Fixed retrieve translation not validating code path and terminology t…

…arget.

Src/java/build.gradle

@@ -3,7 +3,7 @@ allprojects {
     apply plugin: 'eclipse'
 
     group = 'info.cqframework'
-    version = '1.2.2-SNAPSHOT'
+    version = '1.2.4-SNAPSHOT'
 }
 
 subprojects {

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/Cql2ElmVisitor.java

@@ -1499,25 +1499,7 @@ public Object visitMembershipExpression(@NotNull cqlParser.MembershipExpressionC
                 } else {
                     Expression left = parseExpression(ctx.expression(0));
                     Expression right = parseExpression(ctx.expression(1));
-                    if (right instanceof ValueSetRef) {
-                        InValueSet in = of.createInValueSet()
-                                .withCode(left)
-                                .withValueset((ValueSetRef) right);
-                        libraryBuilder.resolveCall("System", "InValueSet", new InValueSetInvocation(in));
-                        return in;
-                    }
-
-                    if (right instanceof CodeSystemRef) {
-                        InCodeSystem in = of.createInCodeSystem()
-                                .withCode(left)
-                                .withCodesystem((CodeSystemRef)right);
-                        libraryBuilder.resolveCall("System", "InCodeSystem", new InCodeSystemInvocation(in));
-                        return in;
-                    }
-
-                    In in = of.createIn().withOperand(left, right);
-                    libraryBuilder.resolveBinaryCall("System", "In", in);
-                    return in;
+                    return libraryBuilder.resolveIn(left, right);
                 }
             case "contains":
                 if (ctx.dateTimePrecisionSpecifier() != null) {
@@ -2690,12 +2672,51 @@ public Retrieve visitRetrieve(@NotNull cqlParser.RetrieveContext ctx) {
                 retrieve.setCodeProperty(classType.getPrimaryCodePath());
             }
 
+            Property property = null;
+            if (retrieve.getCodeProperty() == null) {
+                libraryBuilder.recordParsingException(new CqlSemanticException("Retrieve has a terminology target but does not specify a code path and the type of the retrieve does not have a primary code path defined.",
+                        CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx)));
+            }
+            else {
+                try {
+                    DataType codeType = libraryBuilder.resolvePath((DataType) namedType, retrieve.getCodeProperty());
+                    property = of.createProperty().withPath(retrieve.getCodeProperty());
+                    property.setResultType(codeType);
+                }
+                catch (Exception e) {
+                    libraryBuilder.recordParsingException(new CqlSemanticException(String.format("Could not resolve code path %s for the type of the retrieve %s.",
+                            retrieve.getCodeProperty(), namedType.getName()), CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx), e));
+                }
+            }
+
+            Expression terminology = null;
             if (ctx.terminology().qualifiedIdentifier() != null) {
                 List<String> identifiers = (List<String>) visit(ctx.terminology());
-                retrieve.setCodes(resolveQualifiedIdentifier(identifiers));
+                terminology = resolveQualifiedIdentifier(identifiers);
             }
             else {
-                retrieve.setCodes(parseExpression(ctx.terminology().expression()));
+                terminology = parseExpression(ctx.terminology().expression());
+            }
+
+            // Resolve the terminology target using an in operator
+            try {
+                Expression in = libraryBuilder.resolveIn(property, terminology);
+                if (in instanceof In) {
+                    retrieve.setCodes(((In) in).getOperand().get(1));
+                } else if (in instanceof InValueSet) {
+                    retrieve.setCodes(((InValueSet) in).getValueset());
+                } else if (in instanceof InCodeSystem) {
+                    retrieve.setCodes(((InCodeSystem) in).getCodesystem());
+                } else {
+                    libraryBuilder.recordParsingException(new CqlSemanticException(String.format("Unexpected membership operator %s in retrieve", in.getClass().getSimpleName()),
+                            CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx)));
+                }
+            }
+            catch (Exception e) {
+                // If something goes wrong attempting to resolve, just set to the expression and report it as a warning, it shouldn't prevent translation
+                retrieve.setCodes(terminology);
+                libraryBuilder.recordParsingException(new CqlSemanticException("Could not resolve membership operator for terminology target of the retrieve.",
+                        CqlTranslatorException.ErrorSeverity.Warning, getTrackBack(ctx), e));
             }
         }
 

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/LibraryBuilder.java

@@ -516,6 +516,28 @@ public Expression resolveAggregateCall(String libraryName, String operatorName,
         return resolveCall(libraryName, operatorName, new AggregateExpressionInvocation(expression));
     }
 
+    public Expression resolveIn(Expression left, Expression right) {
+        if (right instanceof ValueSetRef) {
+            InValueSet in = of.createInValueSet()
+                    .withCode(left)
+                    .withValueset((ValueSetRef) right);
+            resolveCall("System", "InValueSet", new InValueSetInvocation(in));
+            return in;
+        }
+
+        if (right instanceof CodeSystemRef) {
+            InCodeSystem in = of.createInCodeSystem()
+                    .withCode(left)
+                    .withCodesystem((CodeSystemRef)right);
+            resolveCall("System", "InCodeSystem", new InCodeSystemInvocation(in));
+            return in;
+        }
+
+        In in = of.createIn().withOperand(left, right);
+        resolveBinaryCall("System", "In", in);
+        return in;
+    }
+
     public Expression resolveCall(String libraryName, String operatorName, Invocation invocation) {
         return resolveCall(libraryName, operatorName, invocation, true);
     }
@@ -1090,6 +1112,14 @@ else if (currentType instanceof ChoiceType) {
                     }
                 }
             }
+            else if (currentType instanceof ListType && listTraversal) {
+                // NOTE: FHIRPath path traversal support
+                // Resolve property as a list of items of property of the element type
+                ListType listType = (ListType)currentType;
+                DataType resultType = resolveProperty(listType.getElementType(), identifier);
+                return new ListType(resultType);
+
+            }
 
             if (currentType.getBaseType() != null) {
                 currentType = currentType.getBaseType();

Src/java/cql-to-elm/src/test/resources/org/cqframework/cql/cql2elm/CMS146v2_Expected.json

@@ -1,5 +1,29 @@
 {
    "library" : {
+      "annotation" : [ {
+         "startLine" : 22,
+         "startChar" : 5,
+         "endLine" : 22,
+         "endChar" : 54,
+         "message" : "Could not resolve code path medication.code for the type of the retrieve QUICK.MedicationPrescription.",
+         "errorType" : "semantic",
+         "errorSeverity" : "warning",
+         "type" : "CqlToElmError"
+      }, {
+         "startLine" : 22,
+         "startChar" : 5,
+         "endLine" : 22,
+         "endChar" : 54,
+         "message" : "Could not resolve membership operator for terminology target of the retrieve.",
+         "errorType" : "semantic",
+         "errorSeverity" : "warning",
+         "type" : "CqlToElmError"
+      }, {
+         "message" : "List-valued expression was demoted to a singleton.",
+         "errorType" : "semantic",
+         "errorSeverity" : "warning",
+         "type" : "CqlToElmError"
+      } ],
       "identifier" : {
          "id" : "CMS146",
          "version" : "2"

Src/java/qdm/src/main/resources/gov/healthit/qdm/qdm-modelinfo-5.0.2.xml

@@ -77,7 +77,7 @@
         <ns4:element name="negationRationale" type="System.Code"/>
         <ns4:element name="lengthOfStay" type="System.Quantity"/>
     </ns4:typeInfo>
-    <ns4:typeInfo xsi:type="ns4:ClassInfo" name="QDM.Diagnosis" retrievable="true" baseType="QDM.QDMBaseType" label="Diagnosis">
+    <ns4:typeInfo xsi:type="ns4:ClassInfo" name="QDM.Diagnosis" retrievable="true" baseType="QDM.QDMBaseType" label="Diagnosis" primaryCodePath="code">
         <ns4:element name="prevalencePeriod" type="interval&lt;System.DateTime&gt;"/>
         <ns4:element name="anatomicalLocationSite" type="System.Code"/>
         <ns4:element name="severity" type="System.Code"/>

Src/java/quick/src/main/resources/org/hl7/fhir/quick-modelinfo.xml

@@ -440,8 +440,7 @@
         <ns4:element name="value" type="System.String"/>
     </ns4:typeInfo>
     <ns4:typeInfo xsi:type="ns4:ClassInfo" name="QUICK.Practitioner" baseType="QUICK.DomainResource"
-                  retrievable="true" identifier="practitioner-qicore-qicore-practitioner" primaryCodePath="practitionerRole[].role">
-                                                                                          <!-- note: primaryCodePath is invalid -->
+                  retrievable="true" identifier="practitioner-qicore-qicore-practitioner" primaryCodePath="practitionerRole.role">
         <ns4:element name="identifier" type="list&lt;QUICK.Identifier&gt;"/>
         <ns4:element name="name" type="QUICK.HumanName"/>
         <ns4:element name="telecom" type="list&lt;QUICK.ContactPoint&gt;"/>
@@ -1523,8 +1522,7 @@
         <ns4:element name="related" type="list&lt;QUICK.Observation.Related&gt;"/>
     </ns4:typeInfo>
     <ns4:typeInfo xsi:type="ns4:ClassInfo" name="QUICK.DiagnosticOrder" baseType="QUICK.DomainResource"
-                  retrievable="true" identifier="diagnosticorder-qicore-qicore-diagnosticorder" primaryCodePath="item[].code">
-                                                                                                <!-- note: primaryCodePath is invalid -->
+                  retrievable="true" identifier="diagnosticorder-qicore-qicore-diagnosticorder" primaryCodePath="item.code">
         <ns4:element name="subject" type="System.Any"/>
         <ns4:element name="orderer" type="System.Any"/>
         <ns4:element name="identifier" type="list&lt;QUICK.Identifier&gt;"/>
@@ -1587,8 +1585,7 @@
         <ns4:element name="value" type="System.String"/>
     </ns4:typeInfo>
     <ns4:typeInfo xsi:type="ns4:ClassInfo" name="QUICK.ImmunizationRecommendation" baseType="QUICK.DomainResource"
-                  retrievable="true" identifier="immunizationrecommendation-qicore-qicore-immunizationrec" primaryCodePath="recommendation[].vaccineType">
-                                                                                                           <!-- note: primaryCodePath is invalid -->
+                  retrievable="true" identifier="immunizationrecommendation-qicore-qicore-immunizationrec" primaryCodePath="recommendation.vaccineType">
         <ns4:element name="identifier" type="list&lt;QUICK.Identifier&gt;"/>
         <ns4:element name="patient" type="System.Any"/>
         <ns4:element name="recommendation" type="list&lt;QUICK.ImmunizationRecommendation.Recommendation&gt;"/>