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

Example 16 with Reference

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

the class FhirObservationAnalyzer method getHPO4ObservationOutcome.

/**
 * A core function that tries three ways to return a LabTestResultInHPO object:
 * first, it tries to return the result through the interpretation field. If it fails,
 * second, it tries to return the result through the quantative value, or
 * third, it tries to return the retult through the coded value (ordinal Loinc)
 * @param loinc2HPOannotationMap
 * @param loincIds
 * @return
 */
public static LabTestResultInHPO getHPO4ObservationOutcome(HashSet<LoincId> loincIds, Map<LoincId, UniversalLoinc2HPOAnnotation> loinc2HPOannotationMap) {
    // first make sure the observation has a valid loinc code; otherwise, we cannot handle it
    if (!hasValidLoincCode(loincIds)) {
        // TODO: consider handling this as a future project
        return null;
    }
    LoincId loincId = null;
    try {
        loincId = getLoincIdOfObservation();
    } catch (MalformedLoincCodeException e) {
        logger.error("malformed loinc code; should never happen");
        return null;
    } catch (LoincCodeNotFoundException e) {
        logger.error("No loinc code was found in the observation; should never happen");
        return null;
    } catch (UnsupportedCodingSystemException e) {
        logger.error("coding system not recognized");
        return null;
    }
    if (!loinc2HPOannotationMap.containsKey(loincId)) {
        return null;
    }
    if (observation.hasInterpretation()) {
        logger.debug("enter analyzer using the interpretation field");
        try {
            // return getHPOFromInterpretation(observation.getInterpretation(), loinc2HPOannotationMap);
            HpoTermId4LoincTest hpoterm = new ObservationAnalysisFromInterpretation(getLoincIdOfObservation(), observation.getInterpretation(), loinc2HPOannotationMap).getHPOforObservation();
            return new BasicLabTestResultInHPO(hpoterm, null);
        } catch (UnrecognizedCodeException e) {
            // this means the interpretation code is not recognized
            logger.info("The interpretation codes for this loinc code is not annotated; system will try using raw values");
        } catch (MalformedLoincCodeException e1) {
            // not going to happen
            logger.error("malformed loinc code.");
            return null;
        } catch (LoincCodeNotFoundException e2) {
            // not going to happen
            logger.error("no loinc code is found in the observation");
            return null;
        } catch (UnsupportedCodingSystemException e3) {
            // not going to happen
            logger.error("The interpretation coding system cannot be recognized.");
            return null;
        } catch (AmbiguousResultsFoundException e) {
            logger.error("The observation has conflicting interpretation codes.");
            return null;
        } catch (AnnotationNotFoundException e) {
            logger.error("There is no annotation for the loinc code used in the observation");
        }
    }
    // Qn will have a value field
    if (observation.hasValueQuantity()) {
        try {
            HpoTermId4LoincTest hpoterm = new ObservationAnalysisFromQnValue(loincId, observation, loinc2HPOannotationMap).getHPOforObservation();
            if (hpoterm != null)
                return new BasicLabTestResultInHPO(hpoterm, null);
        } catch (ReferenceNotFoundException e) {
            // if there is no reference
            logger.error("The observation has no reference field.");
        // TODO: make a list of our own references
        } catch (AmbiguousReferenceException e) {
            logger.info("There are two reference ranges or more");
        } catch (UnrecognizedCodeException e) {
            logger.error("uncognized coding system");
        }
    }
    // Ord will have a ValueCodeableConcept field
    if (observation.hasValueCodeableConcept()) {
        try {
            HpoTermId4LoincTest hpoterm = null;
            hpoterm = new ObservationAnalysisFromCodedValues(loincId, observation.getValueCodeableConcept(), loinc2HPOannotationMap).getHPOforObservation();
            if (hpoterm != null)
                return new BasicLabTestResultInHPO(hpoterm, null);
        } catch (AmbiguousResultsFoundException e) {
            logger.error("multiple results are found");
        } catch (UnrecognizedCodeException e) {
            logger.error("unrecognized codes");
        } catch (FHIRException e) {
            // not going to happen
            logger.error("Could not get HPO term from coded value");
        } catch (AnnotationNotFoundException e) {
            logger.error("There is no annotation for the loinc code used in the observation");
        }
    }
    // if all the above fails, we cannot do nothing
    logger.error("Could not return HPO for observation: " + observation.getId());
    return null;
}

Example 17 with Reference

use of org.hl7.fhir.dstu3.model.Reference 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 18 with Reference

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

the class LocationResourceProvider method locationDetailsToLocation.

/**
 * convert locationDetails to fhir resource
 * @param locationDetails
 * @return Location resource
 */
private Location locationDetailsToLocation(LocationDetails locationDetails) {
    Location location = new Location();
    String resourceId = String.valueOf(locationDetails.getId());
    String versionId = String.valueOf(locationDetails.getLastUpdated().getTime());
    String resourceType = location.getResourceType().toString();
    IdType id = new IdType(resourceType, resourceId, versionId);
    location.setId(id);
    location.getMeta().setVersionId(versionId);
    location.getMeta().setLastUpdated(locationDetails.getLastUpdated());
    location.getMeta().addProfile(SystemURL.SD_GPC_LOCATION);
    location.setName(locationDetails.getName());
    // #207 no site code
    // location.setIdentifier(Collections.singletonList(new Identifier().setSystem(SystemURL.ID_ODS_SITE_CODE).setValue(locationDetails.getSiteOdsCode())));
    // #246 remove type element
    // Coding locationCommTypeCode = new Coding();
    // locationCommTypeCode.setCode("COMM");
    // locationCommTypeCode.setSystem(SystemURL.VS_CC_SER_DEL_LOCROLETYPE);
    // locationCommTypeCode.setDisplay("Community Location");
    // 
    // Coding locationGachTypeCode = new Coding();
    // locationGachTypeCode.setCode("GACH");
    // locationGachTypeCode.setSystem(SystemURL.VS_CC_SER_DEL_LOCROLETYPE);
    // locationGachTypeCode.setDisplay("Hospitals; General Acute Care Hospital");
    // 
    // @SuppressWarnings("deprecation")
    // CodeableConcept locationType = new CodeableConcept();
    // locationType.addCoding(locationCommTypeCode);
    // locationType.addCoding(locationGachTypeCode);
    // location.setType(locationType);
    Organization orgz = FindOrganization(locationDetails.getOrgOdsCode());
    if (orgz != null) {
        Reference mngOrg = new Reference();
        mngOrg.setReference(orgz.getId());
        // #246 remove display element
        // mngOrg.setDisplay(orgz.getName());
        location.setManagingOrganization(mngOrg);
    }
    EnumSet<LocationStatus> statusList = EnumSet.allOf(LocationStatus.class);
    LocationStatus locationStatus = null;
    String status = locationDetails.getStatus();
    if (status != null) {
        for (LocationStatus statusItem : statusList) {
            if (statusItem.toCode().equalsIgnoreCase(status)) {
                locationStatus = statusItem;
                break;
            }
        }
    }
    location.setAddress(createAddress(locationDetails));
    location.setStatus(locationStatus);
    return location;
}

Example 19 with Reference

use of org.hl7.fhir.dstu3.model.Reference 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 20 with Reference

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

the class PopulateSlotBundle method populateBundle.

/**
 * @param bundle Bundle resource to populate
 * @param operationOutcome
 * @param planningHorizonStart Date
 * @param planningHorizonEnd Date
 * @param actorPractitioner boolean
 * @param actorLocation boolean
 * @param managingOrganisation boolean
 * @param bookingOdsCode String
 * @param bookingOrgType String eg "urgent-care"
 */
public void populateBundle(Bundle bundle, OperationOutcome operationOutcome, Date planningHorizonStart, Date planningHorizonEnd, boolean actorPractitioner, boolean actorLocation, boolean managingOrganisation, String bookingOdsCode, String bookingOrgType) {
    bundle.getMeta().addProfile(SystemURL.SD_GPC_SRCHSET_BUNDLE);
    // TODO remove hard coding pick up from providerRouting.json ?
    final String OUR_ODS_CODE = "A20047";
    // find all locations for this ODS practice code and construct Resources for them
    // #144 generalise to handle 1..n locations for a practice
    HashMap<String, BundleEntryComponent> locationEntries = new HashMap<>();
    for (LocationDetails aLocationDetail : locationSearch.findAllLocations()) {
        if (aLocationDetail.getOrgOdsCode().equals(OUR_ODS_CODE)) {
            Location aLocationResource = locationResourceProvider.getLocationById(new IdType(aLocationDetail.getId()));
            BundleEntryComponent locationEntry = new BundleEntryComponent();
            locationEntry.setResource(aLocationResource);
            // #202 use full urls
            // #215 full url removed completely
            // locationEntry.setFullUrl(serverBaseUrl + "Location/" + aLocationResource.getIdElement().getIdPart());
            locationEntries.put(aLocationResource.getIdElement().getIdPart(), locationEntry);
        }
    }
    // find the provider organization from the ods code
    List<OrganizationDetails> ourOrganizationsDetails = organizationSearch.findOrganizationDetailsByOrgODSCode(OUR_ODS_CODE);
    OrganizationDetails ourOrganizationDetails = null;
    if (!ourOrganizationsDetails.isEmpty()) {
        // at 1.2.2 these are added regardless of the status of the relevant parameter
        // Just picks the first organization. There should only be one.
        ourOrganizationDetails = ourOrganizationsDetails.get(0);
    } else {
    // do something here .. should never happen
    }
    // find the bookng organization from the ods code
    List<OrganizationDetails> bookingOrganizationsDetails = organizationSearch.findOrganizationDetailsByOrgODSCode(bookingOdsCode);
    OrganizationDetails bookingOrganizationDetails = null;
    if (!bookingOrganizationsDetails.isEmpty()) {
        // at 1.2.2 these are added regardless of the status of the relevant parameter
        // Just picks the first organization. There should only be one.
        bookingOrganizationDetails = bookingOrganizationsDetails.get(0);
    }
    HashSet<BundleEntryComponent> addedSchedule = new HashSet<>();
    HashSet<BundleEntryComponent> addedLocation = new HashSet<>();
    HashSet<String> addedPractitioner = new HashSet<>();
    HashSet<String> addedOrganization = new HashSet<>();
    // issue #165 don't add duplicate slots, hashSet contains slot id as String
    HashSet<String> addedSlot = new HashSet<>();
    // #144 process all locations
    for (String locationId : locationEntries.keySet()) {
        // process the schedules
        for (Schedule schedule : scheduleResourceProvider.getSchedulesForLocationId(locationId, planningHorizonStart, planningHorizonEnd)) {
            boolean slotsAdded = false;
            schedule.getMeta().addProfile(SystemURL.SD_GPC_SCHEDULE);
            BundleEntryComponent scheduleEntry = new BundleEntryComponent();
            scheduleEntry.setResource(schedule);
            // #202 use full urls
            // #215 full url removed completely
            // scheduleEntry.setFullUrl(serverBaseUrl + "Schedule/" + schedule.getIdElement().getIdPart());
            // This Set does not work as expected because Slot does not implement hashCode
            // so the second set call to getSlots returns different objects with the same slot id
            Set<Slot> slots = new HashSet<>();
            // 
            if (bookingOrgType.isEmpty() && bookingOdsCode.isEmpty()) {
                // OPTION 1 get slots Specfying  neither org type nor org code
                slots.addAll(slotResourceProvider.getSlotsForScheduleIdNoOrganizationTypeOrODS(schedule.getIdElement().getIdPart(), planningHorizonStart, planningHorizonEnd));
            } else if (!bookingOrgType.isEmpty() && bookingOdsCode.isEmpty()) {
                // OPTION 2 organisation type only
                for (Slot slot : slotResourceProvider.getSlotsForScheduleId(schedule.getIdElement().getIdPart(), planningHorizonStart, planningHorizonEnd)) {
                    SlotDetail slotDetail = slotSearch.findSlotByID(Long.parseLong(slot.getId()));
                    if (slotDetail.getOrganizationIds().isEmpty() && (slotDetail.getOrganizationTypes().isEmpty() || slotDetail.getOrganizationTypes().contains(bookingOrgType))) {
                        slots.add(slot);
                    }
                }
            } else if (!bookingOdsCode.isEmpty() && bookingOrgType.isEmpty()) {
                // OPTION 3 org code only
                for (Slot slot : slotResourceProvider.getSlotsForScheduleId(schedule.getIdElement().getIdPart(), planningHorizonStart, planningHorizonEnd)) {
                    SlotDetail slotDetail = slotSearch.findSlotByID(Long.parseLong(slot.getId()));
                    if (slotDetail.getOrganizationTypes().isEmpty() && (slotDetail.getOrganizationIds().isEmpty() || bookingOrganizationDetails != null && slotDetail.getOrganizationIds().contains(bookingOrganizationDetails.getId()))) {
                        slots.add(slot);
                    }
                }
            } else if (!bookingOrgType.isEmpty() && !bookingOdsCode.isEmpty()) {
                // OPTION 4 both org code and org type
                for (Slot slot : slotResourceProvider.getSlotsForScheduleId(schedule.getIdElement().getIdPart(), planningHorizonStart, planningHorizonEnd)) {
                    SlotDetail slotDetail = slotSearch.findSlotByID(Long.parseLong(slot.getId()));
                    if (((slotDetail.getOrganizationTypes().isEmpty() || slotDetail.getOrganizationTypes().contains(bookingOrgType))) && (slotDetail.getOrganizationIds().isEmpty() || bookingOrganizationDetails != null && slotDetail.getOrganizationIds().contains(bookingOrganizationDetails.getId()))) {
                        slots.add(slot);
                    }
                }
            }
            // added at 1.2.2 add the organisation but only if there are some slots available
            if (slots.size() > 0 && ourOrganizationDetails != null && !addedOrganization.contains(ourOrganizationDetails.getOrgCode())) {
                addOrganisation(ourOrganizationDetails, bundle);
                addedOrganization.add(ourOrganizationDetails.getOrgCode());
            }
            String freeBusyType = "FREE";
            // process all the slots to be returned
            for (Slot slot : slots) {
                if (freeBusyType.equalsIgnoreCase(slot.getStatus().toString())) {
                    String slotId = slot.getIdElement().getIdPart();
                    if (!addedSlot.contains(slotId)) {
                        BundleEntryComponent slotEntry = new BundleEntryComponent();
                        slotEntry.setResource(slot);
                        // #202 use full urls
                        // #215 full url removed completely
                        // slotEntry.setFullUrl(serverBaseUrl + "Slot/" + slotId);
                        bundle.addEntry(slotEntry);
                        addedSlot.add(slotId);
                        slotsAdded = true;
                    }
                    if (!addedSchedule.contains(scheduleEntry)) {
                        // only add a schedule if there's a reference to it and only add it once
                        bundle.addEntry(scheduleEntry);
                        addedSchedule.add(scheduleEntry);
                    }
                    if (actorLocation == true) {
                        // only add a unique location once
                        if (!addedLocation.contains(locationEntries.get(locationId))) {
                            bundle.addEntry(locationEntries.get(locationId));
                            addedLocation.add(locationEntries.get(locationId));
                        }
                    }
                }
            // if free/busy status matches
            }
            // # 193 for each schedule only add a practitioner if there have been some slots added.
            if (slotsAdded) {
                // practitioners for this schedule
                List<Reference> practitionerActors = scheduleResourceProvider.getPractitionerReferences(schedule);
                if (!practitionerActors.isEmpty()) {
                    for (Reference practitionerActor : practitionerActors) {
                        Practitioner practitioner = practitionerResourceProvider.getPractitionerById((IdType) practitionerActor.getReferenceElement());
                        if (practitioner == null) {
                            Coding errorCoding = new Coding().setSystem(SystemURL.VS_GPC_ERROR_WARNING_CODE).setCode(SystemCode.REFERENCE_NOT_FOUND);
                            CodeableConcept errorCodableConcept = new CodeableConcept().addCoding(errorCoding);
                            errorCodableConcept.setText("Invalid Reference");
                            operationOutcome.addIssue().setSeverity(IssueSeverity.ERROR).setCode(IssueType.NOTFOUND).setDetails(errorCodableConcept);
                            throw new ResourceNotFoundException("Practitioner Reference returning null");
                        }
                        if (actorPractitioner) {
                            if (!addedPractitioner.contains(practitioner.getIdElement().getIdPart())) {
                                addPractitioner(practitioner, bundle);
                                addedPractitioner.add(practitioner.getIdElement().getIdPart());
                            }
                        }
                    }
                // for practitioner
                }
            // if non empty practitioner list
            }
        // if slots added
        }
    // for schedules
    }
// for location
}