Fix issue with item generation for hidden items (#441)

* Fix element type determination and allow for null if element has children * spotless * Fix tests * cleanup
cqframework · Mar 21, 2024 · 4ee24d3 · 4ee24d3
1 parent a50e8eb
commit 4ee24d3
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Showing 15 changed files with 624 additions and 119 deletions.
diff --git a/cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/LibraryConstructor.java b/cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/LibraryConstructor.java
@@ -7,7 +7,6 @@
 import java.util.List;
 import org.apache.commons.lang3.tuple.Pair;
 import org.hl7.elm.r1.VersionedIdentifier;
-import org.hl7.fhir.instance.model.api.IBaseParameters;
 import org.opencds.cqf.fhir.cql.engine.parameters.CqlParameterDefinition;
 import org.opencds.cqf.fhir.utility.FhirPathCache;
 import org.slf4j.Logger;
@@ -102,27 +101,6 @@ private void constructHeader(StringBuilder sb) {
  sb.append(String.format("library expression version '1.0.0'%n%n"));
  }
 
- private String getFhirVersion(IBaseParameters parameters) {
- if (parameters == null) {
- return null;
- }
-
- switch (parameters.getStructureFhirVersionEnum()) {
- case DSTU3:
- return "3.0.1";
- case R4:
- return "4.0.1";
- case DSTU2:
- case DSTU2_1:
- case DSTU2_HL7ORG:
- case R5:
- default:
- throw new IllegalArgumentException(String.format(
- "Unsupported version of FHIR: %s",
- parameters.getStructureFhirVersionEnum().getFhirVersionString()));
- }
- }
-
  protected VersionedIdentifier getVersionedIdentifier(String url) {
  if (!url.contains("/Library/")) {
  throw new IllegalArgumentException(
@@ -135,7 +113,7 @@ protected VersionedIdentifier getVersionedIdentifier(String url) {
  }
 
  // TODO: Use the namespace manager here to do the mapping?
- String cqlNamespaceUrl = urlSplit[0];
+ // String cqlNamespaceUrl = urlSplit[0];
 
  String cqlName = urlSplit[1];
  VersionedIdentifier versionedIdentifier = new VersionedIdentifier();

diff --git a/cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/model/DynamicModelResolver.java b/cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/model/DynamicModelResolver.java
@@ -30,6 +30,7 @@ public class DynamicModelResolver extends CachingModelResolverDecorator {
 
  private final FhirContext fhirContext;
 
+ @SuppressWarnings("rawtypes")
  public DynamicModelResolver(ModelResolver modelResolver) {
  super(modelResolver);
  this.fhirContext = ((FhirModelResolver) modelResolver).getFhirContext();

diff --git a/.../src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/ElementHasDefaultValue.java b/.../src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/ElementHasDefaultValue.java
@@ -19,6 +19,7 @@ public IBaseBackboneElement addProperties(
  questionnaireItem,
  "extension",
  buildBooleanExt(request.getFhirVersion(), sdcQuestionnaireHidden(Boolean.TRUE)));
+ // Collections.singletonList(buildBooleanExt(request.getFhirVersion(), sdcQuestionnaireHidden(Boolean.TRUE))));
  request.getModelResolver()
  .setValue(questionnaireItem, "readOnly", buildBooleanType(request.getFhirVersion(), Boolean.TRUE));
  return questionnaireItem;

diff --git a/...ir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/IElementProcessor.java b/...ir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/IElementProcessor.java
@@ -12,7 +12,12 @@
 
 public interface IElementProcessor {
  IBaseBackboneElement processElement(
- GenerateRequest request, ICompositeType element, String childLinkId, IBaseResource caseFeature);
+ GenerateRequest request,
+ ICompositeType element,
+ String elementType,
+ String childLinkId,
+ IBaseResource caseFeature,
+ Boolean isGroup);
 
  public static IElementProcessor createProcessor(Repository repository) {
  switch (repository.fhirContext().getVersion().getVersion()) {

diff --git a/cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/ItemGenerator.java b/cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/ItemGenerator.java
@@ -8,7 +8,6 @@
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
 import org.hl7.fhir.instance.model.api.IBaseBooleanDatatype;
-import org.hl7.fhir.instance.model.api.IBaseEnumeration;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.ICompositeType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
@@ -54,7 +53,7 @@ public IBaseBackboneElement generate(GenerateRequest request) {
  processExtensions(request, questionnaireItem);
  int childCount = request.getItems(questionnaireItem).size();
  var caseFeature = getCaseFeature(request, linkId);
- var parentElements = getElementsWithNonNullElementType(request, null, null);
+ var parentElements = getElements(request, null, null);
  processElements(request, questionnaireItem, parentElements, childCount, linkId, caseFeature);
  return questionnaireItem;
  } catch (Exception ex) {
@@ -107,28 +106,32 @@ protected <E extends ICompositeType> void processElements(
  for (var element : elements) {
  childCount++;
  var childLinkId = String.format(CHILD_LINK_ID_FORMAT, itemLinkId, childCount);
- var childItem = processElement(request, element, childLinkId, caseFeature);
- if (request.resolvePath(childItem, "type", IBaseEnumeration.class)
- .getValueAsString()
- .equals("group")) {
- var childElements = getElementsWithNonNullElementType(
- request,
- request.resolvePathString(element, "path"),
- request.resolvePathString(element, "sliceName"));
- if (!childElements.isEmpty()) {
- processElements(request, childItem, childElements, 0, childLinkId, caseFeature);
- request.getModelResolver().setValue(item, "item", Collections.singletonList(childItem));
- }
+ var childElements = getElements(
+ request,
+ request.resolvePathString(element, "path"),
+ request.resolvePathString(element, "sliceName"));
+ // if child elements exist ignore the type and create a group
+ var elementType = getElementType(request, element);
+ var childItem =
+ processElement(request, element, elementType, childLinkId, caseFeature, !childElements.isEmpty());
+ if (childElements.isEmpty()) {
+ request.getModelResolver().setValue(item, "item", Collections.singletonList(childItem));
  } else {
+ processElements(request, childItem, childElements, 0, childLinkId, caseFeature);
  request.getModelResolver().setValue(item, "item", Collections.singletonList(childItem));
  }
  }
  }
 
  protected IBaseBackboneElement processElement(
- GenerateRequest request, ICompositeType element, String childLinkId, IBaseResource caseFeature) {
+ GenerateRequest request,
+ ICompositeType element,
+ String elementType,
+ String childLinkId,
+ IBaseResource caseFeature,
+ Boolean isGroup) {
  try {
- return elementProcessor.processElement(request, element, childLinkId, caseFeature);
+ return elementProcessor.processElement(request, element, elementType, childLinkId, caseFeature, isGroup);
  } catch (Exception ex) {
  final String message = String.format(ITEM_CREATION_ERROR, ex.getMessage());
  logger.warn(message);
@@ -137,7 +140,7 @@ protected IBaseBackboneElement processElement(
  }
 
  @SuppressWarnings("unchecked")
- protected <E extends ICompositeType> List<E> getElementsWithNonNullElementType(
+ protected <E extends ICompositeType> List<E> getElements(
  GenerateRequest request, String parentPath, String sliceName) {
  List<E> elements = new ArrayList<>();
  // Add all elements from the differential
@@ -154,10 +157,7 @@ protected <E extends ICompositeType> List<E> getElementsWithNonNullElementType(
  .filter(e -> filterElement(request, e, elements, parentPath, sliceName, request.getRequiredOnly()))
  .collect(Collectors.toList()));
  }
- // Filter out elements for which a type cannot be derived
- return elements.stream()
- .filter(element -> getElementType(request, element) != null)
- .collect(Collectors.toList());
+ return elements;
  }
 
  protected <E extends ICompositeType> Boolean filterElement(
@@ -173,6 +173,10 @@ protected <E extends ICompositeType> Boolean filterElement(
  return false;
  }
  }
+ // filter out slicing definitions
+ if (request.resolvePath(element, "slicing") != null) {
+ return false;
+ }
  var pathSplit = path.split("\\.");
  if (parentPath == null) {
  // grab only top level elements
@@ -208,9 +212,27 @@ protected IBaseBackboneElement createErrorItem(GenerateRequest request, String l
  return createQuestionnaireItemComponent(request, errorMessage, linkId, null, true);
  }
 
+ protected String resolveElementType(GenerateRequest request, ICompositeType element) {
+ var typeList = request.resolvePathList(element, "type");
+ return typeList.isEmpty() ? null : request.resolvePathString(typeList.get(0), "code");
+ }
+
  protected String getElementType(GenerateRequest request, ICompositeType element) {
- var type = request.resolvePathList(element, "type");
- return type.isEmpty() ? null : request.resolvePathString(type.get(0), "code");
+ var type = resolveElementType(request, element);
+ if (type == null) {
+ // Attempt to resolve the type from the Snapshot if it is available
+ var path = request.resolvePathString(element, "path");
+ var snapshot = request.getSnapshotElements() == null
+ ? null
+ : request.getSnapshotElements().stream()
+ .filter(e -> path.equals(request.resolvePathString(e, "path")))
+ .findFirst()
+ .orElse(null);
+ if (snapshot != null) {
+ type = resolveElementType(request, snapshot);
+ }
+ }
+ return type;
  }
 
  public IBaseBackboneElement createQuestionnaireItem(GenerateRequest request, String linkId) {

diff --git a/.../src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/dstu3/ElementProcessor.java b/.../src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/dstu3/ElementProcessor.java
@@ -33,11 +33,22 @@ public ElementProcessor(Repository repository) {
 
  @Override
  public IBaseBackboneElement processElement(
- GenerateRequest request, ICompositeType baseElement, String childLinkId, IBaseResource caseFeature) {
+ GenerateRequest request,
+ ICompositeType baseElement,
+ String elementType,
+ String childLinkId,
+ IBaseResource caseFeature,
+ Boolean isGroup) {
  var element = (ElementDefinition) baseElement;
- final QuestionnaireItemType itemType = getItemType(element);
- final QuestionnaireItemComponent item =
- initializeQuestionnaireItem(itemType, request.getProfileUrl(), element, childLinkId);
+ final var itemType = isGroup ? QuestionnaireItemType.GROUP : parseItemType(elementType, element.hasBinding());
+ final var item = initializeQuestionnaireItem(itemType, request.getProfileUrl(), element, childLinkId);
+ item.setRequired(element.hasMin() && element.getMin() > 0);
+ item.setRepeats(element.hasMax() && !element.getMax().equals("1"));
+ // set enableWhen based on? use
+ // http:https://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-enableWhenExpression
+ if (itemType == QuestionnaireItemType.GROUP) {
+ return item;
+ }
  if (itemType == QuestionnaireItemType.CHOICE) {
  questionnaireTypeIsChoice.addProperties(element, item);
  }
@@ -55,10 +66,6 @@ public IBaseBackboneElement processElement(
  item.setInitial(transformValueToItem((Type) pathValue));
  }
  }
- item.setRequired(element.hasMin() && element.getMin() > 0);
- item.setRepeats(element.hasMax() && !element.getMax().equals("1"));
- // set enableWhen based on? use
- // http:https://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-enableWhenExpression
  return item;
  }
 
@@ -72,20 +79,13 @@ protected QuestionnaireItemComponent initializeQuestionnaireItem(
  .setText(getElementText(element));
  }
 
- public QuestionnaireItemType getItemType(ElementDefinition element) {
- final String elementType = element.getType().get(0).getCode();
- final QuestionnaireItemType itemType = parseItemType(elementType, element.hasBinding());
- if (itemType == null) {
- final String message = String.format(ITEM_TYPE_ERROR, element.getId());
- throw new IllegalArgumentException(message);
- }
- return itemType;
- }
-
  public QuestionnaireItemType parseItemType(String elementType, Boolean hasBinding) {
  if (Boolean.TRUE.equals(hasBinding)) {
  return QuestionnaireItemType.CHOICE;
  }
+ if (elementType == null) {
+ throw new IllegalArgumentException("Unable to determine item type.");
+ }
  switch (elementType) {
  case "code":
  case "coding":

diff --git a/...-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/r4/ElementProcessor.java b/...-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/r4/ElementProcessor.java
@@ -33,11 +33,22 @@ public ElementProcessor(Repository repository) {
 
  @Override
  public IBaseBackboneElement processElement(
- GenerateRequest request, ICompositeType baseElement, String childLinkId, IBaseResource caseFeature) {
+ GenerateRequest request,
+ ICompositeType baseElement,
+ String elementType,
+ String childLinkId,
+ IBaseResource caseFeature,
+ Boolean isGroup) {
  var element = (ElementDefinition) baseElement;
- final QuestionnaireItemType itemType = getItemType(element);
- final QuestionnaireItemComponent item =
- initializeQuestionnaireItem(itemType, request.getProfileUrl(), element, childLinkId);
+ final var itemType = isGroup ? QuestionnaireItemType.GROUP : parseItemType(elementType, element.hasBinding());
+ final var item = initializeQuestionnaireItem(itemType, request.getProfileUrl(), element, childLinkId);
+ item.setRequired(element.hasMin() && element.getMin() > 0);
+ item.setRepeats(element.hasMax() && !element.getMax().equals("1"));
+ // set enableWhen based on? use
+ // http:https://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-enableWhenExpression
+ if (itemType == QuestionnaireItemType.GROUP) {
+ return item;
+ }
  if (itemType == QuestionnaireItemType.CHOICE) {
  questionnaireTypeIsChoice.addProperties(element, item);
  }
@@ -53,10 +64,6 @@ public IBaseBackboneElement processElement(
  item.addInitial().setValue(transformValueToItem((Type) pathValue));
  }
  }
- item.setRequired(element.hasMin() && element.getMin() > 0);
- item.setRepeats(element.hasMax() && !element.getMax().equals("1"));
- // set enableWhen based on? use
- // http:https://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-enableWhenExpression
  return item;
  }
 
@@ -70,21 +77,13 @@ protected QuestionnaireItemComponent initializeQuestionnaireItem(
  .setText(getElementText(element));
  }
 
- public QuestionnaireItemType getItemType(ElementDefinition element) {
- final String elementType = element.getType().get(0).getCode();
- QuestionnaireItemType itemType = null;
- try {
- itemType = parseItemType(elementType, element.hasBinding());
- } catch (Exception e) {
- itemType = QuestionnaireItemType.GROUP;
- }
- return itemType;
- }
-
  public QuestionnaireItemType parseItemType(String elementType, Boolean hasBinding) {
  if (Boolean.TRUE.equals(hasBinding)) {
  return QuestionnaireItemType.CHOICE;
  }
+ if (elementType == null) {
+ throw new IllegalArgumentException("Unable to determine item type.");
+ }
  switch (elementType) {
  case "code":
  case "coding":
@@ -112,7 +111,7 @@ public QuestionnaireItemType parseItemType(String elementType, Boolean hasBindin
  }
  }
 
- public String getElementText(ElementDefinition element) {
+ protected String getElementText(ElementDefinition element) {
  return element.hasLabel() ? element.getLabel() : getElementDescription(element);
  }
 

diff --git a/...-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/r5/ElementProcessor.java b/...-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/generate/r5/ElementProcessor.java
@@ -33,11 +33,22 @@ public ElementProcessor(Repository repository) {
 
  @Override
  public IBaseBackboneElement processElement(
- GenerateRequest request, ICompositeType baseElement, String childLinkId, IBaseResource caseFeature) {
+ GenerateRequest request,
+ ICompositeType baseElement,
+ String elementType,
+ String childLinkId,
+ IBaseResource caseFeature,
+ Boolean isGroup) {
  var element = (ElementDefinition) baseElement;
- final QuestionnaireItemType itemType = getItemType(element);
- final QuestionnaireItemComponent item =
- initializeQuestionnaireItem(itemType, request.getProfileUrl(), element, childLinkId);
+ final var itemType = isGroup ? QuestionnaireItemType.GROUP : parseItemType(elementType, element.hasBinding());
+ final var item = initializeQuestionnaireItem(itemType, request.getProfileUrl(), element, childLinkId);
+ item.setRequired(element.hasMin() && element.getMin() > 0);
+ item.setRepeats(element.hasMax() && !element.getMax().equals("1"));
+ // set enableWhen based on? use
+ // http:https://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-enableWhenExpression
+ if (itemType == QuestionnaireItemType.GROUP) {
+ return item;
+ }
  if (itemType == QuestionnaireItemType.QUESTION) {
  questionnaireTypeIsChoice.addProperties(element, item);
  }
@@ -53,10 +64,6 @@ public IBaseBackboneElement processElement(
  item.addInitial().setValue(transformValueToItem((DataType) pathValue));
  }
  }
- item.setRequired(element.hasMin() && element.getMin() > 0);
- item.setRepeats(element.hasMax() && !element.getMax().equals("1"));
- // set enableWhen based on? use
- // http:https://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-enableWhenExpression
  return item;
  }
 
@@ -70,20 +77,13 @@ protected QuestionnaireItemComponent initializeQuestionnaireItem(
  .setText(getElementText(element));
  }
 
- public QuestionnaireItemType getItemType(ElementDefinition element) {
- final String elementType = element.getType().get(0).getCode();
- final QuestionnaireItemType itemType = parseItemType(elementType, element.hasBinding());
- if (itemType == null) {
- final String message = String.format(ITEM_TYPE_ERROR, element.getId());
- throw new IllegalArgumentException(message);
- }
- return itemType;
- }
-
  public QuestionnaireItemType parseItemType(String elementType, Boolean hasBinding) {
  if (Boolean.TRUE.equals(hasBinding)) {
  return QuestionnaireItemType.QUESTION;
  }
+ if (elementType == null) {
+ throw new IllegalArgumentException("Unable to determine item type.");
+ }
  switch (elementType) {
  case "code":
  case "coding":