Refactor how Questionnaires are generated during the $apply operation

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/LibraryConstructor.java

@@ -5,7 +5,9 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.fhirpath.IFhirPath;
+import java.util.Arrays;
 import java.util.List;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.opencds.cqf.fhir.cql.engine.parameters.CqlParameterDefinition;
 import org.opencds.cqf.fhir.utility.FhirPathCache;
@@ -28,25 +30,38 @@ public LibraryConstructor(FhirContext fhirContext) {
     public String constructCqlLibrary(
             String expression, List<Pair<String, String>> libraries, List<CqlParameterDefinition> parameters) {
         logger.debug("Constructing expression for local evaluation");
+        return constructCqlLibrary(
+                "expression",
+                "1.0.0",
+                Arrays.asList(String.format("%ndefine \"return\":%n       %s", expression)),
+                libraries,
+                parameters);
+    }
+
+    public String constructCqlLibrary(
+            String name,
+            String version,
+            List<String> expressions,
+            List<Pair<String, String>> libraries,
+            List<CqlParameterDefinition> parameters) {
 
         StringBuilder sb = new StringBuilder();
 
-        constructHeader(sb);
+        constructHeader(sb, name, version);
         constructUsings(sb);
         constructIncludes(sb, libraries);
         constructParameters(sb, parameters);
-        constructExpression(sb, expression);
+        constructContext(sb, null);
+        for (var expression : expressions) {
+            sb.append(String.format("%s%n%n", expression));
+        }
 
         String cql = sb.toString();
 
         logger.debug(cql);
         return cql;
     }
 
-    private void constructExpression(StringBuilder sb, String expression) {
-        sb.append(String.format("%ndefine \"return\":%n       %s", expression));
-    }
-
     private String getFhirVersionString(FhirVersionEnum fhirVersion) {
         // The version of the DSTU3 enum is 3.0.2 which the CQL Engine does not support.
         return fhirVersion == FhirVersionEnum.DSTU3 ? "3.0.1" : fhirVersion.getFhirVersionString();
@@ -70,6 +85,7 @@ private void constructIncludes(StringBuilder sb, List<Pair<String, String>> libr
                 sb.append("\n");
             }
         }
+        sb.append("\n");
     }
 
     private void constructParameters(StringBuilder sb, List<CqlParameterDefinition> parameters) {
@@ -98,11 +114,16 @@ private String getTypeDeclaration(String type, Boolean isList) {
 
     private void constructUsings(StringBuilder sb) {
         sb.append(String.format(
-                "using FHIR version '%s'%n",
+                "using FHIR version '%s'%n%n",
                 getFhirVersionString(fhirContext.getVersion().getVersion())));
     }
 
-    private void constructHeader(StringBuilder sb) {
-        sb.append(String.format("library expression version '1.0.0'%n%n"));
+    private void constructHeader(StringBuilder sb, String name, String version) {
+        sb.append(String.format("library %s version '%s'%n%n", name, version));
+    }
+
+    private void constructContext(StringBuilder sb, String contextType) {
+        sb.append(String.format(
+                String.format("context %s%n%n", StringUtils.isBlank(contextType) ? "Patient" : contextType)));
     }
 }

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/LibraryEngine.java

@@ -56,6 +56,10 @@ public Repository getRepository() {
         return repository;
     }
 
+    public EvaluationSettings getSettings() {
+        return settings;
+    }
+
     private Pair<String, Object> buildContextParameter(String patientId) {
         Pair<String, Object> contextParameter = null;
         if (patientId != null) {

cqf-fhir-cql/src/test/java/org/opencds/cqf/fhir/cql/LibraryEngineTests.java

@@ -1,6 +1,7 @@
 package org.opencds.cqf.fhir.cql;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.opencds.cqf.fhir.test.Resources.getResourcePath;
 import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
 import static org.opencds.cqf.fhir.utility.r4.Parameters.part;
@@ -16,9 +17,12 @@
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Encounter;
+import org.hl7.fhir.r4.model.Encounter.EncounterStatus;
 import org.hl7.fhir.r4.model.HumanName;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Practitioner;
+import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.Task;
 import org.junit.jupiter.api.BeforeEach;
@@ -79,13 +83,35 @@ void fhirPathWithResource() {
                 ((CodeableConcept) result.get(0)).getCodingFirstRep().getCode());
     }
 
+    @Test
+    void fhirPathWithContextAndResource() {
+        var patientId = "Patient/Patient1";
+        var patient = new Patient().addName(new HumanName().addGiven("Alice")).setId(patientId);
+        var encounter = new Encounter()
+                .setSubject(new Reference(patient.getIdElement()))
+                .setStatus(EncounterStatus.FINISHED);
+        var params = parameters();
+        params.addParameter(part("%subject", patient));
+        params.addParameter(part("%practitioner", new Practitioner().addName(new HumanName().addGiven("Michael"))));
+        var expression = new CqfExpression(
+                "text/fhirpath",
+                "'Encounter: ' + %context.status + ' ' + %resource.code.coding[0].system + ' ' + %resource.code.coding[0].code",
+                null);
+
+        var task = new Task().setCode(new CodeableConcept(new Coding("test-system", "test-code", null)));
+
+        var result = libraryEngine.resolveExpression(patientId, expression, params, null, encounter, task);
+        assertNotNull(result);
+        assertEquals("Encounter: finished test-system test-code", ((StringType) result.get(0)).getValueAsString());
+    }
+
     @Test
     void expressionWithLibraryReference() {
         var patientId = "Patient/Patient1";
         var expression =
                 new CqfExpression("text/cql", "TestLibrary.testExpression", "http://fhir.test/Library/TestLibrary");
         var result = libraryEngine.resolveExpression(patientId, expression, null, null, null, null);
-        assertEquals(((StringType) result.get(0)).getValue(), "I am a test");
+        assertEquals("I am a test", ((StringType) result.get(0)).getValue());
     }
 
     String libraryCql = "library MyLibrary version '1.0.0'\n"

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/activitydefinition/ActivityDefinitionProcessor.java

@@ -29,13 +29,12 @@
 import org.opencds.cqf.fhir.utility.repository.operations.IActivityDefinitionProcessor;
 
 public class ActivityDefinitionProcessor implements IActivityDefinitionProcessor {
-    // private static final Logger logger = LoggerFactory.getLogger(ActivityDefinitionProcessor.class);
     protected final ModelResolver modelResolver;
     protected final EvaluationSettings evaluationSettings;
     protected final FhirVersionEnum fhirVersion;
     protected final ResourceResolver resourceResolver;
-    protected final IApplyProcessor applyProcessor;
-    protected final IRequestResolverFactory requestResolverFactory;
+    protected IApplyProcessor applyProcessor;
+    protected IRequestResolverFactory requestResolverFactory;
     protected Repository repository;
     protected ExtensionResolver extensionResolver;
 
@@ -57,12 +56,8 @@ public ActivityDefinitionProcessor(
         this.resourceResolver = new ResourceResolver("ActivityDefinition", this.repository);
         fhirVersion = repository.fhirContext().getVersion().getVersion();
         modelResolver = FhirModelResolverCache.resolverForVersion(fhirVersion);
-        this.requestResolverFactory = requestResolverFactory == null
-                ? IRequestResolverFactory.getDefault(fhirVersion)
-                : requestResolverFactory;
-        this.applyProcessor = applyProcessor != null
-                ? applyProcessor
-                : new ApplyProcessor(this.repository, this.requestResolverFactory);
+        this.requestResolverFactory = requestResolverFactory;
+        this.applyProcessor = applyProcessor;
     }
 
     @Override
@@ -109,8 +104,8 @@ public <C extends IPrimitiveType<String>, R extends IBaseResource> IBaseResource
             IBaseDatatype setting,
             IBaseDatatype settingContext,
             IBaseParameters parameters,
-            Boolean useServerData,
-            IBaseBundle bundle,
+            boolean useServerData,
+            IBaseBundle data,
             IBaseResource dataEndpoint,
             IBaseResource contentEndpoint,
             IBaseResource terminologyEndpoint) {
@@ -127,7 +122,7 @@ public <C extends IPrimitiveType<String>, R extends IBaseResource> IBaseResource
                 settingContext,
                 parameters,
                 useServerData,
-                bundle,
+                data,
                 createRestRepository(repository.fhirContext(), dataEndpoint),
                 createRestRepository(repository.fhirContext(), contentEndpoint),
                 createRestRepository(repository.fhirContext(), terminologyEndpoint));
@@ -145,8 +140,8 @@ public <C extends IPrimitiveType<String>, R extends IBaseResource> IBaseResource
             IBaseDatatype setting,
             IBaseDatatype settingContext,
             IBaseParameters parameters,
-            Boolean useServerData,
-            IBaseBundle bundle,
+            boolean useServerData,
+            IBaseBundle data,
             Repository dataRepository,
             Repository contentRepository,
             Repository terminologyRepository) {
@@ -164,7 +159,7 @@ public <C extends IPrimitiveType<String>, R extends IBaseResource> IBaseResource
                 settingContext,
                 parameters,
                 useServerData,
-                bundle,
+                data,
                 new LibraryEngine(repository, evaluationSettings));
     }
 
@@ -180,8 +175,8 @@ public <C extends IPrimitiveType<String>, R extends IBaseResource> IBaseResource
             IBaseDatatype setting,
             IBaseDatatype settingContext,
             IBaseParameters parameters,
-            Boolean useServerData,
-            IBaseBundle bundle,
+            boolean useServerData,
+            IBaseBundle data,
             LibraryEngine libraryEngine) {
         if (StringUtils.isBlank(subjectId)) {
             throw new IllegalArgumentException("Missing required parameter: 'subject'");
@@ -203,12 +198,23 @@ public <C extends IPrimitiveType<String>, R extends IBaseResource> IBaseResource
                 settingContext,
                 parameters,
                 useServerData,
-                bundle,
+                data,
                 libraryEngine,
                 modelResolver);
+        initApplyProcessor();
         return applyProcessor.apply(request);
     }
 
+    protected void initApplyProcessor() {
+        if (applyProcessor == null) {
+            applyProcessor = new ApplyProcessor(
+                    repository,
+                    requestResolverFactory != null
+                            ? requestResolverFactory
+                            : IRequestResolverFactory.getDefault(fhirVersion));
+        }
+    }
+
     protected <C extends IPrimitiveType<String>, R extends IBaseResource> R resolveActivityDefinition(
             Either3<C, IIdType, R> activityDefinition) {
         return resourceResolver.resolve(activityDefinition);

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/activitydefinition/apply/ApplyRequest.java

@@ -13,6 +13,7 @@
 import org.opencds.cqf.fhir.cql.LibraryEngine;
 import org.opencds.cqf.fhir.cr.common.ICpgRequest;
 import org.opencds.cqf.fhir.cr.inputparameters.IInputParameterResolver;
+import org.opencds.cqf.fhir.utility.adapter.QuestionnaireAdapter;
 
 public class ApplyRequest implements ICpgRequest {
     private final IBaseResource activityDefinition;
@@ -27,7 +28,7 @@ public class ApplyRequest implements ICpgRequest {
     private final IBaseDatatype settingContext;
     private final IBaseParameters parameters;
     private final Boolean useServerData;
-    private final IBaseBundle bundle;
+    private final IBaseBundle data;
     private final LibraryEngine libraryEngine;
     private final ModelResolver modelResolver;
     private final FhirVersionEnum fhirVersion;
@@ -47,11 +48,13 @@ public ApplyRequest(
             IBaseDatatype setting,
             IBaseDatatype settingContext,
             IBaseParameters parameters,
-            Boolean useServerData,
-            IBaseBundle bundle,
+            boolean useServerData,
+            IBaseBundle data,
             LibraryEngine libraryEngine,
             ModelResolver modelResolver) {
+        checkNotNull(activityDefinition, "expected non-null value for activityDefinition");
         checkNotNull(libraryEngine, "expected non-null value for libraryEngine");
+        checkNotNull(modelResolver, "expected non-null value for modelResolver");
         this.activityDefinition = activityDefinition;
         this.subjectId = subjectId;
         this.encounterId = encounterId;
@@ -64,7 +67,7 @@ public ApplyRequest(
         this.settingContext = settingContext;
         this.parameters = parameters;
         this.useServerData = useServerData;
-        this.bundle = bundle;
+        this.data = data;
         this.libraryEngine = libraryEngine;
         this.modelResolver = modelResolver;
         fhirVersion = activityDefinition.getStructureFhirVersionEnum();
@@ -76,7 +79,7 @@ public ApplyRequest(
                 this.practitionerId,
                 this.parameters,
                 this.useServerData,
-                this.bundle);
+                this.data);
     }
 
     public IBaseResource getActivityDefinition() {
@@ -134,12 +137,12 @@ public IBaseDatatype getSettingContext() {
     }
 
     @Override
-    public IBaseBundle getBundle() {
-        return bundle;
+    public IBaseBundle getData() {
+        return data;
     }
 
     @Override
-    public Boolean getUseServerData() {
+    public boolean getUseServerData() {
         return useServerData;
     }
 
@@ -210,4 +213,9 @@ protected final String resolveDefaultLibraryUrl() {
     public IBaseResource getQuestionnaire() {
         return null;
     }
+
+    @Override
+    public QuestionnaireAdapter getQuestionnaireAdapter() {
+        return null;
+    }
 }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/activitydefinition/apply/resolvers/dstu3/ReferralRequestResolver.java

@@ -32,7 +32,7 @@ public ReferralRequest resolve(ICpgRequest request) {
         if (request.hasPractitionerId()) {
             referralRequest.setRequester(
                     new ReferralRequestRequesterComponent(new Reference(request.getPractitionerId())));
-        } else if (request.hasOrganizationId() != null) {
+        } else if (request.hasOrganizationId()) {
             referralRequest.setRequester(
                     new ReferralRequestRequesterComponent(new Reference(request.getOrganizationId())));
         }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/common/DataRequirementsProcessor.java

@@ -0,0 +1,36 @@
+package org.opencds.cqf.fhir.cr.common;
+
+import static org.opencds.cqf.fhir.utility.Parameters.newParameters;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IDomainResource;
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.cql.EvaluationSettings;
+import org.opencds.cqf.fhir.cr.visitor.DataRequirementsVisitor;
+import org.opencds.cqf.fhir.utility.adapter.AdapterFactory;
+
+public class DataRequirementsProcessor implements IDataRequirementsProcessor {
+    protected final Repository repository;
+    protected final FhirVersionEnum fhirVersion;
+    protected final DataRequirementsVisitor dataRequirementsVisitor;
+
+    public DataRequirementsProcessor(Repository repository) {
+        this(repository, EvaluationSettings.getDefault());
+    }
+
+    public DataRequirementsProcessor(Repository repository, EvaluationSettings evaluationSettings) {
+        this.repository = repository;
+        this.fhirVersion = this.repository.fhirContext().getVersion().getVersion();
+        dataRequirementsVisitor = new DataRequirementsVisitor(evaluationSettings);
+    }
+
+    @Override
+    public IBaseResource getDataRequirements(IBaseResource resource, IBaseParameters parameters) {
+        return (IBaseResource) dataRequirementsVisitor.visit(
+                AdapterFactory.forFhirVersion(fhirVersion).createKnowledgeArtifactAdapter((IDomainResource) resource),
+                repository,
+                parameters == null ? newParameters(repository.fhirContext()) : parameters);
+    }
+}

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/common/DynamicValueProcessor.java

@@ -130,7 +130,7 @@ protected List<IBase> getDynamicValueExpressionResult(
                         request.getSubjectId().getIdPart(),
                         cqfExpression,
                         request.getParameters(),
-                        request.getBundle(),
+                        request.getData(),
                         context,
                         resource);
     }