use of org.hl7.fhir.r4b.elementmodel.Element 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;
}
use of org.hl7.fhir.r4b.elementmodel.Element in project quality-measure-and-cohort-service by Alvearie.
the class ModelUtilsTest method testFHIR400Model.
@Test
public void testFHIR400Model() throws Exception {
ModelInfo modelInfo = loadFromClasspath("org/hl7/fhir/fhir-modelinfo-4.0.0.xml");
Map<QName, TypeNode> typeMap = ModelUtils.buildTypeMap(modelInfo);
assertEquals(892, typeMap.size());
TypeNode node = typeMap.get(new QName(modelInfo.getUrl(), "MoneyQuantity"));
assertNotNull(node);
assertEquals("Missing parent type", 1, node.getParentTypes().size());
assertEquals("Quantity", node.getParentTypes().iterator().next().getTypeName().getLocalPart());
node = typeMap.get(new QName(modelInfo.getUrl(), "Quantity"));
assertNotNull(node);
assertEquals(5, node.getChildTypes().size());
assertEquals(1, node.getChildTypes().stream().filter(n -> n.getTypeName().getLocalPart().equals("MoneyQuantity")).collect(Collectors.counting()).longValue());
node = typeMap.get(new QName(modelInfo.getUrl(), "Element"));
assertNotNull(node);
// The actual parent is System.Any, but we exclude included types from the type map
assertEquals(0, node.getParentTypes().size());
}
use of org.hl7.fhir.r4b.elementmodel.Element in project Gravity-SDOH-Exchange-RI by FHIR.
the class ConvertService method convertToBundle.
private String convertToBundle(JSONObject questionnaireResponse, String mapUri) {
try (ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
Element element = validationEngine.transform(questionnaireResponse.toString().getBytes(), Manager.FhirFormat.JSON, mapUri);
new JsonParser(validationEngine.getContext()).compose(element, byteArrayOutputStream, org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY, null);
return byteArrayOutputStream.toString();
} catch (IOException e) {
throw new IllegalStateException("QuestionnaireResponse with id cannot be parsed.", e.getCause());
}
}
use of org.hl7.fhir.r4b.elementmodel.Element in project org.hl7.fhir.core by hapifhir.
the class SpecDifferenceEvaluator method analyseTypes.
private void analyseTypes(JsonObject element, ElementDefinition rev, ElementDefinition orig) {
JsonArray oa = new JsonArray();
JsonArray ra = new JsonArray();
if (rev.getType().size() == 1 && orig.getType().size() == 1) {
String r = describeType(rev.getType().get(0));
if (Utilities.noString(r) && Utilities.existsInList(rev.getId(), "Element.id", "Extension.url"))
r = "string";
String o = describeType(orig.getType().get(0));
if (Utilities.noString(o) && Utilities.existsInList(orig.getId(), "Element.id", "Extension.url"))
o = "string";
if (!o.equals(r)) {
oa.add(new JsonPrimitive(o));
ra.add(new JsonPrimitive(r));
}
} else {
for (TypeRefComponent tr : orig.getType()) {
if (!hasType(rev.getType(), tr))
oa.add(new JsonPrimitive(describeType(tr)));
}
for (TypeRefComponent tr : rev.getType()) {
if (!hasType(orig.getType(), tr) && !isAbstractType(tr.getWorkingCode()))
ra.add(new JsonPrimitive(describeType(tr)));
}
for (TypeRefComponent tr : rev.getType()) {
TypeRefComponent tm = getType(rev.getType(), tr);
if (tm != null) {
compareParameters(element, tr, tm);
}
}
}
if (oa.size() > 0)
element.add("removed-types", oa);
if (ra.size() > 0)
element.add("added-types", ra);
}
use of org.hl7.fhir.r4b.elementmodel.Element in project org.hl7.fhir.core by hapifhir.
the class SpecDifferenceEvaluator method compareBindings.
private boolean compareBindings(JsonObject element, ElementDefinitionBindingComponent rev, ElementDefinitionBindingComponent orig) {
boolean res = false;
if (rev.getStrength() != orig.getStrength()) {
element.addProperty("binding-strength-changed", true);
res = true;
}
if (!Base.compareDeep(rev.getValueSet(), orig.getValueSet(), false)) {
element.addProperty("binding-valueset-changed", true);
res = true;
}
if (!maxValueSetsMatch(rev, orig)) {
element.addProperty("max-valueset-changed", true);
res = true;
}
if (rev.getStrength() == BindingStrength.REQUIRED && orig.getStrength() == BindingStrength.REQUIRED) {
JsonArray oa = new JsonArray();
JsonArray ra = new JsonArray();
ValueSet vrev = getValueSet(rev.getValueSet(), revision.getExpansions());
ValueSet vorig = getValueSet(rev.getValueSet(), original.getExpansions());
if (vrev != null && vorig != null) {
for (ValueSetExpansionContainsComponent cc : vorig.getExpansion().getContains()) {
if (!hasCode(vrev, cc))
oa.add(new JsonPrimitive(cc.getCode()));
}
for (ValueSetExpansionContainsComponent cc : vrev.getExpansion().getContains()) {
if (!hasCode(vorig, cc))
ra.add(new JsonPrimitive(cc.getCode()));
}
}
if (oa.size() > 0 || ra.size() > 0) {
element.addProperty("binding-codes-changed", true);
res = true;
}
if (oa.size() > 0)
element.add("removed-codes", oa);
if (ra.size() > 0)
element.add("added-codes", ra);
}
return res;
}
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