Br fixes 2023 07 10 (cqframework#1177)

* cqframework#1156: Added test cases for CMS143 and CMS149 to validate data requirements output

* cqframework#1147: Fixed invalid let ref during data requirements inference

* cqframework#1146: Added test for MedicationRequest to ensure expected ELM output

* cqframework#1109: Fixed newlines being stripped incorrectly in mixed single- and multi-line comments

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

@@ -576,25 +576,32 @@ private Narrative buildNarrative(Chunk chunk) {
         else {
             String chunkContent = tokenStream.getText(chunk.getInterval());
             if (chunk.isHeaderChunk()) {
-                chunkContent = chunkContent.trim();
+                chunkContent = stripLeading(chunkContent);
             }
             chunkContent = normalizeWhitespace(chunkContent);
-            chunkContent = makeSeparationBetweenCommentAndDefinition(chunkContent);
             narrative.getContent().add(chunkContent);
         }
 
         return narrative;
     }
 
-    private String normalizeWhitespace(String input) {
-        return input.replace("\r\n", "\n");
+    // TODO: Should just use String.stripLeading() but that is only available in 11+
+    private String stripLeading(String s) {
+        int index = 0;
+        while (index < s.length()) {
+            if (!Character.isWhitespace(s.charAt(index))) {
+                break;
+            }
+            index++;
+        }
+        if (index == s.length()) {
+            return "";
+        }
+        return s.substring(index);
     }
 
-    private String makeSeparationBetweenCommentAndDefinition(String input) {
-        if(StringUtils.startsWith(input, "//") || StringUtils.endsWith(input, "*/")) {
-            return input + "\n";
-        }
-        return input;
+    private String normalizeWhitespace(String input) {
+        return input.replace("\r\n", "\n");
     }
 
     private boolean hasChunks(Narrative narrative) {

Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/CommentTests.java

@@ -2,16 +2,22 @@
 
 import org.cqframework.cql.cql2elm.model.CompiledLibrary;
 import org.hl7.cql_annotations.r1.Annotation;
+import org.hl7.cql_annotations.r1.CqlToElmBase;
+import org.hl7.cql_annotations.r1.Narrative;
 import org.hl7.cql_annotations.r1.Tag;
 import org.hl7.elm.r1.ExpressionDef;
 import org.hl7.elm.r1.FunctionDef;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import javax.xml.bind.JAXBElement;
 import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.assertTrue;
 
 public class CommentTests {
     @BeforeClass
@@ -25,6 +31,57 @@ public void testComments() throws IOException {
         CqlTranslator translator = TestUtils.runSemanticTest("TestComments.cql", 0, CqlTranslatorOptions.Options.EnableAnnotations);
         CompiledLibrary library = translator.getTranslatedLibrary();
         assertThat(library.getLibrary().getAnnotation(), notNullValue());
+
+        Map<String, ExpressionDef> defs = new HashMap<>();
+
+        if (library.getLibrary().getStatements() != null) {
+            for (ExpressionDef def : library.getLibrary().getStatements().getDef()) {
+                defs.put(def.getName(), def);
+            }
+        }
+
+        // Validate that boolIpp has appropriate comment value
+        // Comment should be: "/* Multi-line works fine */\n// Single-line comment does not work\n"
+        ExpressionDef def = defs.get("boolIpp");
+        assertThat(def, notNullValue());
+        assertThat(def.getAnnotation(), notNullValue());
+        assertThat(def.getAnnotation().size(), is(1));
+        assertThat(def.getAnnotation().get(0), instanceOf(Annotation.class));
+        Annotation a = (Annotation)def.getAnnotation().get(0);
+        assertThat(a.getS().getContent(), notNullValue());
+        assertThat(a.getS().getContent().size(), is(2));
+        assertThat(a.getS().getContent().get(0), instanceOf(JAXBElement.class));
+        JAXBElement e = (JAXBElement)a.getS().getContent().get(0);
+        assertThat(e, notNullValue());
+        assertThat(e.getValue(), instanceOf(Narrative.class));
+        Narrative n = (Narrative)e.getValue();
+        assertThat(n.getContent(), notNullValue());
+        assertThat(n.getContent().size(), is(4));
+        assertThat(n.getContent().get(0), instanceOf(String.class));
+        String s = (String)n.getContent().get(0);
+        assertThat(s, is("/* Multi-line works fine */\n// Single-line comment does not work\n"));
+
+
+        // Validate that singleLineCommentTest has appropriate comment value
+        // Comment should be: "// Unmixed single-line comment works\n"
+        def = defs.get("singleLineCommentTest");
+        assertThat(def, notNullValue());
+        assertThat(def.getAnnotation(), notNullValue());
+        assertThat(def.getAnnotation().size(), is(1));
+        assertThat(def.getAnnotation().get(0), instanceOf(Annotation.class));
+        a = (Annotation)def.getAnnotation().get(0);
+        assertThat(a.getS().getContent(), notNullValue());
+        assertThat(a.getS().getContent().size(), is(2));
+        assertThat(a.getS().getContent().get(0), instanceOf(JAXBElement.class));
+        e = (JAXBElement)a.getS().getContent().get(0);
+        assertThat(e, notNullValue());
+        assertThat(e.getValue(), instanceOf(Narrative.class));
+        n = (Narrative)e.getValue();
+        assertThat(n.getContent(), notNullValue());
+        assertThat(n.getContent().size(), is(4));
+        assertThat(n.getContent().get(0), instanceOf(String.class));
+        s = (String)n.getContent().get(0);
+        assertThat(s, is("// Unmixed single-line comment works\n"));
     }
 
     @Test

Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/qicore/v411/BaseTest.java

@@ -292,6 +292,33 @@ public void testPapTestWithResults() throws IOException {
         assertThat(p.getScope(), equalTo("PapTest"));
     }
 
+    @Test
+    public void TestMedicationRequest() throws IOException {
+        CqlTranslator translator = TestUtils.runSemanticTest("qicore/v411/TestMedicationRequest.cql", 0);
+        Library library = translator.toELM();
+        Map<String, ExpressionDef> defs = new HashMap<>();
+
+        if (library.getStatements() != null) {
+            for (ExpressionDef def : library.getStatements().getDef()) {
+                defs.put(def.getName(), def);
+            }
+        }
+
+        ExpressionDef def = defs.get("Antithrombotic Therapy at Discharge");
+        assertThat(def, notNullValue());
+        assertThat(def.getExpression(), instanceOf(Query.class));
+        Query q = (Query)def.getExpression();
+        assertThat(q.getSource().size(), is(1));
+        assertThat(q.getSource().get(0).getExpression(), instanceOf(Retrieve.class));
+        Retrieve r = (Retrieve)q.getSource().get(0).getExpression();
+        assertThat(r.getTemplateId(), is("http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationrequest"));
+        assertThat(r.getCodeProperty(), is("medication"));
+        assertThat(r.getCodeComparator(), is("in"));
+        assertThat(r.getCodes(), instanceOf(ValueSetRef.class));
+        ValueSetRef vsr = (ValueSetRef)r.getCodes();
+        assertThat(vsr.getName(), is("Antithrombotic Therapy"));
+    }
+
     @Test
     public void TestChoiceUnion() throws IOException {
         CqlTranslator translator = TestUtils.runSemanticTest("qicore/v411/TestChoiceUnion.cql", 0);

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

@@ -49,3 +49,11 @@ to ensure overlapping intervals do not contribute multiple times to the result#
 define function CumulativeDuration(Intervals List<Interval<DateTime>>):
   Sum((collapse Intervals) X return all duration in days of X)
 
+/* Multi-line works fine */
+// Single-line comment does not work
+define "boolIpp":
+  exists ["Encounter"] E where E.period.start during MeasurementPeriod
+
+// Unmixed single-line comment works
+define "singleLineCommentTest":
+  exists ["Encounter"] E where E.period.start during "MeasurementPeriod"

Src/java/cql-to-elm/src/test/resources/org/cqframework/cql/cql2elm/qicore/v411/TestMedicationRequest.cql

@@ -0,0 +1,12 @@
+library TestMedicationRequest
+
+using QICore version '4.1.1'
+
+include FHIRHelpers version '4.0.1'
+
+valueset "Antithrombotic Therapy": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1110.62'
+
+context Patient
+
+define "Antithrombotic Therapy at Discharge":
+  ["MedicationRequest": medication in "Antithrombotic Therapy"] Antithrombotic

Src/java/elm-fhir/src/main/java/org/cqframework/cql/elm/requirements/ElmExpressionDefContext.java

@@ -62,7 +62,7 @@ public ElmQueryLetContext resolveLet(String letName) {
         ElmQueryLetContext letContext = null;
         for (ElmQueryContext queryContext : queryStack) {
             letContext = queryContext.resolveLet(letName);
-            if (letName != null) {
+            if (letContext != null) {
                 break;
             }
         }

Src/java/elm-fhir/src/test/java/org/cqframework/cql/elm/requirements/fhir/DataRequirementsProcessorTest.java

@@ -1661,6 +1661,7 @@ private void assertEqualToExpectedModuleDefinitionLibrary(org.hl7.fhir.r5.model.
         IParser parser = context.newJsonParser();
         org.hl7.fhir.r5.model.Library expectedModuleDefinitionLibrary = (org.hl7.fhir.r5.model.Library)parser.parseResource(DataRequirementsProcessorTest.class.getResourceAsStream(pathToExpectedModuleDefinitionLibrary));
         assertNotNull(expectedModuleDefinitionLibrary);
+        //outputModuleDefinitionLibrary(actualModuleDefinitionLibrary);
         actualModuleDefinitionLibrary.setDate(null);
         expectedModuleDefinitionLibrary.setDate(null);
         assertTrue(actualModuleDefinitionLibrary.equalsDeep(expectedModuleDefinitionLibrary));
@@ -1690,6 +1691,42 @@ public void TestWithDependencies() throws IOException {
         //outputModuleDefinitionLibrary(moduleDefinitionLibrary);
     }
 
+    @Test
+    public void TestCMS645() throws IOException {
+        CqlTranslatorOptions translatorOptions = getTranslatorOptions();
+        translatorOptions.setAnalyzeDataRequirements(false);
+        CqlTranslator translator = setupDataRequirementsAnalysis("CMS645/CMS645Test.cql", translatorOptions);
+        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = getModuleDefinitionLibrary(translator, translatorOptions, new HashMap<String, Object>(), ZonedDateTime.of(2023, 1, 16, 0, 0, 0, 0, ZoneId.of("UTC")));
+        assertNotNull(moduleDefinitionLibrary);
+        assertEqualToExpectedModuleDefinitionLibrary(moduleDefinitionLibrary, "CMS645/CMS645-ModuleDefinitionLibrary.json");
+
+        //outputModuleDefinitionLibrary(moduleDefinitionLibrary);
+    }
+
+    @Test
+    public void TestCMS143() throws IOException {
+        CqlTranslatorOptions translatorOptions = getTranslatorOptions();
+        translatorOptions.setAnalyzeDataRequirements(false);
+        CqlTranslator translator = setupDataRequirementsAnalysis("CMS143/cql/POAGOpticNerveEvaluationFHIR-0.0.003.cql", translatorOptions);
+        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = getModuleDefinitionLibrary(translator, translatorOptions, new HashMap<String, Object>(), ZonedDateTime.of(2023, 1, 16, 0, 0, 0, 0, ZoneId.of("UTC")));
+        assertNotNull(moduleDefinitionLibrary);
+        assertEqualToExpectedModuleDefinitionLibrary(moduleDefinitionLibrary, "CMS143/resources/Library-EffectiveDataRequirements.json");
+
+        //outputModuleDefinitionLibrary(moduleDefinitionLibrary);
+    }
+
+    @Test
+    public void TestCMS149() throws IOException {
+        CqlTranslatorOptions translatorOptions = getTranslatorOptions();
+        translatorOptions.setAnalyzeDataRequirements(false);
+        CqlTranslator translator = setupDataRequirementsAnalysis("CMS149/cql/DementiaCognitiveAssessmentFHIR-0.0.003.cql", translatorOptions);
+        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = getModuleDefinitionLibrary(translator, translatorOptions, new HashMap<String, Object>(), ZonedDateTime.of(2023, 1, 16, 0, 0, 0, 0, ZoneId.of("UTC")));
+        assertNotNull(moduleDefinitionLibrary);
+        assertEqualToExpectedModuleDefinitionLibrary(moduleDefinitionLibrary, "CMS149/resources/Library-EffectiveDataRequirements.json");
+
+        //outputModuleDefinitionLibrary(moduleDefinitionLibrary);
+    }
+
     @Test
     public void TestDataRequirementsProcessorWithPertinence() {
         CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();