Populate and evaluate enhancements

cqf-fhir-benchmark/src/test/java/org/opencds/cqf/fhir/benchmark/helpers/RequestHelpers.java

@@ -6,7 +6,7 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.opencds.cqf.cql.engine.model.ModelResolver;
 import org.opencds.cqf.fhir.cql.LibraryEngine;
-import org.opencds.cqf.fhir.cr.inputparameters.IInputParameterResolver;
+import org.opencds.cqf.fhir.cr.common.IInputParameterResolver;
 import org.opencds.cqf.fhir.cr.library.evaluate.EvaluateRequest;
 import org.opencds.cqf.fhir.cr.questionnaire.generate.GenerateRequest;
 import org.opencds.cqf.fhir.cr.questionnaire.populate.PopulateRequest;
@@ -118,7 +118,6 @@ public static org.opencds.cqf.fhir.cr.plandefinition.apply.ApplyRequest newPDApp
                 null,
                 null,
                 null,
-                true,
                 null,
                 null,
                 libraryEngine,
@@ -156,7 +155,6 @@ public static PopulateRequest newPopulateRequestForVersion(
                 null,
                 null,
                 null,
-                true,
                 libraryEngine,
                 FhirModelResolverCache.resolverForVersion(fhirVersion));
     }
@@ -172,7 +170,6 @@ public static ExtractRequest newExtractRequestForVersion(
                 Ids.newId(fhirVersion, Ids.ensureIdType(PATIENT_ID, "Patient")),
                 null,
                 null,
-                true,
                 libraryEngine,
                 FhirModelResolverCache.resolverForVersion(fhirVersion),
                 null);
@@ -185,7 +182,6 @@ public static EvaluateRequest newEvaluateRequestForVersion(
                 Ids.newId(fhirVersion, Ids.ensureIdType(PATIENT_ID, "Patient")),
                 null,
                 null,
-                true,
                 null,
                 null,
                 libraryEngine,

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

@@ -1,7 +1,7 @@
 package org.opencds.cqf.fhir.cql;
 
 import java.util.List;
-import java.util.stream.Collectors;
+import java.util.Map;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseDatatype;
@@ -31,54 +31,40 @@ public ExtensionResolver(
 
     @SuppressWarnings({"unchecked", "rawtypes"})
     public <E extends IBaseExtension> void resolveExtensions(
-            IBase resource, List<E> extensions, String defaultLibraryUrl) {
+            IBase resource, List<E> extensions, Map<String, String> referencedLibraries) {
         for (var extension : extensions) {
             var nestedExtensions = extension.getExtension();
             if (nestedExtensions != null && !nestedExtensions.isEmpty()) {
-                resolveExtensions(resource, nestedExtensions, defaultLibraryUrl);
+                resolveExtensions(resource, nestedExtensions, referencedLibraries);
             }
             var value = extension.getValue();
             if (value instanceof IBaseHasExtensions) {
                 var valueExtensions = ((IBaseHasExtensions) value).getExtension();
                 if (valueExtensions != null) {
                     var expressionExtensions = valueExtensions.stream()
                             .filter(e -> e.getUrl() != null && e.getUrl().equals(Constants.CQF_EXPRESSION))
-                            .collect(Collectors.toList());
-                    if (expressionExtensions != null && !expressionExtensions.isEmpty()) {
-                        var expression = expressionExtensions.get(0).getValue();
-                        if (expression != null) {
-                            var result = getExpressionResult(expression, defaultLibraryUrl, resource);
-                            if (result != null) {
-                                extension.setValue(result);
-                            }
+                            .findFirst();
+                    if (expressionExtensions.isPresent()) {
+                        var result = getExpressionResult(expressionExtensions.get(), referencedLibraries, resource);
+                        if (result != null) {
+                            extension.setValue(result);
                         }
                     }
                 }
             }
         }
     }
 
-    protected IBaseDatatype getExpressionResult(IBaseDatatype expression, String defaultLibraryUrl, IBase resource) {
-        List<IBase> result = null;
-        if (expression instanceof org.hl7.fhir.r4.model.Expression) {
-            result = libraryEngine.resolveExpression(
-                    subjectId.getIdPart(),
-                    CqfExpression.of((org.hl7.fhir.r4.model.Expression) expression, defaultLibraryUrl),
-                    parameters,
-                    bundle,
-                    resource,
-                    null);
-        }
-
-        if (expression instanceof org.hl7.fhir.r5.model.Expression) {
-            result = libraryEngine.resolveExpression(
-                    subjectId.getIdPart(),
-                    CqfExpression.of((org.hl7.fhir.r5.model.Expression) expression, defaultLibraryUrl),
-                    parameters,
-                    bundle,
-                    resource,
-                    null);
-        }
+    protected <E extends IBaseExtension<?, ?>> IBaseDatatype getExpressionResult(
+            E expressionExtension, Map<String, String> referencedLibraries, IBase resource) {
+        var result = libraryEngine.resolveExpression(
+                subjectId.getIdPart(),
+                CqfExpression.of(expressionExtension, referencedLibraries),
+                parameters,
+                null,
+                bundle,
+                resource,
+                null);
 
         return result != null && !result.isEmpty() ? (IBaseDatatype) result.get(0) : null;
     }

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

@@ -5,10 +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 java.util.Map;
 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;
 import org.slf4j.Logger;
@@ -28,12 +27,16 @@ public LibraryConstructor(FhirContext fhirContext) {
     }
 
     public String constructCqlLibrary(
-            String expression, List<Pair<String, String>> libraries, List<CqlParameterDefinition> parameters) {
+            String name,
+            String version,
+            String expression,
+            Map<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)),
+                name,
+                version,
+                List.of(String.format("%ndefine \"return\":%n       %s", expression)),
                 libraries,
                 parameters);
     }
@@ -42,7 +45,7 @@ public String constructCqlLibrary(
             String name,
             String version,
             List<String> expressions,
-            List<Pair<String, String>> libraries,
+            Map<String, String> libraries,
             List<CqlParameterDefinition> parameters) {
 
         StringBuilder sb = new StringBuilder();
@@ -67,21 +70,19 @@ private String getFhirVersionString(FhirVersionEnum fhirVersion) {
         return fhirVersion == FhirVersionEnum.DSTU3 ? "3.0.1" : fhirVersion.getFhirVersionString();
     }
 
-    private void constructIncludes(StringBuilder sb, List<Pair<String, String>> libraries) {
+    private void constructIncludes(StringBuilder sb, Map<String, String> libraries) {
         sb.append(String.format(
                 "include FHIRHelpers version '%s' called FHIRHelpers%n",
                 getFhirVersionString(fhirContext.getVersion().getVersion())));
 
         if (libraries != null) {
-            for (Pair<String, String> library : libraries) {
-                var vi = VersionedIdentifiers.forUrl(library.getLeft());
+            for (var library : libraries.entrySet()) {
+                var vi = VersionedIdentifiers.forUrl(library.getValue());
                 sb.append(String.format("include \"%s\"", vi.getId()));
                 if (vi.getVersion() != null) {
                     sb.append(String.format(" version '%s'", vi.getVersion()));
                 }
-                if (library.getRight() != null) {
-                    sb.append(String.format(" called \"%s\"", library.getRight()));
-                }
+                sb.append(String.format(" called \"%s\"", library.getKey()));
                 sb.append("\n");
             }
         }

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

@@ -8,12 +8,14 @@
 import jakarta.annotation.Nullable;
 import java.time.ZonedDateTime;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
 import org.cqframework.cql.cql2elm.StringLibrarySourceProvider;
 import org.hl7.elm.r1.VersionedIdentifier;
@@ -25,14 +27,13 @@
 import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cql.engine.parameters.CqlFhirParametersConverter;
 import org.opencds.cqf.fhir.cql.engine.parameters.CqlParameterDefinition;
-import org.opencds.cqf.fhir.utility.Canonicals;
 import org.opencds.cqf.fhir.utility.CqfExpression;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 public class LibraryEngine {
 
-    private static Logger logger = LoggerFactory.getLogger(LibraryEngine.class);
+    private static final Logger logger = LoggerFactory.getLogger(LibraryEngine.class);
 
     protected final Repository repository;
     protected final FhirContext fhirContext;
@@ -96,50 +97,67 @@ public IBaseParameters evaluate(
         return cqlFhirParametersConverter.toFhirParameters(result);
     }
 
+    protected String getModelName(Object base) {
+        if (base instanceof List<?> list) {
+            return getModelName(list.get(0));
+        }
+        var fhirType = ((IBase) base).fhirType();
+        if (fhirType.contains(".")) {
+            var split = fhirType.split("\\.");
+            fhirType = Arrays.stream(split).map(StringUtils::capitalize).collect(Collectors.joining("."));
+        }
+        return String.format("FHIR.%s", fhirType);
+    }
+
     public IBaseParameters evaluateExpression(
             String expression,
             IBaseParameters parameters,
+            Map<String, Object> rawParameters,
             String patientId,
-            List<Pair<String, String>> libraries,
+            Map<String, String> referencedLibraries,
             IBaseBundle bundle,
             IBase contextParameter,
             IBase resourceParameter) {
         var libraryConstructor = new LibraryConstructor(fhirContext);
         var cqlFhirParametersConverter = Engines.getCqlFhirParametersConverter(fhirContext);
         var cqlParameters = cqlFhirParametersConverter.toCqlParameterDefinitions(parameters);
+        var fhirPathContextName = "%fhirpathcontext";
         if (contextParameter != null) {
-            var contextType = contextParameter.getClass().getSimpleName();
-            cqlParameters.add(new CqlParameterDefinition("%fhirpathcontext", contextType, false, contextParameter));
-            var resourceType = resourceParameter == null
-                    ? contextType
-                    : resourceParameter.getClass().getSimpleName();
-            cqlParameters.add(new CqlParameterDefinition(
-                    "%resource",
-                    resourceType, false, resourceParameter == null ? contextParameter : resourceParameter));
+            var contextType = getModelName(contextParameter);
+            cqlParameters.add(new CqlParameterDefinition(fhirPathContextName, contextType, false));
+            var resourceType = resourceParameter == null ? contextType : getModelName(resourceParameter);
+            cqlParameters.add(new CqlParameterDefinition("%resource", resourceType, false));
+        }
+        if (rawParameters != null) {
+            rawParameters.forEach(
+                    (k, v) -> cqlParameters.add(new CqlParameterDefinition(k, getModelName(v), v instanceof List<?>)));
         }
         // There is currently a bug in the CQL compiler that causes the FHIRPath %context variable to fail.
         // This bit of hackery finds any uses of %context in the expression being evaluated and switches it to
         // fhirpathcontext to allow for successful evaluation.
         if (expression.contains("%context")) {
-            expression = expression.replace("%context", "%fhirpathcontext");
+            expression = expression.replace("%context", fhirPathContextName);
         }
-        var cql = libraryConstructor.constructCqlLibrary(expression, libraries, cqlParameters);
-
+        var libraryName = "expression";
+        var libraryVersion = "1.0.0";
+        var cql = libraryConstructor.constructCqlLibrary(
+                libraryName, libraryVersion, expression, referencedLibraries, cqlParameters);
         Set<String> expressions = new HashSet<>();
         expressions.add("return");
 
         var requestSettings = new EvaluationSettings(settings);
-
         requestSettings.getLibrarySourceProviders().add(new StringLibrarySourceProvider(Lists.newArrayList(cql)));
-
         var engine = Engines.forRepository(repository, requestSettings, bundle);
 
         var evaluationParameters = cqlFhirParametersConverter.toCqlParameters(parameters);
         if (contextParameter != null) {
-            evaluationParameters.put("%fhirpathcontext", contextParameter);
+            evaluationParameters.put(fhirPathContextName, contextParameter);
             evaluationParameters.put("%resource", resourceParameter == null ? contextParameter : resourceParameter);
         }
-        var id = new VersionedIdentifier().withId("expression").withVersion("1.0.0");
+        if (rawParameters != null) {
+            evaluationParameters.putAll(rawParameters);
+        }
+        var id = new VersionedIdentifier().withId(libraryName).withVersion(libraryVersion);
         var result = engine.evaluate(id.getId(), expressions, buildContextParameter(patientId), evaluationParameters);
 
         return cqlFhirParametersConverter.toFhirParameters(result);
@@ -150,7 +168,9 @@ public List<IBase> getExpressionResult(
             String expression,
             String language,
             String libraryToBeEvaluated,
+            Map<String, String> referencedLibraries,
             IBaseParameters parameters,
+            Map<String, Object> rawParameters,
             IBaseBundle bundle,
             IBase contextParameter,
             IBase resourceParameter) {
@@ -162,13 +182,15 @@ public List<IBase> getExpressionResult(
             case "text/cql.expression":
             case "text/cql-expression":
             case "text/fhirpath":
-                var libraries = new ArrayList<Pair<String, String>>();
-                if (!StringUtils.isBlank(libraryToBeEvaluated)) {
-                    libraries.add(
-                            new ImmutablePair<>(libraryToBeEvaluated, Canonicals.getIdPart(libraryToBeEvaluated)));
-                }
                 parametersResult = this.evaluateExpression(
-                        expression, parameters, subjectId, libraries, bundle, contextParameter, resourceParameter);
+                        expression,
+                        parameters,
+                        rawParameters,
+                        subjectId,
+                        referencedLibraries,
+                        bundle,
+                        contextParameter,
+                        resourceParameter);
                 // The expression is assumed to be the parameter component name
                 // The expression evaluator creates a library with a single expression defined as "return"
                 results = resolveParameterValues(
@@ -256,6 +278,7 @@ public List<IBase> resolveExpression(
             String patientId,
             CqfExpression expression,
             IBaseParameters params,
+            Map<String, Object> rawParameters,
             IBaseBundle bundle,
             IBase contextParameter,
             IBase resourceParameter) {
@@ -264,7 +287,9 @@ public List<IBase> resolveExpression(
                 expression.getExpression(),
                 expression.getLanguage(),
                 expression.getLibraryUrl(),
+                expression.getReferencedLibraries(),
                 params,
+                rawParameters,
                 bundle,
                 contextParameter,
                 resourceParameter);
@@ -274,7 +299,9 @@ public List<IBase> resolveExpression(
                     expression.getAltExpression(),
                     expression.getAltLanguage(),
                     expression.getAltLibraryUrl(),
+                    expression.getReferencedLibraries(),
                     params,
+                    rawParameters,
                     bundle,
                     contextParameter,
                     resourceParameter);