalsIgnoreCase("R4")) {
        ctx = new org.hl7.davinci.r4.FhirComponents().getFhirContext();
    } else {
        logger.warn("unsupported FHIR version: " + fhirVersion + ", skipping folder");
        return;
    }
    IParser parser = ctx.newJsonParser();
    // suppress the unknown element warnings
    parser.setParserErrorHandler(new SuppressParserErrorHandler());
    for (String folder : connection.getDirectory(fhirPath)) {
        if (folder.equalsIgnoreCase("resources")) {
            String fullFolderPath = fhirPath + "/" + folder;
            for (String resource : connection.getDirectory(fullFolderPath)) {
                String filename = resource;
                String fullFilePath = fullFolderPath + "/" + filename;
                logger.info("        process: FHIR Resource: " + filename);
                String[] parts = filename.split("-");
                if (parts.length > 2) {
                    // = parts[0];
                    String resourceType;
                    if (!parts[1].equalsIgnoreCase(fhirVersion)) {
                        logger.warn("GitHubFileStore::processFhirFolder() warning: FhirVersion doesn't match!");
                        continue;
                    }
                    InputStream inputStream = connection.getFile(fullFilePath);
                    if (inputStream != null) {
                        IBaseResource baseResource = parser.parseResource(inputStream);
                        processFhirResource(baseResource, filename, filename, fhirVersion, topic);
                    } else {
                        logger.warn("could not find file: " + fullFilePath);
                        continue;
                    }
                }
            }
        }
    }
}

Example 58 with ResourceType

use of org.hl7.fhir.dstu3.model.ResourceType in project gpconnect-demonstrator by nhsconnect.

the class MedicationAdministrationResourceProvider method getMedicationAdministrationsForPatientId.

@Search
public List<MedicationAdministration> getMedicationAdministrationsForPatientId(@RequiredParam(name = "patient") String patientId) {
    ArrayList<MedicationAdministration> medicationAdministrations = new ArrayList<>();
    List<MedicationAdministrationDetail> medicationAdministrationDetailList = medicationAdministrationSearch.findMedicationAdministrationForPatient(Long.parseLong(patientId));
    if (medicationAdministrationDetailList != null && !medicationAdministrationDetailList.isEmpty()) {
        for (MedicationAdministrationDetail medicationAdministrationDetail : medicationAdministrationDetailList) {
            MedicationAdministration medicationAdministration = new MedicationAdministration();
            String resourceId = String.valueOf(medicationAdministrationDetail.getId());
            String versionId = String.valueOf(medicationAdministrationDetail.getLastUpdated().getTime());
            String resourceType = medicationAdministration.getResourceType().toString();
            IdType id = new IdType(resourceType, resourceId, versionId);
            medicationAdministration.setId(id);
            medicationAdministration.getMeta().setVersionId(versionId);
            medicationAdministration.getMeta().setLastUpdated(medicationAdministrationDetail.getLastUpdated());
            medicationAdministration.addDefinition(new Reference("Patient/" + medicationAdministrationDetail.getPatientId()));
            medicationAdministration.addDefinition(new Reference("Practitioner/" + medicationAdministrationDetail.getPractitionerId()));
            medicationAdministration.setPrescription(new Reference("MedicationOrder/" + medicationAdministrationDetail.getPrescriptionId()));
            medicationAdministration.setEffective(new DateType(medicationAdministrationDetail.getAdministrationDate()));
            medicationAdministration.setMedication(new Reference("Medication/" + medicationAdministrationDetail.getMedicationId()));
            medicationAdministrations.add(medicationAdministration);
        }
    }
    return medicationAdministrations;
}

Example 59 with ResourceType

use of org.hl7.fhir.dstu3.model.ResourceType in project gpconnect-demonstrator by nhsconnect.

the class MedicationOrderResourceProvider method medicationOrderDetailsToMedicationOrderResourceConverter.

private MedicationRequest medicationOrderDetailsToMedicationOrderResourceConverter(MedicationOrderDetails medicationOrderDetails) {
    MedicationRequest medicationOrder = new MedicationRequest();
    String resourceId = String.valueOf(medicationOrderDetails.getId());
    String versionId = String.valueOf(medicationOrderDetails.getLastUpdated().getTime());
    String resourceType = medicationOrder.getResourceType().toString();
    IdType id = new IdType(resourceType, resourceId, versionId);
    medicationOrder.setId(id);
    medicationOrder.getMeta().setVersionId(versionId);
    medicationOrder.getMeta().setLastUpdated(medicationOrderDetails.getLastUpdated());
    switch(medicationOrderDetails.getOrderStatus().toLowerCase(Locale.UK)) {
        case "active":
            medicationOrder.setStatus(MedicationRequestStatus.ACTIVE);
            break;
        case "completed":
            medicationOrder.setStatus(MedicationRequestStatus.COMPLETED);
            break;
        case "draft":
            medicationOrder.setStatus(MedicationRequestStatus.DRAFT);
            break;
        case "entered_in_error":
            medicationOrder.setStatus(MedicationRequestStatus.ENTEREDINERROR);
            break;
        case "on_hold":
            medicationOrder.setStatus(MedicationRequestStatus.ONHOLD);
            break;
        case "stopped":
            medicationOrder.setStatus(MedicationRequestStatus.STOPPED);
            break;
    }
    if (medicationOrderDetails.getPatientId() != null) {
        medicationOrder.setSubject(new Reference("Patient/" + medicationOrderDetails.getPatientId()));
    } else {
        medicationOrder.setSubject(new Reference());
    }
    medicationOrder.setRecorder(new Reference("Practitioner/" + medicationOrderDetails.getAutherId()));
    medicationOrder.setMedication(new Reference("Medication/" + medicationOrderDetails.getMedicationId()));
    medicationOrder.addDosageInstruction().setText(medicationOrderDetails.getDosageText());
    MedicationRequestDispenseRequestComponent dispenseRequest = new MedicationRequestDispenseRequestComponent();
    dispenseRequest.addExtension(new Extension(SystemURL.SD_EXTENSION_MEDICATION_QUANTITY_TEXT, new StringDt(medicationOrderDetails.getDispenseQuantityText())));
    dispenseRequest.addExtension(new Extension(SystemURL.SD_EXTENSION_PERSCRIPTION_REPEAT_REVIEW_DATE, new DateTimeDt(medicationOrderDetails.getDispenseReviewDate())));
    dispenseRequest.setId("Medication/" + medicationOrderDetails.getDispenseMedicationId());
    dispenseRequest.setNumberOfRepeatsAllowed(medicationOrderDetails.getDispenseRepeatsAllowed());
    medicationOrder.setDispenseRequest(dispenseRequest);
    return medicationOrder;
}

Example 60 with ResourceType

use of org.hl7.fhir.dstu3.model.ResourceType in project gpconnect-demonstrator by nhsconnect.

the class MedicationResourceProvider method getMedicationById.

@Read()
public Medication getMedicationById(@IdParam IdType medicationId) {
    MedicationEntity medicationEntity = medicationRepository.findOne(medicationId.getIdPartAsLong());
    if (medicationEntity == null) {
        OperationOutcome operationalOutcome = new OperationOutcome();
        operationalOutcome.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics("No medication details found for ID: " + medicationId.getIdPart());
        throw new InternalErrorException("No medication details found for ID: " + medicationId.getIdPart(), operationalOutcome);
    }
    Medication medication = new Medication();
    String resourceId = String.valueOf(medicationEntity.getId());
    String versionId = String.valueOf(medicationEntity.getLastUpdated().getTime());
    String resourceType = medication.getResourceType().toString();
    IdType id = new IdType(resourceType, resourceId, versionId);
    medication.setId(id);
    medication.getMeta().setVersionId(versionId);
    medication.getMeta().setLastUpdated(medicationEntity.getLastUpdated());
    return medication;
}