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CqlFhirParametersConverter EmptyList and Null support (#597)
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* Handle Empty Lists and Null EvaluationResults in CqlFhirParametersConverter

* Ran spotless

* Make types version independent

* Fix author ext being added to item instead of responseItem

* Perf fixes

* Remove uneeded cast

* Remove duplicate code

* Debug CI failure

* Debug

* Sorted paths so behavior is consistent between machines

---------

Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
Co-authored-by: Brenin Rhodes <brenin@alphora.com>
Co-authored-by: JP <jonathan.percival@smilecdr.com>
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@jreyno77 @JPercival @barhodes
4 people authored Dec 3, 2024
1 parent 3916f70 commit fb1b126
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Showing 10 changed files with 335 additions and 184 deletions.
56 changes: 55 additions & 1 deletion .../src/main/java/org/opencds/cqf/fhir/cql/engine/parameters/CqlFhirParametersConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import static java.util.Objects.requireNonNull;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
Expand All @@ -11,8 +12,10 @@
import java.util.Optional;
import java.util.stream.Collectors;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseBooleanDatatype;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
Expand All @@ -36,6 +39,9 @@ public class CqlFhirParametersConverter {
// private IFhirPath fhirPath;
private ModelResolver modelResolver;

/*
* Converts both CQL parameters and CQL Evaluation Results into Fhir Parameters Resources
*/
public CqlFhirParametersConverter(
FhirContext fhirContext, IAdapterFactory adapterFactory, FhirTypeConverter fhirTypeConverter) {
this.fhirContext = requireNonNull(fhirContext);
Expand All @@ -47,6 +53,42 @@ public CqlFhirParametersConverter(
// this.fhirPath = FhirPathCache.cachedForContext(fhirContext);
}

// This is basically a copy and paste from R4FhirTypeConverter, but it's not exposed.
static final String EMPTY_LIST_EXT_URL = "http://hl7.org/fhir/StructureDefinition/cqf-isEmptyList";
static final String DATA_ABSENT_REASON_EXT_URL = "http://hl7.org/fhir/StructureDefinition/data-absent-reason";
static final String DATA_ABSENT_REASON_UNKNOWN_CODE = "unknown";

private static IBaseBooleanDatatype booleanType(FhirContext context, Boolean value) {
try {
return (IBaseBooleanDatatype) context.getElementDefinition("Boolean")
.getImplementingClass()
.getDeclaredConstructor(Boolean.class)
.newInstance(value);
} catch (Exception e) {
throw new InternalErrorException("error creating BooleanType", e);
}
}

private static IBaseDatatype codeType(FhirContext context, String value) {
try {
return (IBaseDatatype) context.getElementDefinition("Code")
.getImplementingClass()
.getDeclaredConstructor(String.class)
.newInstance(value);
} catch (Exception e) {
throw new InternalErrorException("error creating CodeType", e);
}
}

private static IBaseBooleanDatatype emptyBooleanWithExtension(
FhirContext context, String url, IBaseDatatype value) {
var result = booleanType(context, null);
var ext = ((IBaseHasExtensions) result).addExtension();
ext.setUrl(url);
ext.setValue(value);
return result;
}

public IBaseParameters toFhirParameters(EvaluationResult evaluationResult) {
IBaseParameters params = null;
try {
Expand All @@ -67,11 +109,23 @@ public IBaseParameters toFhirParameters(EvaluationResult evaluationResult) {
Object value = entry.getValue().value();

if (value == null) {
this.addPart(pa, name);
// Null value, add a single empty value with an extension indicating the reason
var dataAbsentValue = emptyBooleanWithExtension(
fhirContext,
DATA_ABSENT_REASON_EXT_URL,
codeType(fhirContext, DATA_ABSENT_REASON_UNKNOWN_CODE));
addPart(pa, name, dataAbsentValue);
continue;
}

if (value instanceof Iterable) {
var iterable = (Iterable<?>) value;
if (!iterable.iterator().hasNext()) {
// Empty list
var emptyListValue =
emptyBooleanWithExtension(fhirContext, EMPTY_LIST_EXT_URL, booleanType(fhirContext, true));
addPart(pa, name, emptyListValue);
}
Iterable<?> values = (Iterable<?>) value;
for (Object o : values) {
this.addPart(pa, name, o);
Expand Down
37 changes: 37 additions & 0 deletions ...test/java/org/opencds/cqf/fhir/cql/engine/parameters/CqlFhirParametersConverterTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,12 @@

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Encounter;
import org.hl7.fhir.r4.model.ParameterDefinition;
Expand Down Expand Up @@ -59,6 +61,41 @@ void TestEvaluationResultToParameters() {
assertTrue(expected.equalsDeep(actual));
}

@Test
void TestEvaluationResultToEmptyListParameters() {
Parameters expected = new Parameters();
expected.addParameter().setName("Patient").setResource(new Patient());
BooleanType nullBooleanValue = new BooleanType((String) null);
nullBooleanValue.addExtension("http://hl7.org/fhir/StructureDefinition/cqf-isEmptyList", new BooleanType(true));
expected.addParameter().setName("Encounters").setValue(nullBooleanValue);

EvaluationResult testData = new EvaluationResult();
testData.expressionResults.put("Patient", new ExpressionResult(new Patient(), null));
testData.expressionResults.put("Encounters", new ExpressionResult(Collections.emptyList(), null));

Parameters actual = (Parameters) cqlFhirParametersConverter.toFhirParameters(testData);

assertTrue(expected.equalsDeep(actual));
}

@Test
void TestEvaluationResultNullParameters() {
Parameters expected = new Parameters();
expected.addParameter().setName("Patient").setResource(new Patient());
BooleanType nullBooleanValue = new BooleanType((String) null);
nullBooleanValue.addExtension(
"http://hl7.org/fhir/StructureDefinition/data-absent-reason", new CodeType("unknown"));
expected.addParameter().setName("Null").setValue(nullBooleanValue);

EvaluationResult testData = new EvaluationResult();
testData.expressionResults.put("Patient", new ExpressionResult(new Patient(), null));
testData.expressionResults.put("Null", new ExpressionResult(null, null));

Parameters actual = (Parameters) cqlFhirParametersConverter.toFhirParameters(testData);

assertTrue(expected.equalsDeep(actual));
}

@Test
void TestFhirParametersToCqlParameters() {
Map<String, Object> expected = new HashMap<>();
Expand Down
7 changes: 4 additions & 3 deletions cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/populate/ProcessItem.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ public ProcessItem(ExpressionProcessor expressionProcessor) {

public IBaseBackboneElement processItem(PopulateRequest request, IBaseBackboneElement item) {
final var responseItem = createResponseItem(request.getFhirVersion(), item);
populateAnswer(request, responseItem, getInitialValue(request, item));
populateAnswer(request, responseItem, getInitialValue(request, item, responseItem));
return responseItem;
}

Expand All @@ -44,15 +44,16 @@ protected void populateAnswer(PopulateRequest request, IBaseBackboneElement resp
request.getModelResolver().setValue(responseItem, "answer", answers);
}

protected List<IBase> getInitialValue(PopulateRequest request, IBaseBackboneElement item) {
protected List<IBase> getInitialValue(
PopulateRequest request, IBaseBackboneElement item, IBaseBackboneElement responseItem) {
List<IBase> results;
var expression = expressionProcessor.getItemInitialExpression(request, item);
if (expression != null) {
var itemLinkId = request.getItemLinkId(item);
try {
results = expressionProcessor.getExpressionResultForItem(request, expression, itemLinkId);
if (results != null && !results.isEmpty()) {
addAuthorExtension(request, item);
addAuthorExtension(request, responseItem);
}
} catch (Exception e) {
var message = String.format(
Expand Down
2 changes: 1 addition & 1 deletion .../src/main/java/org/opencds/cqf/fhir/cr/questionnaire/populate/ProcessItemWithContext.java
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Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,7 @@ IBaseBackboneElement createResponseContextItem(
if (extension != null) {
// pass the context resource(s) as a parameter to the evaluation
request.addContextParameter("%" + contextName, context);
populateAnswer(request, responseItem, getInitialValue(request, item));
populateAnswer(request, responseItem, getInitialValue(request, item, responseItem));
}
}
return responseItem;
Expand Down
6 changes: 3 additions & 3 deletions cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/library/LibraryProcessorTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,7 @@ void evaluateDstu3() {
.libraryId("OutpatientPriorAuthorizationPrepopulation")
.subjectId("OPA-Patient1")
.thenEvaluate()
.hasResults(47);
.hasResults(48);
}

@Test
Expand All @@ -137,7 +137,7 @@ void evaluateR4() {
.libraryId("OutpatientPriorAuthorizationPrepopulation")
.subjectId("OPA-Patient1")
.thenEvaluate()
.hasResults(50);
.hasResults(51);
}

@Test
Expand All @@ -147,7 +147,7 @@ void evaluateR5() {
.libraryId("OutpatientPriorAuthorizationPrepopulation")
.subjectId("OPA-Patient1")
.thenEvaluate()
.hasResults(48);
.hasResults(49);
}

@Test
Expand Down
11 changes: 9 additions & 2 deletions ...hir-cr/src/test/java/org/opencds/cqf/fhir/cr/questionnaire/populate/ProcessItemTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.r4.model.Questionnaire;
import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemComponent;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
Expand Down Expand Up @@ -132,11 +133,14 @@ void getExpressionResultsShouldReturnEmptyListIfInitialExpressionIsNull() {
final PopulateRequest prePopulateRequest =
newPopulateRequestForVersion(FhirVersionEnum.R4, libraryEngine, questionnaire);
final QuestionnaireItemComponent questionnaireItemComponent = new QuestionnaireItemComponent();
final QuestionnaireResponseItemComponent questionnaireResponseItemComponent =
new QuestionnaireResponseItemComponent();
doReturn(null)
.when(expressionProcessor)
.getItemInitialExpression(prePopulateRequest, questionnaireItemComponent);
// execute
final List<IBase> actual = processItem.getInitialValue(prePopulateRequest, questionnaireItemComponent);
final List<IBase> actual = processItem.getInitialValue(
prePopulateRequest, questionnaireItemComponent, questionnaireResponseItemComponent);
// validate
assertTrue(actual.isEmpty());
verify(expressionProcessor).getItemInitialExpression(prePopulateRequest, questionnaireItemComponent);
Expand All @@ -153,6 +157,8 @@ void getExpressionResultsShouldReturnListOfResourcesIfInitialExpressionIsNotNull
newPopulateRequestForVersion(FhirVersionEnum.R4, libraryEngine, questionnaire);
final QuestionnaireItemComponent questionnaireItemComponent = new QuestionnaireItemComponent();
questionnaireItemComponent.setLinkId("linkId");
final QuestionnaireResponseItemComponent questionnaireResponseItemComponent =
new QuestionnaireResponseItemComponent();
final CqfExpression expression = withExpression();
doReturn(expression)
.when(expressionProcessor)
Expand All @@ -161,7 +167,8 @@ void getExpressionResultsShouldReturnListOfResourcesIfInitialExpressionIsNotNull
.when(expressionProcessor)
.getExpressionResultForItem(prePopulateRequest, expression, "linkId");
// execute
final List<IBase> actual = processItem.getInitialValue(prePopulateRequest, questionnaireItemComponent);
final List<IBase> actual = processItem.getInitialValue(
prePopulateRequest, questionnaireItemComponent, questionnaireResponseItemComponent);
// validate
assertEquals(expected, actual);
verify(expressionProcessor).getItemInitialExpression(prePopulateRequest, questionnaireItemComponent);
Expand Down
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