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

Example 6 with Annotation

use of org.hl7.fhir.dstu3.model.Annotation 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 7 with Annotation

use of org.hl7.fhir.dstu3.model.Annotation 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;
}

Example 8 with Annotation

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

the class PopulateMedicationBundle method createListEntry.

private ListResource createListEntry(List<MedicationStatementDetail> medicationStatements, String nhsNumber) {
    ListResource medicationStatementsList = new ListResource();
    // #179 dont populate List.id
    // medicationStatementsList.setId(new IdType(1));
    medicationStatementsList.setMeta(new Meta().addProfile(SystemURL.SD_GPC_LIST));
    medicationStatementsList.setStatus(ListStatus.CURRENT);
    // #179 dont populate List.id
    // medicationStatementsList.setId(new IdDt(1));
    medicationStatementsList.setMode(ListMode.SNAPSHOT);
    medicationStatementsList.setTitle(SystemConstants.MEDICATION_LIST);
    medicationStatementsList.setCode(new CodeableConcept().addCoding(new Coding(SystemURL.VS_SNOMED, "933361000000108", MEDICATION_LIST)));
    medicationStatementsList.setSubject(new Reference(new IdType("Patient", 1L)).setIdentifier(new Identifier().setValue(nhsNumber).setSystem(SystemURL.ID_NHS_NUMBER)));
    medicationStatementsList.setDate(new Date());
    medicationStatementsList.setOrderedBy(new CodeableConcept().addCoding(new Coding(SystemURL.CS_LIST_ORDER, "event-date", "Sorted by Event Date")));
    medicationStatementsList.addExtension(setClinicalSetting());
    if (medicationStatements.isEmpty()) {
        medicationStatementsList.setEmptyReason(new CodeableConcept().setText(SystemConstants.NO_CONTENT));
        medicationStatementsList.setNote(Arrays.asList(new Annotation(new StringType(SystemConstants.INFORMATION_NOT_AVAILABLE))));
    }
    Set<String> warningCodes = new HashSet<>();
    medicationStatements.forEach(statement -> {
        Reference statementRef = new Reference(new IdType("MedicationStatement", statement.getId()));
        ListEntryComponent listEntryComponent = new ListEntryComponent(statementRef);
        medicationStatementsList.addEntry(listEntryComponent);
        if (statement.getWarningCode() != null) {
            warningCodes.add(statement.getWarningCode());
        }
    });
    WarningCodeExtHelper.addWarningCodeExtensions(warningCodes, medicationStatementsList, patientRepository, medicationStatementRepository, structuredAllergySearch);
    return medicationStatementsList;
}