62 create unit tests for questionnaire processor

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/plandefinition/r4/PlanDefinitionProcessor.java

@@ -55,8 +55,8 @@
 import org.opencds.cqf.fhir.cql.ExtensionResolver;
 import org.opencds.cqf.fhir.cr.activitydefinition.r4.ActivityDefinitionProcessor;
 import org.opencds.cqf.fhir.cr.plandefinition.BasePlanDefinitionProcessor;
-import org.opencds.cqf.fhir.cr.questionnaire.r4.QuestionnaireProcessor;
 import org.opencds.cqf.fhir.cr.questionnaire.r4.generator.questionnaireitem.QuestionnaireItemGenerator;
+import org.opencds.cqf.fhir.cr.questionnaire.r4.processor.QuestionnaireProcessor;
 import org.opencds.cqf.fhir.cr.questionnaireresponse.r4.QuestionnaireResponseProcessor;
 import org.opencds.cqf.fhir.utility.Constants;
 import org.opencds.cqf.fhir.utility.client.Clients;
@@ -73,7 +73,7 @@ public class PlanDefinitionProcessor extends BasePlanDefinitionProcessor<PlanDef
     private static final Logger logger = LoggerFactory.getLogger(PlanDefinitionProcessor.class);
 
     private final ActivityDefinitionProcessor activityDefinitionProcessor;
-    private final QuestionnaireProcessor questionnaireProcessor;
+    private final QuestionnaireProcessor myQuestionnaireProcessor;
     private final QuestionnaireResponseProcessor questionnaireResponseProcessor;
     private ExtensionResolver extensionResolver;
     private InputParameterResolver inputParameterResolver;
@@ -88,7 +88,7 @@ public PlanDefinitionProcessor(Repository repository) {
     public PlanDefinitionProcessor(Repository repository, EvaluationSettings evaluationSettings) {
         super(repository, evaluationSettings);
         this.activityDefinitionProcessor = new ActivityDefinitionProcessor(this.repository, evaluationSettings);
-        this.questionnaireProcessor = new QuestionnaireProcessor(this.repository, evaluationSettings);
+        this.myQuestionnaireProcessor = new QuestionnaireProcessor(this.repository, evaluationSettings);
         this.questionnaireResponseProcessor = new QuestionnaireResponseProcessor(this.repository, evaluationSettings);
     }
 
@@ -660,7 +660,7 @@ private void resolvePrepopulateAction(
                 valueSets.forEach(
                         valueSet -> additionalData.addEntry(new Bundle.BundleEntryComponent().setResource(valueSet)));
 
-                var populatedQuestionnaire = questionnaireProcessor.prePopulate(
+                var populatedQuestionnaire = myQuestionnaireProcessor.prePopulate(
                         toPopulate, subjectId, this.parameters, additionalData, libraryEngine);
                 if (Boolean.TRUE.equals(containResources)) {
                     requestGroup.addContained(populatedQuestionnaire);

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/r4/QuestionnaireProcessor.java → cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/r4/DepreciatedQuestionnaireProcessor.java

@@ -1,6 +1,6 @@
 package org.opencds.cqf.fhir.cr.questionnaire.r4;
 
-import static org.opencds.cqf.fhir.cr.questionnaire.r4.ItemValueTransformer.transformValue;
+import static org.opencds.cqf.fhir.cr.questionnaire.r4.processor.utils.ItemValueTransformer.transformValue;
 
 import java.util.ArrayList;
 import java.util.Collections;
@@ -35,15 +35,15 @@
 import org.opencds.cqf.fhir.utility.r4.PackageHelper;
 import org.opencds.cqf.fhir.utility.r4.SearchHelper;
 
-public class QuestionnaireProcessor extends BaseQuestionnaireProcessor<Questionnaire> {
+public class DepreciatedQuestionnaireProcessor extends BaseQuestionnaireProcessor<Questionnaire> {
     protected OperationOutcome oc;
     protected Questionnaire populatedQuestionnaire;
 
-    public QuestionnaireProcessor(Repository repository) {
+    public DepreciatedQuestionnaireProcessor(Repository repository) {
         this(repository, EvaluationSettings.getDefault());
     }
 
-    public QuestionnaireProcessor(Repository repository, EvaluationSettings evaluationSettings) {
+    public DepreciatedQuestionnaireProcessor(Repository repository, EvaluationSettings evaluationSettings) {
         super(repository, evaluationSettings);
     }
 
@@ -81,6 +81,7 @@ public Questionnaire prePopulate(
         this.parameters = parameters;
         this.bundle = bundle;
         this.libraryEngine = libraryEngine;
+
         libraryUrl = questionnaire.hasExtension(Constants.CQF_LIBRARY)
                 ? ((CanonicalType) questionnaire
                                 .getExtensionByUrl(Constants.CQF_LIBRARY)
@@ -237,7 +238,6 @@ public IBaseResource populate(
         var responseItems = new ArrayList<QuestionnaireResponseItemComponent>();
         processResponseItems(populatedQuestionnaire.getItem(), responseItems);
         response.setItem(responseItems);
-
         return response;
     }
 
@@ -267,10 +267,8 @@ protected void processResponseItems(
 
     @Override
     public Questionnaire generateQuestionnaire(String id) {
-
         var questionnaire = new Questionnaire();
         questionnaire.setId(new IdType("Questionnaire", id));
-
         return questionnaire;
     }
 
@@ -290,7 +288,6 @@ public Bundle packageQuestionnaire(Questionnaire questionnaire, boolean isPut) {
                 }
             }
         }
-
         return bundle;
     }
 }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/r4/generator/nestedquestionnaireitem/ElementHasCqfExpression.java

@@ -1,6 +1,6 @@
 package org.opencds.cqf.fhir.cr.questionnaire.r4.generator.nestedquestionnaireitem;
 
-import static org.opencds.cqf.fhir.cr.questionnaire.r4.ItemValueTransformer.transformValue;
+import static org.opencds.cqf.fhir.cr.questionnaire.r4.processor.utils.ItemValueTransformer.transformValue;
 
 import java.util.List;
 import org.hl7.fhir.instance.model.api.IAnyResource;

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/r4/generator/nestedquestionnaireitem/ElementHasDefaultValue.java

@@ -1,6 +1,6 @@
 package org.opencds.cqf.fhir.cr.questionnaire.r4.generator.nestedquestionnaireitem;
 
-import static org.opencds.cqf.fhir.cr.questionnaire.r4.ItemValueTransformer.transformValue;
+import static org.opencds.cqf.fhir.cr.questionnaire.r4.processor.utils.ItemValueTransformer.transformValue;
 
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemComponent;

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/r4/generator/nestedquestionnaireitem/NestedQuestionnaireItemService.java

@@ -1,6 +1,6 @@
 package org.opencds.cqf.fhir.cr.questionnaire.r4.generator.nestedquestionnaireitem;
 
-import static org.opencds.cqf.fhir.cr.questionnaire.r4.ItemValueTransformer.transformValue;
+import static org.opencds.cqf.fhir.cr.questionnaire.r4.processor.utils.ItemValueTransformer.transformValue;
 
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseParameters;

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/r4/processor/QuestionnaireProcessor.java

@@ -0,0 +1,101 @@
+package org.opencds.cqf.fhir.cr.questionnaire.r4.processor;
+
+import static java.util.Objects.requireNonNull;
+
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Questionnaire;
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.cql.EvaluationSettings;
+import org.opencds.cqf.fhir.cql.LibraryEngine;
+import org.opencds.cqf.fhir.cr.questionnaire.BaseQuestionnaireProcessor;
+import org.opencds.cqf.fhir.cr.questionnaire.r4.processor.packager.PackageService;
+import org.opencds.cqf.fhir.cr.questionnaire.r4.processor.populate.PopulateService;
+import org.opencds.cqf.fhir.cr.questionnaire.r4.processor.prepopulate.PrePopulateRequest;
+import org.opencds.cqf.fhir.cr.questionnaire.r4.processor.prepopulate.PrePopulateService;
+import org.opencds.cqf.fhir.cr.questionnaire.r4.processor.resolve.ResolveService;
+
+public class QuestionnaireProcessor extends BaseQuestionnaireProcessor<Questionnaire> {
+    protected PopulateService populateService;
+    protected ResolveService resolveService;
+    protected PackageService packageService;
+    protected PrePopulateService prePopulateService;
+
+    public QuestionnaireProcessor(Repository repository, EvaluationSettings evaluationSettings) {
+        this(repository,
+            evaluationSettings,
+            new ResolveService(repository),
+            new PackageService(repository),
+            new PopulateService(),
+            new PrePopulateService()
+        );
+    }
+
+    public QuestionnaireProcessor(Repository repository) {
+       this(repository, EvaluationSettings.getDefault());
+    }
+
+    private QuestionnaireProcessor(
+            Repository repository,
+            EvaluationSettings evaluationSettings,
+            ResolveService resolveService,
+            PackageService packageService,
+            PopulateService populateService,
+            PrePopulateService prePopulateService
+    ) {
+        super(repository, evaluationSettings);
+        this.resolveService = resolveService;
+        this.packageService = packageService;
+        this.populateService = populateService;
+        this.prePopulateService = prePopulateService;
+    }
+
+    @Override
+    public <C extends IPrimitiveType<String>> Questionnaire resolveQuestionnaire(
+            IIdType id, C canonical, IBaseResource questionnaire) {
+        return resolveService.resolve(id, canonical, questionnaire);
+    }
+
+    @Override
+    public Questionnaire prePopulate(
+            Questionnaire questionnaire,
+            String patientId,
+            IBaseParameters parameters,
+            IBaseBundle bundle,
+            LibraryEngine libraryEngine) {
+        requireNonNull(questionnaire);
+        requireNonNull(libraryEngine);
+        final PrePopulateRequest prePopulateRequest =
+                new PrePopulateRequest(questionnaire, patientId, parameters, bundle, libraryEngine);
+        return prePopulateService.prePopulate(prePopulateRequest);
+    }
+
+    @Override
+    public IBaseResource populate(
+            Questionnaire questionnaire,
+            String patientId,
+            IBaseParameters parameters,
+            IBaseBundle bundle,
+            LibraryEngine libraryEngine) {
+        final Questionnaire prePopulatedQuestionnaire =
+                prePopulate(questionnaire, patientId, parameters, bundle, libraryEngine);
+        return populateService.populate(questionnaire, prePopulatedQuestionnaire, patientId);
+    }
+
+    @Override
+    public Questionnaire generateQuestionnaire(String id) {
+        var questionnaire = new Questionnaire();
+        questionnaire.setId(new IdType("Questionnaire", id));
+        return questionnaire;
+    }
+
+    @Override
+    public Bundle packageQuestionnaire(Questionnaire questionnaire, boolean isPut) {
+        return packageService.packageQuestionnaire(questionnaire, isPut);
+    }
+}

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/r4/processor/packager/PackageService.java

@@ -0,0 +1,39 @@
+package org.opencds.cqf.fhir.cr.questionnaire.r4.processor.packager;
+
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleType;
+import org.hl7.fhir.r4.model.CanonicalType;
+import org.hl7.fhir.r4.model.Library;
+import org.hl7.fhir.r4.model.Questionnaire;
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.utility.Constants;
+import org.opencds.cqf.fhir.utility.r4.PackageHelper;
+import org.opencds.cqf.fhir.utility.r4.SearchHelper;
+
+public class PackageService {
+    final Repository repository;
+
+    public PackageService(Repository  repository) {
+        this.repository = repository;
+    }
+
+    public Bundle packageQuestionnaire(Questionnaire questionnaire, boolean isPut) {
+        // TODO: this is incomplete and needs to be abstracted further
+        final Bundle bundle = new Bundle();
+        bundle.setType(BundleType.TRANSACTION);
+        bundle.addEntry(PackageHelper.createEntry(questionnaire, isPut));
+        var libraryExtension = questionnaire.getExtensionByUrl(Constants.CQF_LIBRARY);
+        if (libraryExtension != null) {
+            var libraryCanonical = (CanonicalType) libraryExtension.getValue();
+            var library = (Library) SearchHelper.searchRepositoryByCanonical(repository, libraryCanonical);
+            if (library != null) {
+                bundle.addEntry(PackageHelper.createEntry(library, isPut));
+                if (library.hasRelatedArtifact()) {
+                    PackageHelper.addRelatedArtifacts(bundle, library.getRelatedArtifact(),
+                        repository, isPut);
+                }
+            }
+        }
+        return bundle;
+    }
+}

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/questionnaire/r4/processor/populate/PopulateService.java

@@ -0,0 +1,94 @@
+package org.opencds.cqf.fhir.cr.questionnaire.r4.processor.populate;
+
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.Collectors;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.OperationOutcome;
+import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
+import org.hl7.fhir.r4.model.Questionnaire;
+import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemComponent;
+import org.hl7.fhir.r4.model.QuestionnaireResponse;
+import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemAnswerComponent;
+import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemComponent;
+import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r4.model.ResourceType;
+import org.opencds.cqf.fhir.cr.questionnaire.r4.processor.utils.ExtensionBuilders;
+import org.opencds.cqf.fhir.utility.Constants;
+
+public class PopulateService {
+    public QuestionnaireResponse populate(
+            Questionnaire originalQuestionnaire, Questionnaire prePopulatedQuestionnaire, String patientId) {
+        final QuestionnaireResponse response = new QuestionnaireResponse();
+        response.setId(prePopulatedQuestionnaire.getIdPart() + "-response");
+        final Optional<OperationOutcome> operationOutcome =
+                getOperationOutcomeFromPrePopulatedQuestionnaire(prePopulatedQuestionnaire);
+        if (prePopulatedQuestionnaire.hasExtension(Constants.EXT_CRMI_MESSAGES) && operationOutcome.isPresent()) {
+            response.addContained(operationOutcome.get());
+            response.addExtension(ExtensionBuilders.crmiMessagesExtension(
+                    operationOutcome.get().getIdPart()));
+        }
+        response.addContained(prePopulatedQuestionnaire);
+        response.addExtension(ExtensionBuilders.dtrQuestionnaireResponseExtension(prePopulatedQuestionnaire));
+        response.setQuestionnaire(originalQuestionnaire.getUrl());
+        response.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.INPROGRESS);
+        response.setSubject(new Reference(new IdType("Patient", patientId)));
+        response.setItem(processResponseItems(prePopulatedQuestionnaire.getItem()));
+        return response;
+    }
+
+    protected Optional<OperationOutcome> getOperationOutcomeFromPrePopulatedQuestionnaire(
+            Questionnaire prePopulatedQuestionnaire) {
+        return prePopulatedQuestionnaire.getContained().stream()
+                .filter(theResource -> theResource.getResourceType() == ResourceType.OperationOutcome)
+                .map(OperationOutcome.class::cast)
+                .filter(this::filterOperationOutcome)
+                .findFirst();
+    }
+
+    protected boolean filterOperationOutcome(OperationOutcome operationOutcome) {
+        if (operationOutcome.hasIssue()) {
+            final List<OperationOutcomeIssueComponent> filteredIssues = operationOutcome.getIssue().stream()
+                    .filter(theIssue -> theIssue.getCode() == OperationOutcome.IssueType.EXCEPTION
+                            && theIssue.getSeverity() == OperationOutcome.IssueSeverity.ERROR)
+                    .collect(Collectors.toList());
+            return !filteredIssues.isEmpty();
+        }
+        return false;
+    }
+
+    protected List<QuestionnaireResponseItemComponent> processResponseItems(
+            List<QuestionnaireItemComponent> questionnaireItems) {
+        return questionnaireItems.stream().map(this::processResponseItem).collect(Collectors.toList());
+    }
+
+    protected QuestionnaireResponseItemComponent processResponseItem(QuestionnaireItemComponent questionnaireItem) {
+        QuestionnaireResponseItemComponent responseItem =
+                new QuestionnaireResponseItemComponent(questionnaireItem.getLinkIdElement());
+        responseItem.setDefinition(questionnaireItem.getDefinition());
+        responseItem.setTextElement(questionnaireItem.getTextElement());
+        if (questionnaireItem.hasItem()) {
+            final List<QuestionnaireResponseItemComponent> nestedResponseItems =
+                    processResponseItems(questionnaireItem.getItem());
+            responseItem.setItem(nestedResponseItems);
+        } else if (questionnaireItem.hasInitial()) {
+            responseItem = setAnswersForInitial(questionnaireItem, responseItem);
+        }
+        return responseItem;
+    }
+
+    protected QuestionnaireResponseItemComponent setAnswersForInitial(
+            QuestionnaireItemComponent questionnaireItem,
+            QuestionnaireResponseItemComponent questionnaireResponseItem) {
+        if (questionnaireItem.hasExtension(Constants.QUESTIONNAIRE_RESPONSE_AUTHOR)) {
+            questionnaireResponseItem.addExtension(
+                    questionnaireItem.getExtensionByUrl(Constants.QUESTIONNAIRE_RESPONSE_AUTHOR));
+        }
+        questionnaireItem.getInitial().forEach(initial -> {
+            final QuestionnaireResponseItemAnswerComponent answer =
+                    new QuestionnaireResponseItemAnswerComponent().setValue(initial.getValue());
+            questionnaireResponseItem.addAnswer(answer);
+        });
+        return questionnaireResponseItem;
+    }
+}