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

Example 6 with Resource

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

the class PopulateSlotBundle method addOrganisation.

/**
 * Add OrganizationResource to Bundle
 *
 * @param organization OrganizationDetails object to add to bundle
 * @param bundle Bundle Resource to add organisation to
 */
private void addOrganisation(OrganizationDetails organization, Bundle bundle) {
    BundleEntryComponent organizationEntry = new BundleEntryComponent();
    Long organizationId = organization.getId();
    OrganizationDetails organizationDetails = organizationSearch.findOrganizationDetails(organizationId);
    Organization organizationResource = organizationResourceProvider.convertOrganizationDetailsToOrganization(organizationDetails);
    organizationEntry.setResource(organizationResource);
    // #202 use full urls
    // #215 full url removed completely
    // organizationEntry.setFullUrl(serverBaseUrl + "Organization/" + organization.getId());
    bundle.addEntry(organizationEntry);
}

Example 7 with Resource

use of org.hl7.fhir.dstu3.model.Resource in project bunsen by cerner.

the class Functions method toBundle.

/**
 * Returns a bundle containing all resources in the dataset. This should be used
 * with caution for large datasets, since the returned bundle will include all data.
 *
 * @param dataset a dataset of FHIR resoruces
 * @return a bundle containing those resources.
 */
public static Bundle toBundle(Dataset<? extends Resource> dataset) {
    List<Resource> resources = (List<Resource>) dataset.collectAsList();
    Bundle bundle = new Bundle();
    for (Resource resource : resources) {
        bundle.addEntry().setResource(resource);
    }
    return bundle;
}

Example 8 with Resource

use of org.hl7.fhir.dstu3.model.Resource 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 9 with Resource

use of org.hl7.fhir.dstu3.model.Resource 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
}

Example 10 with Resource

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

the class StructuredAllergyIntoleranceBuilder method buildStructuredAllergyIntolerence.

public Bundle buildStructuredAllergyIntolerence(String NHS, Set<String> practitionerIds, Bundle bundle, Boolean includedResolved) {
    List<StructuredAllergyIntoleranceEntity> allergyData = structuredAllergySearch.getAllergyIntollerence(NHS);
    ListResource activeList = initiateListResource(NHS, ACTIVE_ALLERGIES_DISPLAY, allergyData);
    ListResource resolvedList = initiateListResource(NHS, RESOLVED_ALLERGIES_DISPLAY, allergyData);
    // This is patient 5 example 2 only
    if (allergyData.size() == 1 && allergyData.get(0).getClinicalStatus().equals(SystemConstants.NO_KNOWN)) {
        StructuredAllergyIntoleranceEntity noKnownAllergy = allergyData.get(0);
        // #214 had incorrect code and value for no known allergies
        CodeableConcept noKnownAllergies = createCoding(SystemURL.VS_LIST_EMPTY_REASON_CODE, NO_CONTENT_RECORDED, NO_CONTENT_RECORDED_DISPLAY);
        noKnownAllergies.setText("No Known Allergies");
        // activeList.setEmptyReason(noKnownAllergies);
        // see spec example 2 no known allergies positively asserted
        Reference patient = new Reference(SystemConstants.PATIENT_REFERENCE_URL + allergyData.get(0).getPatientRef());
        String noKnownAllergyId = noKnownAllergy.getGuid();
        Reference allergyIntolerance = new Reference("AllergyIntolerance/" + noKnownAllergyId);
        Resource noKnownAllergyResource = createNoKnownAllergy(noKnownAllergy);
        activeList.setSubject(patient);
        // reference to AllergyIntolerance item
        activeList.addEntry().setItem(allergyIntolerance);
        activeList.setOrderedBy(createCoding(SystemURL.CS_LIST_ORDER, "event-date", "Sorted by Event Date"));
        bundle.addEntry().setResource(activeList);
        bundle.addEntry().setResource(noKnownAllergyResource);
        if (includedResolved) {
            resolvedList.setSubject(patient);
            resolvedList.setEmptyReason(noKnownAllergies);
            bundle.addEntry().setResource(resolvedList);
        }
        return bundle;
    }
    for (StructuredAllergyIntoleranceEntity allergyIntoleranceEntity : allergyData) {
        AllergyIntolerance allergyIntolerance = new AllergyIntolerance();
        allergyIntolerance.setOnset(new DateTimeType(allergyIntoleranceEntity.getOnSetDateTime()));
        allergyIntolerance.setMeta(createMeta(SystemURL.SD_CC_ALLERGY_INTOLERANCE));
        allergyIntolerance.setId(allergyIntoleranceEntity.getId().toString());
        List<Identifier> identifiers = new ArrayList<>();
        Identifier identifier1 = new Identifier().setSystem("https://fhir.nhs.uk/Id/cross-care-setting-identifier").setValue(allergyIntoleranceEntity.getGuid());
        identifiers.add(identifier1);
        allergyIntolerance.setIdentifier(identifiers);
        if (allergyIntoleranceEntity.getClinicalStatus().equals(SystemConstants.ACTIVE)) {
            allergyIntolerance.setClinicalStatus(AllergyIntoleranceClinicalStatus.ACTIVE);
        } else {
            allergyIntolerance.setClinicalStatus(AllergyIntoleranceClinicalStatus.RESOLVED);
        }
        if (allergyIntoleranceEntity.getCategory().equals(SystemConstants.MEDICATION)) {
            allergyIntolerance.addCategory(AllergyIntoleranceCategory.MEDICATION);
        } else {
            allergyIntolerance.addCategory(AllergyIntoleranceCategory.ENVIRONMENT);
        }
        allergyIntolerance.setVerificationStatus(AllergyIntoleranceVerificationStatus.UNCONFIRMED);
        // CODE
        codeableConceptBuilder.addConceptCode(SystemConstants.SNOMED_URL, allergyIntoleranceEntity.getConceptCode(), allergyIntoleranceEntity.getConceptDisplay()).addDescription(allergyIntoleranceEntity.getDescCode(), allergyIntoleranceEntity.getDescDisplay()).addTranslation(allergyIntoleranceEntity.getCodeTranslationRef());
        allergyIntolerance.setCode(codeableConceptBuilder.build());
        codeableConceptBuilder.clear();
        allergyIntolerance.setAssertedDate(allergyIntoleranceEntity.getAssertedDate());
        Reference patient = new Reference(SystemConstants.PATIENT_REFERENCE_URL + allergyIntoleranceEntity.getPatientRef());
        allergyIntolerance.setPatient(patient);
        Annotation noteAnnotation = new Annotation(new StringType(allergyIntoleranceEntity.getNote()));
        allergyIntolerance.setNote(Collections.singletonList(noteAnnotation));
        AllergyIntoleranceReactionComponent reaction = new AllergyIntoleranceReactionComponent();
        // MANIFESTATION
        List<CodeableConcept> theManifestation = new ArrayList<>();
        codeableConceptBuilder.addConceptCode(SystemConstants.SNOMED_URL, allergyIntoleranceEntity.getManifestationCoding(), allergyIntoleranceEntity.getManifestationDisplay()).addDescription(allergyIntoleranceEntity.getManifestationDescCoding(), allergyIntoleranceEntity.getManifestationDescDisplay()).addTranslation(allergyIntoleranceEntity.getManTranslationRef());
        theManifestation.add(codeableConceptBuilder.build());
        codeableConceptBuilder.clear();
        reaction.setManifestation(theManifestation);
        reaction.setDescription(allergyIntoleranceEntity.getNote());
        // SEVERITY
        try {
            reaction.setSeverity(AllergyIntoleranceSeverity.fromCode(allergyIntoleranceEntity.getSeverity()));
        } catch (FHIRException e) {
            throw OperationOutcomeFactory.buildOperationOutcomeException(new UnprocessableEntityException("Unknown severity: " + allergyIntoleranceEntity.getSeverity()), SystemCode.INVALID_RESOURCE, IssueType.INVALID);
        }
        // EXPOSURE
        CodeableConcept exposureRoute = new CodeableConcept();
        reaction.setExposureRoute(exposureRoute);
        allergyIntolerance.addReaction(reaction);
        // RECORDER
        final Reference refValue = new Reference();
        final Identifier identifier = new Identifier();
        final String recorder = allergyIntoleranceEntity.getRecorder();
        // This is just an example to demonstrate using Reference element instead of Identifier element
        if (recorder.equals(patient2NhsNo.trim())) {
            Reference rec = new Reference(SystemConstants.PATIENT_REFERENCE_URL + allergyIntoleranceEntity.getPatientRef());
            allergyIntolerance.setRecorder(rec);
        } else if (patientRepository.findByNhsNumber(recorder) != null) {
            identifier.setSystem(SystemURL.ID_NHS_NUMBER);
            identifier.setValue(recorder);
            refValue.setIdentifier(identifier);
            allergyIntolerance.setRecorder(refValue);
        } else if (practitionerSearch.findPractitionerByUserId(recorder) != null) {
            refValue.setReference("Practitioner/" + recorder);
            allergyIntolerance.setRecorder(refValue);
            practitionerIds.add(recorder);
        }
        // CLINICAL STATUS
        List<Extension> extensions = new ArrayList<>();
        if (allergyIntolerance.getClinicalStatus().getDisplay().contains("Active")) {
            listResourceBuilder(activeList, allergyIntolerance, false);
            bundle.addEntry().setResource(allergyIntolerance);
        } else if (allergyIntolerance.getClinicalStatus().getDisplay().equals("Resolved") && includedResolved.equals(true)) {
            listResourceBuilder(resolvedList, allergyIntolerance, true);
            allergyIntolerance.setLastOccurrence(allergyIntoleranceEntity.getEndDate());
            final Extension allergyEndExtension = createAllergyEndExtension(allergyIntoleranceEntity);
            extensions.add(allergyEndExtension);
        }
        if (!extensions.isEmpty()) {
            allergyIntolerance.setExtension(extensions);
        }
        // ASSERTER
        Reference asserter = allergyIntolerance.getAsserter();
        if (asserter != null && asserter.getReference() != null && asserter.getReference().startsWith("Practitioner")) {
            String[] split = asserter.getReference().split("/");
            practitionerIds.add(split[1]);
        }
    }
    if (!activeList.hasEntry()) {
        addEmptyListNote(activeList);
        addEmptyReasonCode(activeList);
    }
    bundle.addEntry().setResource(activeList);
    if (includedResolved && !resolvedList.hasEntry()) {
        addEmptyListNote(resolvedList);
        addEmptyReasonCode(resolvedList);
    }
    if (includedResolved) {
        bundle.addEntry().setResource(resolvedList);
    }
    return bundle;
}