Examples with ListEntryComponent org.hl7.fhir.r4.model.ListResource.ListEntryComponent used on opensource projects

Example 1 with ListEntryComponent

use of org.hl7.fhir.r4.model.ListResource.ListEntryComponent in project quality-measure-and-cohort-service by Alvearie.

the class MeasureEvaluation method evaluate.

protected MeasureReport evaluate(Measure measure, Context context, List<Patient> patients, MeasureReport.MeasureReportType type, boolean isSingle, boolean includeEvaluatedResources) {
    MeasureReportBuilder reportBuilder = new MeasureReportBuilder();
    reportBuilder.buildStatus("complete");
    reportBuilder.buildType(type);
    reportBuilder.buildMeasureReference(measure.getIdElement().getResourceType() + "/" + measure.getIdElement().getIdPart());
    if (type == MeasureReport.MeasureReportType.INDIVIDUAL && CollectionUtils.isNotEmpty(patients)) {
        IdType patientId = patients.get(0).getIdElement();
        reportBuilder.buildPatientReference(patientId.getResourceType() + "/" + patientId.getIdPart());
    }
    reportBuilder.buildPeriod(measurementPeriod);
    MeasureReport report = reportBuilder.build();
    Map<String, Resource> resources = new HashMap<>();
    Map<String, Set<String>> codeToResourceMap = new HashMap<>();
    MeasureScoring measureScoring = MeasureScoring.fromCode(measure.getScoring().getCodingFirstRep().getCode());
    if (measureScoring == null) {
        throw new RuntimeException("Measure scoring is required in order to calculate.");
    }
    List<Measure.MeasureSupplementalDataComponent> sde = measure.getSupplementalData();
    Map<String, Map<String, Integer>> sdeAccumulators = new HashMap<>();
    for (Measure.MeasureGroupComponent group : measure.getGroup()) {
        MeasureReport.MeasureReportGroupComponent reportGroup = new MeasureReport.MeasureReportGroupComponent();
        reportGroup.setId(group.getId());
        report.getGroup().add(reportGroup);
        // Declare variables to avoid a hash lookup on every patient
        // TODO: Isn't quite right, there may be multiple initial populations for a
        // ratio measure...
        Measure.MeasureGroupPopulationComponent initialPopulationCriteria = null;
        Measure.MeasureGroupPopulationComponent numeratorCriteria = null;
        Measure.MeasureGroupPopulationComponent numeratorExclusionCriteria = null;
        Measure.MeasureGroupPopulationComponent denominatorCriteria = null;
        Measure.MeasureGroupPopulationComponent denominatorExclusionCriteria = null;
        Measure.MeasureGroupPopulationComponent denominatorExceptionCriteria = null;
        Map<String, Resource> initialPopulation = null;
        Map<String, Resource> numerator = null;
        Map<String, Resource> numeratorExclusion = null;
        Map<String, Resource> denominator = null;
        Map<String, Resource> denominatorExclusion = null;
        Map<String, Resource> denominatorException = null;
        Map<String, Patient> initialPopulationPatients = null;
        Map<String, Patient> numeratorPatients = null;
        Map<String, Patient> numeratorExclusionPatients = null;
        Map<String, Patient> denominatorPatients = null;
        Map<String, Patient> denominatorExclusionPatients = null;
        Map<String, Patient> denominatorExceptionPatients = null;
        for (Measure.MeasureGroupPopulationComponent pop : group.getPopulation()) {
            MeasurePopulationType populationType = MeasurePopulationType.fromCode(pop.getCode().getCodingFirstRep().getCode());
            if (populationType != null) {
                switch(populationType) {
                    case INITIALPOPULATION:
                        initialPopulationCriteria = pop;
                        initialPopulation = new HashMap<>();
                        if (type == MeasureReport.MeasureReportType.SUBJECTLIST) {
                            initialPopulationPatients = new HashMap<>();
                        }
                        break;
                    case NUMERATOR:
                        numeratorCriteria = pop;
                        numerator = new HashMap<>();
                        if (type == MeasureReport.MeasureReportType.SUBJECTLIST) {
                            numeratorPatients = new HashMap<>();
                        }
                        break;
                    case NUMERATOREXCLUSION:
                        numeratorExclusionCriteria = pop;
                        numeratorExclusion = new HashMap<>();
                        if (type == MeasureReport.MeasureReportType.SUBJECTLIST) {
                            numeratorExclusionPatients = new HashMap<>();
                        }
                        break;
                    case DENOMINATOR:
                        denominatorCriteria = pop;
                        denominator = new HashMap<>();
                        if (type == MeasureReport.MeasureReportType.SUBJECTLIST) {
                            denominatorPatients = new HashMap<>();
                        }
                        break;
                    case DENOMINATOREXCLUSION:
                        denominatorExclusionCriteria = pop;
                        denominatorExclusion = new HashMap<>();
                        if (type == MeasureReport.MeasureReportType.SUBJECTLIST) {
                            denominatorExclusionPatients = new HashMap<>();
                        }
                        break;
                    case DENOMINATOREXCEPTION:
                        denominatorExceptionCriteria = pop;
                        denominatorException = new HashMap<>();
                        if (type == MeasureReport.MeasureReportType.SUBJECTLIST) {
                            denominatorExceptionPatients = new HashMap<>();
                        }
                        break;
                    default:
                        throw new UnsupportedOperationException("Measure population, observation and measure population exclusion are used for continuous-variable scoring measures which are not supported");
                }
            }
        }
        switch(measureScoring) {
            case PROPORTION:
            case RATIO:
                {
                    // For each patient in the initial population
                    for (Patient patient : patients) {
                        // Are they in the initial population?
                        boolean inInitialPopulation = evaluatePopulationCriteria(context, patient, initialPopulationCriteria, initialPopulation, initialPopulationPatients, null, null, null);
                        populateResourceMap(context, MeasurePopulationType.INITIALPOPULATION, resources, codeToResourceMap, includeEvaluatedResources);
                        if (inInitialPopulation) {
                            // Are they in the denominator?
                            boolean inDenominator = evaluatePopulationCriteria(context, patient, denominatorCriteria, denominator, denominatorPatients, denominatorExclusionCriteria, denominatorExclusion, denominatorExclusionPatients);
                            populateResourceMap(context, MeasurePopulationType.DENOMINATOR, resources, codeToResourceMap, includeEvaluatedResources);
                            if (inDenominator) {
                                // Are they in the numerator?
                                boolean inNumerator = evaluatePopulationCriteria(context, patient, numeratorCriteria, numerator, numeratorPatients, numeratorExclusionCriteria, numeratorExclusion, numeratorExclusionPatients);
                                populateResourceMap(context, MeasurePopulationType.NUMERATOR, resources, codeToResourceMap, includeEvaluatedResources);
                                if (!inNumerator && inDenominator && (denominatorExceptionCriteria != null)) {
                                    // Are they in the denominator exception?
                                    boolean inException = false;
                                    for (Resource resource : evaluateCriteria(context, patient, denominatorExceptionCriteria)) {
                                        inException = true;
                                        denominatorException.put(resource.getIdElement().getIdPart(), resource);
                                        denominator.remove(resource.getIdElement().getIdPart());
                                        populateResourceMap(context, MeasurePopulationType.DENOMINATOREXCEPTION, resources, codeToResourceMap, includeEvaluatedResources);
                                    }
                                    if (inException) {
                                        if (denominatorExceptionPatients != null) {
                                            denominatorExceptionPatients.put(patient.getIdElement().getIdPart(), patient);
                                        }
                                        if (denominatorPatients != null) {
                                            denominatorPatients.remove(patient.getIdElement().getIdPart());
                                        }
                                    }
                                }
                            }
                        }
                        MeasureSupplementalDataEvaluation.populateSDEAccumulators(context, patient, sdeAccumulators, sde);
                    }
                    // Calculate actual measure score, Count(numerator) / Count(denominator)
                    if (numerator != null && MapUtils.isNotEmpty(denominator)) {
                        reportGroup.setMeasureScore(new Quantity(numerator.size() / (double) denominator.size()));
                    }
                    break;
                }
            case COHORT:
                {
                    // For each patient in the patient list
                    for (Patient patient : patients) {
                        evaluatePopulationCriteria(context, patient, initialPopulationCriteria, initialPopulation, initialPopulationPatients, null, null, null);
                        populateResourceMap(context, MeasurePopulationType.INITIALPOPULATION, resources, codeToResourceMap, includeEvaluatedResources);
                        MeasureSupplementalDataEvaluation.populateSDEAccumulators(context, patient, sdeAccumulators, sde);
                    }
                    break;
                }
            case CONTINUOUSVARIABLE:
                throw new UnsupportedOperationException("Scoring type CONTINUOUSVARIABLE is not supported");
        }
        // Add population reports for each group
        addPopulationCriteriaReport(report, reportGroup, initialPopulationCriteria, initialPopulation != null ? initialPopulation.size() : 0, initialPopulationPatients != null ? initialPopulationPatients.values() : null);
        addPopulationCriteriaReport(report, reportGroup, numeratorCriteria, numerator != null ? numerator.size() : 0, numeratorPatients != null ? numeratorPatients.values() : null);
        addPopulationCriteriaReport(report, reportGroup, numeratorExclusionCriteria, numeratorExclusion != null ? numeratorExclusion.size() : 0, numeratorExclusionPatients != null ? numeratorExclusionPatients.values() : null);
        addPopulationCriteriaReport(report, reportGroup, denominatorCriteria, denominator != null ? denominator.size() : 0, denominatorPatients != null ? denominatorPatients.values() : null);
        addPopulationCriteriaReport(report, reportGroup, denominatorExclusionCriteria, denominatorExclusion != null ? denominatorExclusion.size() : 0, denominatorExclusionPatients != null ? denominatorExclusionPatients.values() : null);
        addPopulationCriteriaReport(report, reportGroup, denominatorExceptionCriteria, denominatorException != null ? denominatorException.size() : 0, denominatorExceptionPatients != null ? denominatorExceptionPatients.values() : null);
    }
    for (Entry<String, Set<String>> entry : codeToResourceMap.entrySet()) {
        ListResource list = new ListResource();
        for (String element : entry.getValue()) {
            ListResource.ListEntryComponent comp = new ListEntryComponent();
            comp.setItem(new Reference('#' + element));
            list.addEntry(comp);
        }
        if (!list.isEmpty()) {
            list.setId(UUID.randomUUID().toString());
            list.setTitle(entry.getKey());
            resources.put(list.getId(), list);
        }
    }
    if (MapUtils.isNotEmpty(resources)) {
        List<Reference> evaluatedResourceIds = new ArrayList<>();
        resources.forEach((key, resource) -> {
            evaluatedResourceIds.add(new Reference(resource.getId()));
        });
        report.setEvaluatedResource(evaluatedResourceIds);
    }
    if (MapUtils.isNotEmpty(sdeAccumulators)) {
        report = MeasureSupplementalDataEvaluation.processAccumulators(report, sdeAccumulators, isSingle, patients);
    }
    return report;
}

Example 2 with ListEntryComponent

use of org.hl7.fhir.r4.model.ListResource.ListEntryComponent in project org.hl7.fhir.core by hapifhir.

the class CCDAConverter method processAllergyProblemAct.

protected void processAllergyProblemAct(ListResource list, Element concern) throws Exception {
    cda.checkTemplateId(concern, "2.16.840.1.113883.10.20.22.4.30");
    // Allergy Problem Act - this is a concern - we treat the concern as information about it's place in the list
    checkNoNegationOrNullFlavor(concern, "Allergy Problem Act");
    checkNoSubject(concern, "Allergy Problem Act");
    // SHALL contain exactly one [1..1] Allergy - intolerance Observation
    for (Element entry : cda.getChildren(concern, "entryRelationship")) {
        Element obs = cda.getChild(entry, "observation");
        cda.checkTemplateId(obs, "2.16.840.1.113883.10.20.22.4.7");
        checkNoNegationOrNullFlavor(obs, "Allergy - intolerance Observation");
        checkNoSubject(obs, "Allergy Problem Act");
        AllergyIntolerance ai = new AllergyIntolerance();
        ListEntryComponent item = addItemToList(list, ai);
        // SHALL contain at least one [1..*] id (CONF:7472).
        for (Element e : cda.getChildren(concern, "id")) ai.getIdentifier().add(convert.makeIdentifierFromII(e));
        // SHALL contain exactly one [1..1] statusCode, which SHALL be selected from ValueSet 2.16.840.1.113883.3.88.12.80.68 HITSPProblemStatus DYNAMIC (CONF:7485)
        // the status code is about the concern (e.g. the entry in the list)
        // possible values: active, suspended, aborted, completed, with an effective time
        String s = cda.getStatus(concern);
        item.setFlag(Factory.newCodeableConcept(s, "http://hl7.org/fhir/v3/ActStatus", s));
        if (// only on this condition?
        s.equals("aborted"))
            item.setDeleted(true);
        // SHALL contain exactly one [1..1] effectiveTime (CONF:7498)
        Period p = convert.makePeriodFromIVL(cda.getChild(concern, "effectiveTime"));
        item.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/list-period", p, false));
        if (p.getEnd() != null)
            item.setDate(p.getEnd());
        else
            item.setDate(p.getStart());
        // SHALL contain at least one [1..*] id (CONF:7382)
        for (Element e : cda.getChildren(obs, "id")) ai.getIdentifier().add(convert.makeIdentifierFromII(e));
        // SHALL contain exactly one [1..1] effectiveTime (CONF:7387)
        ai.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/allergyintolerance-period", convert.makePeriodFromIVL(cda.getChild(obs, "effectiveTime")), false));
        // SHALL contain exactly one [1..1] value with @xsi:type="CD" (CONF:7390)
        CodeableConcept type = convert.makeCodeableConceptFromCD(cda.getChild(obs, "value"));
        // This value SHALL contain @code, which SHALL be selected from ValueSet 2.16.840.1.113883.3.88.12.3221.6.2 Allergy/Adverse Event Type
        String ss = type.getCoding().get(0).getCode();
        if (ss.equals("416098002") || ss.equals("414285001"))
            ai.setType(AllergyIntoleranceType.ALLERGY);
        else if (ss.equals("59037007") || ss.equals("235719002"))
            ai.setType(AllergyIntoleranceType.INTOLERANCE);
        ai.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/allergy-category", type, false));
        // SHOULD contain zero or one [0..1] participant (CONF:7402) such that it
        // ......This playingEntity SHALL contain exactly one [1..1] code
        ai.setCode(convert.makeCodeableConceptFromCD(cda.getDescendent(obs, "participant/participantRole/playingEntity/code")));
        // SHOULD contain zero or more [0..*] entryRelationship (CONF:7447) such that it SHALL contain exactly one [1..1] Reaction Observation (templateId:2.16.840.1.113883.10.20.22.4.9) (CONF:7450).
        for (Element e : cda.getChildren(obs, "entryRelationship")) {
            Element child = cda.getChild(e, "observation");
            if (cda.hasTemplateId(child, "2.16.840.1.113883.10.20.22.4.28") && ai.getClinicalStatus() == null) {
                // SHALL contain exactly one [1..1] value with @xsi:type="CE", where the @code SHALL be selected from ValueSet Problem Status Value Set 2.16.840.1.113883.3.88.12.80.68 DYNAMIC (CONF:7322).
                // 55561003  SNOMED CT  Active
                // 73425007  SNOMED CT  Inactive
                // 413322009  SNOMED CT  Resolved
                String sc = cda.getChild(child, "value").getAttribute("code");
                if (sc.equals("55561003")) {
                    ai.setClinicalStatus(AllergyIntoleranceClinicalStatus.ACTIVE);
                    ai.setVerificationStatus(AllergyIntoleranceVerificationStatus.CONFIRMED);
                } else
                    ai.setClinicalStatus(AllergyIntoleranceClinicalStatus.RESOLVED);
            } else if (cda.hasTemplateId(child, "2.16.840.1.113883.10.20.22.4.9")) {
                ai.getReaction().add(processAdverseReactionObservation(child));
            }
        }
        // SHOULD contain zero or one [0..1] entryRelationship (CONF:9961) such that it SHALL contain exactly one [1..1] Severity Observation (templateId:2.16.840.1.113883.10.20.22.4.8) (CONF:9963).
        ai.setCriticality(readCriticality(cda.getSeverity(obs)));
    }
}

Example 3 with ListEntryComponent

use of org.hl7.fhir.r4.model.ListResource.ListEntryComponent in project nia-patient-switching-standard-adaptor by NHSDigital.

the class EncounterMapper method generateLinkSetTopicLists.

private void generateLinkSetTopicLists(RCMRMT030101UK04EhrComposition ehrComposition, ListResource consultation, List<ListResource> topics) {
    var linkSetList = getLinkSets(ehrComposition);
    if (!CollectionUtils.isEmpty(linkSetList)) {
        var linkSetTopic = consultationListMapper.mapToTopic(consultation, null);
        addLinkSetsAsTopicEntries(linkSetList, linkSetTopic);
        consultation.addEntry(new ListEntryComponent(new Reference(linkSetTopic)));
        topics.add(linkSetTopic);
    }
}

Example 4 with ListEntryComponent

use of org.hl7.fhir.r4.model.ListResource.ListEntryComponent in project nia-patient-switching-standard-adaptor by NHSDigital.

the class EncounterMapper method generateCategoryLists.

private void generateCategoryLists(RCMRMT030101UK04CompoundStatement topicCompoundStatement, ListResource topic, List<ListResource> categories) {
    var categoryCompoundStatements = getCategoryCompoundStatements(topicCompoundStatement);
    categoryCompoundStatements.forEach(categoryCompoundStatement -> {
        var category = consultationListMapper.mapToCategory(topic, categoryCompoundStatement);
        List<Reference> entryReferences = new ArrayList<>();
        resourceReferenceUtil.extractChildReferencesFromCompoundStatement(categoryCompoundStatement, entryReferences);
        entryReferences.forEach(reference -> addEntry(category, reference));
        topic.addEntry(new ListEntryComponent(new Reference(category)));
        categories.add(category);
    });
}

Example 5 with ListEntryComponent

use of org.hl7.fhir.r4.model.ListResource.ListEntryComponent in project gpconnect-demonstrator by nhsconnect.

the class StructuredAllergyIntoleranceBuilder method listResourceBuilder.

private void listResourceBuilder(ListResource buildingListResource, AllergyIntolerance allergyIntolerance, boolean isResolved) {
    ListEntryComponent comp = new ListEntryComponent();
    if (isResolved) {
        buildingListResource.addContained(allergyIntolerance);
        Reference allergyReference = new Reference("#" + allergyIntolerance.getId());
        comp.setItem(allergyReference);
    } else {
        Reference allergyReference = new Reference("AllergyIntolerance/" + allergyIntolerance.getId());
        comp.setItem(allergyReference);
    }
    buildingListResource.addEntry(comp);
}