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

Example 21 with Patient

use of org.hl7.fhir.dstu3.model.Patient in project loinc2hpo by monarch-initiative.

the class FhirResourceRetriever method retrievePatientFromServer.

/**
 * Retrieve a patient from the reference field of an observation
 * @param subject
 * @return
 */
public static Patient retrievePatientFromServer(Reference subject) throws SubjectNotFoundException, AmbiguousSubjectException {
    List<Patient> patients = new ArrayList<>();
    if (subject.hasReference()) {
        String ref = subject.getReference();
        if (!ref.startsWith(BASEURL) && ref.startsWith("Patient")) {
            ref = BASEURL + "/" + ref;
        }
        Bundle patientBundle = client.search().byUrl(ref).returnBundle(Bundle.class).execute();
        while (true) {
            patientBundle.getEntry().forEach(p -> patients.add((Patient) p.getResource()));
            if (patientBundle.getLink(IBaseBundle.LINK_NEXT) != null) {
                patientBundle = client.loadPage().next(patientBundle).execute();
            } else {
                break;
            }
        }
    } else if (subject.hasIdentifier()) {
        Identifier identifier = subject.getIdentifier();
    // TODO: find patient through the identifier
    }
    if (patients.size() == 1) {
        return patients.iterator().next();
    } else if (patients.isEmpty()) {
        throw new SubjectNotFoundException("Expect one subject, but found none");
    } else {
        throw new AmbiguousSubjectException("Except one subject, but found multiple");
    }
}

Example 22 with Patient

use of org.hl7.fhir.dstu3.model.Patient in project loinc2hpo by monarch-initiative.

the class FhirResourceRetriever method retrieveObservationFromServer.

/**
 * @TODO: implement it
 * retrieve a patient's observations from FHIR server
 * @param patient
 * @return
 */
public static List<Observation> retrieveObservationFromServer(Patient patient) {
    List<Observation> observationList = new ArrayList<>();
    String id = patient.getId();
    if (id != null) {
        Bundle observationBundle = client.search().forResource(Observation.class).where(new ReferenceClientParam("subject").hasId(id)).prettyPrint().returnBundle(Bundle.class).execute();
        while (true) {
            observationBundle.getEntry().forEach(p -> observationList.add((Observation) p.getResource()));
            if (observationBundle.getLink(IBaseBundle.LINK_NEXT) != null) {
                observationBundle = client.loadPage().next(observationBundle).execute();
            } else {
                break;
            }
        }
    }
    return observationList;
}

Example 23 with Patient

use of org.hl7.fhir.dstu3.model.Patient in project syndesis-qe by syndesisio.

the class FhirUtils method insertPatientToFhir.

// entity PATIENT:
public String insertPatientToFhir(MyPatientSpecification ps) {
    Patient patient = new Patient();
    patient.addName().setFamily(ps.getFamilyName()).addGiven(ps.getGivenName());
    checkConnection();
    MethodOutcome outcome = fhirClient.createPatient(patient);
    lastPatientId = this.extractSimpleId(outcome.getId().getValue(), FhirEntity.PATIENT.getName());
    log.info("Patient *{}* has been inserted with id:*{}*", ps.toString(), lastPatientId);
    return lastPatientId;
}

Example 24 with Patient

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

the class MedicationStatementResourceProvider method getMedicationStatementResource.

public MedicationStatement getMedicationStatementResource(MedicationStatementDetail statementDetail) {
    MedicationStatement medicationStatement = new MedicationStatement();
    medicationStatement.setId(statementDetail.getId().toString());
    List<Identifier> identifiers = new ArrayList<>();
    Identifier identifier = new Identifier().setSystem("https://fhir.nhs.uk/Id/cross-care-setting-identifier").setValue(statementDetail.getGuid());
    identifiers.add(identifier);
    medicationStatement.setIdentifier(identifiers);
    medicationStatement.setMeta(new Meta().addProfile(SystemURL.SD_GPC_MEDICATION_STATEMENT));
    medicationStatement.addExtension(new Extension(SystemURL.SD_CC_EXT_MEDICATION_STATEMENT_LAST_ISSUE, new DateTimeType(statementDetail.getLastIssueDate(), TemporalPrecisionEnum.DAY)));
    if (statementDetail.getMedicationRequestPlanId() != null) {
        medicationStatement.addBasedOn(new Reference(new IdType("MedicationRequest", statementDetail.getMedicationRequestPlanId())));
    }
    try {
        medicationStatement.setStatus(MedicationStatementStatus.fromCode(statementDetail.getStatusCode()));
    } catch (FHIRException e) {
        throw new UnprocessableEntityException(e.getMessage());
    }
    if (statementDetail.getMedicationId() != null) {
        medicationStatement.setMedication(new Reference(new IdType("Medication", statementDetail.getMedicationId())));
    }
    medicationStatement.setEffective(new Period().setStart(statementDetail.getStartDate()).setEnd(statementDetail.getEndDate()));
    medicationStatement.setDateAsserted(statementDetail.getDateAsserted());
    if (statementDetail.getPatientId() != null)
        medicationStatement.setSubject(new Reference(new IdType("Patient", statementDetail.getPatientId())));
    try {
        medicationStatement.setTaken(statementDetail.getTakenCode() != null ? MedicationStatementTaken.fromCode(statementDetail.getTakenCode()) : MedicationStatementTaken.UNK);
    } catch (FHIRException e) {
        throw new UnprocessableEntityException(e.getMessage());
    }
    setReasonCodes(medicationStatement, statementDetail);
    setNotes(medicationStatement, statementDetail);
    String dosageText = statementDetail.getDosageText();
    medicationStatement.addDosage(new Dosage().setText(dosageText == null || dosageText.trim().isEmpty() ? NO_INFORMATION_AVAILABLE : dosageText).setPatientInstruction(statementDetail.getDosagePatientInstruction()));
    String prescribingAgency = statementDetail.getPrescribingAgency();
    if (prescribingAgency != null && !prescribingAgency.trim().isEmpty()) {
        String prescribingAgencyDisplay = "";
        if (prescribingAgency.equalsIgnoreCase("prescribed-at-gp-practice")) {
            prescribingAgencyDisplay = "Prescribed at GP practice";
        } else if (prescribingAgency.equalsIgnoreCase("prescribed-by-another-organisation")) {
            prescribingAgencyDisplay = "Prescribed by another organisation";
        }
        Coding coding = new Coding(SystemURL.CS_CC_PRESCRIBING_AGENCY_STU3, prescribingAgency, prescribingAgencyDisplay);
        CodeableConcept codeableConcept = new CodeableConcept().addCoding(coding);
        medicationStatement.addExtension(new Extension(SystemURL.SD_EXTENSION_CC_PRESCRIBING_AGENCY, codeableConcept));
    }
    // #281 1.2.5 add dosageLastChanged
    Date dosageLastChanged = statementDetail.getDosageLastChanged();
    if (dosageLastChanged != null) {
        medicationStatement.addExtension(new Extension(SystemURL.SD_EXTENSION_CC_DOSAGE_LAST_CHANGED, new DateTimeType(dosageLastChanged)));
    }
    return medicationStatement;
}

Example 25 with Patient

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

the class PatientResourceProvider method registerPatientResourceConverterToPatientDetail.

private PatientDetails registerPatientResourceConverterToPatientDetail(Patient patientResource) {
    PatientDetails patientDetails = new PatientDetails();
    HumanName name = patientResource.getNameFirstRep();
    String givenNames = name.getGiven().stream().map(n -> n.getValue()).collect(Collectors.joining(","));
    patientDetails.setForename(givenNames);
    patientDetails.setSurname(name.getFamily());
    patientDetails.setDateOfBirth(patientResource.getBirthDate());
    if (patientResource.getGender() != null) {
        patientDetails.setGender(patientResource.getGender().toString());
    }
    patientDetails.setNhsNumber(patientResource.getIdentifierFirstRep().getValue());
    DateTimeType deceased = (DateTimeType) patientResource.getDeceased();
    if (deceased != null) {
        try {
            patientDetails.setDeceased((deceased.getValue()));
        } catch (ClassCastException cce) {
            throwUnprocessableEntity422_InvalidResourceException("The multiple deceased property is expected to be a datetime");
        }
    }
    // activate patient as temporary
    patientDetails.setRegistrationStartDateTime(new Date());
    // patientDetails.setRegistrationEndDateTime(getRegistrationEndDate(patientResource));
    patientDetails.setRegistrationStatus(ACTIVE_REGISTRATION_STATUS);
    patientDetails.setRegistrationType(TEMPORARY_RESIDENT_REGISTRATION_TYPE);
    updateAddressAndTelecom(patientResource, patientDetails);
    // set some standard values for defaults, ensure managing org is always returned
    // added at 1.2.2 7 is A20047 the default GP Practice
    patientDetails.setManagingOrganization("7");
    return patientDetails;
}