Merge pull request #235 from cqframework/spelling-and-warning-fixes

Fixes for various spelling issues and warnings

.vscode/settings.json

@@ -1,3 +1,8 @@
 {
-    "java.configuration.updateBuildConfiguration": "automatic"
+    "java.configuration.updateBuildConfiguration": "automatic",
+    "cSpell.words": [
+        "Careand",
+        "pagecontent",
+        "plandefinition"
+    ]
 }

src/main/java/org/opencds/cqf/tooling/library/r4/R4LibraryProcessor.java

@@ -1,7 +1,6 @@
 package org.opencds.cqf.tooling.library.r4;
 
 import java.io.File;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;

src/main/java/org/opencds/cqf/tooling/measure/MeasureProcessor.java

@@ -18,7 +18,6 @@
 import org.opencds.cqf.tooling.utilities.*;
 import org.opencds.cqf.tooling.utilities.IOUtils.Encoding;
 
-import java.io.IOException;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -32,7 +31,6 @@ public static String getId(String baseId) {
     public static List<String> refreshIgMeasureContent(BaseProcessor parentContext, Encoding outputEncoding, Boolean versioned, FhirContext fhirContext, String measureToRefreshPath) {
 
         System.out.println("Refreshing measures...");
-        ArrayList<String> refreshedMeasureNames = new ArrayList<String>();
 
         MeasureProcessor measureProcessor;
         switch (fhirContext.getVersion().getVersion()) {

src/main/java/org/opencds/cqf/tooling/measure/r4/R4MeasureProcessor.java

@@ -1,6 +1,5 @@
 package org.opencds.cqf.tooling.measure.r4;
 
-import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.convertors.VersionConvertor_40_50;
 import org.hl7.fhir.r4.formats.FormatUtilities;
 import org.opencds.cqf.tooling.common.r4.CqfmSoftwareSystemHelper;
@@ -9,7 +8,6 @@
 import org.opencds.cqf.tooling.utilities.IOUtils;
 
 import java.io.File;
-import java.io.IOException;
 import java.util.*;
 
 public class R4MeasureProcessor extends MeasureProcessor {

src/main/java/org/opencds/cqf/tooling/measure/r4/RefreshR4MeasureOperation.java

@@ -75,7 +75,7 @@ private void refreshMeasureFromFile(File f) {
 
     public Measure refreshMeasure(Measure measure) {
         cqfmHelper.ensureCQFToolingExtensionAndDevice(measure, this.getFhirContext());
-        R4MeasureProcessor refresher = new R4MeasureProcessor();
+        // R4MeasureProcessor refresher = new R4MeasureProcessor();
         //refresher.refreshMeasure(measure, );
         return measure;
     }

src/main/java/org/opencds/cqf/tooling/processor/CqlProcessor.java

@@ -3,39 +3,29 @@
 import java.io.File;
 import java.io.FilenameFilter;
 import java.nio.file.Paths;
-import java.util.*;
-import java.util.concurrent.atomic.AtomicBoolean;
-
-import org.cqframework.cql.cql2elm.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.cqframework.cql.cql2elm.CqlTranslator;
+import org.cqframework.cql.cql2elm.CqlTranslatorException;
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
+import org.cqframework.cql.cql2elm.DefaultLibrarySourceProvider;
+import org.cqframework.cql.cql2elm.DefaultModelInfoProvider;
+import org.cqframework.cql.cql2elm.FhirLibrarySourceProvider;
+import org.cqframework.cql.cql2elm.LibraryManager;
+import org.cqframework.cql.cql2elm.ModelManager;
+import org.cqframework.cql.cql2elm.NamespaceInfo;
+import org.cqframework.cql.cql2elm.NamespaceManager;
 import org.cqframework.cql.cql2elm.model.TranslatedLibrary;
 import org.cqframework.cql.elm.tracking.TrackBack;
 import org.fhir.ucum.UcumService;
-import org.hl7.cql.model.IntervalType;
-import org.hl7.cql.model.ListType;
-import org.hl7.cql.model.NamedType;
-import org.hl7.elm.r1.AccessModifier;
-import org.hl7.elm.r1.Code;
-import org.hl7.elm.r1.CodeDef;
-import org.hl7.elm.r1.CodeRef;
-import org.hl7.elm.r1.CodeSystemDef;
-import org.hl7.elm.r1.CodeSystemRef;
-import org.hl7.elm.r1.Concept;
-import org.hl7.elm.r1.ConceptDef;
-import org.hl7.elm.r1.ConceptRef;
-import org.hl7.elm.r1.Expression;
-import org.hl7.elm.r1.ExpressionDef;
-import org.hl7.elm.r1.FunctionDef;
-import org.hl7.elm.r1.IncludeDef;
-import org.hl7.elm.r1.ParameterDef;
-import org.hl7.elm.r1.Retrieve;
-import org.hl7.elm.r1.UsingDef;
-import org.hl7.elm.r1.ValueSetDef;
-import org.hl7.elm.r1.ValueSetRef;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService;
 import org.hl7.fhir.r5.model.DataRequirement;
-import org.hl7.fhir.r5.model.Enumerations;
 import org.hl7.fhir.r5.model.ParameterDefinition;
 import org.hl7.fhir.r5.model.RelatedArtifact;
 import org.hl7.fhir.utilities.npm.NpmPackage;

src/main/java/org/opencds/cqf/tooling/processor/IGProcessor.java

@@ -7,7 +7,6 @@
 
 import org.apache.commons.io.FilenameUtils;
 import org.hl7.fhir.utilities.Utilities;
-import org.opencds.cqf.tooling.library.LibraryProcessor;
 import org.opencds.cqf.tooling.measure.MeasureProcessor;
 import org.opencds.cqf.tooling.parameter.RefreshIGParameters;
 import org.opencds.cqf.tooling.utilities.IGUtils;
@@ -56,7 +55,7 @@ public void publishIG(RefreshIGParameters params) {
         //ScaffoldProcessor.scaffold(ScaffoldParameters);
 
         //Use case 2 while developing in Atom refresh content and run tests for either entire IG or targeted Artifact
-        //refreshcontent
+        //refreshContent
         LogUtils.info("IGProcessor.publishIG - refreshIG");
         refreshIG(params);
         //validate

src/main/java/org/opencds/cqf/tooling/visitor/ElmDataRequirement.java

@@ -206,7 +206,7 @@ else if (context.getTypeResolver().isDateType(comparisonType)) {
                 }
                 // Determine operation and appropriate range
                 // If right is interval-valued
-                // If the operation is equal, equivalent, sameas, in, or included in, the date range is the comparand
+                // If the operation is equal, equivalent, same as, in, or included in, the date range is the comparand
                 Expression comparand = conditionRequirement.getComparand().getExpression();
                 if (context.getTypeResolver().isIntervalType(comparisonType)) {
                     switch (conditionRequirement.getElement().getClass().getSimpleName()) {
@@ -317,7 +317,7 @@ private void applyJoinRequirementTo(ElmJoinRequirement joinRequirement, Retrieve
                 }
 
                 // Search from the model info should be used to inform the selection, but will in general resolve to multiple choices
-                // May be a choice better left to the capabilitystatement-informed planning phase anyway
+                // May be a choice better left to the capabilityStatement-informed planning phase anyway
             }
 
             // In the absence of search information, either of these formulations is correct, favor primary query sources over withs

src/main/java/org/opencds/cqf/tooling/visitor/ElmPropertyRequirement.java

@@ -1,7 +1,6 @@
 package org.opencds.cqf.tooling.visitor;
 
 import org.hl7.elm.r1.Element;
-import org.hl7.elm.r1.Expression;
 import org.hl7.elm.r1.Property;
 import org.hl7.elm.r1.VersionedIdentifier;
 

src/main/java/org/opencds/cqf/tooling/visitor/ElmQueryAliasContext.java

@@ -1,7 +1,6 @@
 package org.opencds.cqf.tooling.visitor;
 
 import org.hl7.elm.r1.AliasedQuerySource;
-import org.hl7.elm.r1.Property;
 import org.hl7.elm.r1.Retrieve;
 import org.hl7.elm.r1.VersionedIdentifier;
 

src/main/java/org/opencds/cqf/tooling/visitor/ElmRequirements.java

@@ -1,14 +1,21 @@
 package org.opencds.cqf.tooling.visitor;
 
-import org.hl7.elm.r1.*;
-
-import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.LinkedHashSet;
-import java.util.List;
 import java.util.stream.Collectors;
 
-import static java.util.stream.Collectors.toList;
+import org.hl7.elm.r1.CodeDef;
+import org.hl7.elm.r1.CodeSystemDef;
+import org.hl7.elm.r1.ConceptDef;
+import org.hl7.elm.r1.Element;
+import org.hl7.elm.r1.ExpressionDef;
+import org.hl7.elm.r1.FunctionDef;
+import org.hl7.elm.r1.IncludeDef;
+import org.hl7.elm.r1.ParameterDef;
+import org.hl7.elm.r1.Retrieve;
+import org.hl7.elm.r1.UsingDef;
+import org.hl7.elm.r1.ValueSetDef;
+import org.hl7.elm.r1.VersionedIdentifier;
 
 public class ElmRequirements extends ElmRequirement {
 

src/main/java/org/opencds/cqf/tooling/visitor/ElmRequirementsVisitor.java

@@ -3,8 +3,6 @@
 import org.cqframework.cql.elm.visiting.ElmBaseLibraryVisitor;
 import org.hl7.elm.r1.*;
 
-import javax.xml.namespace.QName;
-
 public class ElmRequirementsVisitor extends ElmBaseLibraryVisitor <ElmRequirement, ElmRequirementsContext>{
 
     public ElmRequirementsVisitor() {
@@ -105,7 +103,7 @@ public ElmRequirement visitParameterRef(ParameterRef elm, ElmRequirementsContext
     @Override
     public ElmRequirement visitRetrieve(Retrieve elm, ElmRequirementsContext context) {
         // TODO: childResult reporting?
-        ElmRequirement childResult = super.visitRetrieve(elm, context);
+        super.visitRetrieve(elm, context);
         ElmDataRequirement result = new ElmDataRequirement(context.getCurrentLibraryIdentifier(), elm);
         // If not in a query context, report the data requirement
         // If in a query context, the requirement will be reported as an inferred requirement at the query boundary
@@ -324,7 +322,7 @@ public ElmRequirement visitChildren(BinaryExpression elm, ElmRequirementsContext
             case "ProperIncludes":
             case "ProperIncludedIn":
             default: {
-                ElmRequirement childResult = super.visitChildren(elm, context);
+                super.visitChildren(elm, context);
                 return new ElmExpressionRequirement(context.getCurrentLibraryIdentifier(), elm);
             }
         }
@@ -337,13 +335,13 @@ public ElmRequirement visitBinaryExpression(BinaryExpression elm, ElmRequirement
 
     @Override
     public ElmRequirement visitTernaryExpression(TernaryExpression elm, ElmRequirementsContext context) {
-        ElmRequirement childResult = super.visitTernaryExpression(elm, context);
+        super.visitTernaryExpression(elm, context);
         return new ElmExpressionRequirement(context.getCurrentLibraryIdentifier(), elm);
     }
 
     @Override
     public ElmRequirement visitNaryExpression(NaryExpression elm, ElmRequirementsContext context) {
-        ElmRequirement childResult = super.visitNaryExpression(elm, context);
+        super.visitNaryExpression(elm, context);
         return new ElmExpressionRequirement(context.getCurrentLibraryIdentifier(), elm);
     }
 
@@ -659,7 +657,7 @@ public ElmRequirement visitCombine(Combine elm, ElmRequirementsContext context)
 
     @Override
     public ElmRequirement visitSplit(Split elm, ElmRequirementsContext context) {
-        // If the separtor is a literal, infer based only on the string to split argument
+        // If the separator is a literal, infer based only on the string to split argument
         if (elm.getSeparator() instanceof Literal) {
             return visitElement(elm.getStringToSplit(), context);
         }

src/test/java/org/opencds/cqf/tooling/utilities/DataRequirementsProcessorTest.java

@@ -1,17 +1,7 @@
 package org.opencds.cqf.tooling.utilities;
 
-import ca.uhn.fhir.context.FhirContext;
-import org.cqframework.cql.cql2elm.*;
-import org.cqframework.cql.cql2elm.model.TranslatedLibrary;
-import org.fhir.ucum.UcumEssenceService;
-import org.fhir.ucum.UcumException;
-import org.fhir.ucum.UcumService;
-import org.hl7.elm.r1.*;
-import ca.uhn.fhir.parser.IParser;
-import org.hl7.elm.r1.Library;
-import org.hl7.fhir.r5.model.*;
-import org.junit.Test;
-import org.opencds.cqf.tooling.processor.DataRequirementsProcessor;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 import java.io.File;
 import java.io.IOException;
@@ -20,8 +10,43 @@
 import java.util.List;
 import java.util.Set;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import org.cqframework.cql.cql2elm.CqlTranslator;
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
+import org.cqframework.cql.cql2elm.DefaultLibrarySourceProvider;
+import org.cqframework.cql.cql2elm.FhirLibrarySourceProvider;
+import org.cqframework.cql.cql2elm.LibraryManager;
+import org.cqframework.cql.cql2elm.ModelManager;
+import org.cqframework.cql.cql2elm.NamespaceInfo;
+import org.cqframework.cql.cql2elm.NamespaceManager;
+import org.cqframework.cql.cql2elm.model.TranslatedLibrary;
+import org.fhir.ucum.UcumEssenceService;
+import org.fhir.ucum.UcumException;
+import org.fhir.ucum.UcumService;
+import org.hl7.elm.r1.AliasedQuerySource;
+import org.hl7.elm.r1.CodeFilterElement;
+import org.hl7.elm.r1.DateFilterElement;
+import org.hl7.elm.r1.Exists;
+import org.hl7.elm.r1.ExpressionDef;
+import org.hl7.elm.r1.IncludeElement;
+import org.hl7.elm.r1.LetClause;
+import org.hl7.elm.r1.Literal;
+import org.hl7.elm.r1.ParameterRef;
+import org.hl7.elm.r1.Query;
+import org.hl7.elm.r1.Retrieve;
+import org.hl7.elm.r1.SingletonFrom;
+import org.hl7.elm.r1.ValueSetRef;
+import org.hl7.elm.r1.With;
+import org.hl7.fhir.r5.model.Coding;
+import org.hl7.fhir.r5.model.DataRequirement;
+import org.hl7.fhir.r5.model.Enumerations;
+import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.ParameterDefinition;
+import org.hl7.fhir.r5.model.RelatedArtifact;
+import org.junit.Test;
+import org.opencds.cqf.tooling.processor.DataRequirementsProcessor;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
 
 public class DataRequirementsProcessorTest {
     private static ModelManager modelManager;
@@ -56,7 +81,7 @@ public void TestDataRequirementsProcessor() {
                 PreventiveCareandWellness-v0-0-001-FHIR-4-0-1.xml
              */
             CqlTranslator translator = createTranslator("CompositeMeasures/cql/EXM124-9.0.000.cql", cqlTranslatorOptions);//"OpioidCDS/cql/OpioidCDSCommon.cql", cqlTranslatorOptions);
-            Library elmLibrary = translator.toELM();
+            translator.toELM();
             assertTrue(translator.getErrors().isEmpty());
             cacheLibrary(translator.getTranslatedLibrary());
 
@@ -89,7 +114,7 @@ public void TestDataRequirementsProcessorWithExpressions() {
             // TODO - add expressions to expressions
             expressions.add("Conditions Indicating End of Life or With Limited Life Expectancy");//Active Ambulatory Opioid Rx");
             CqlTranslator translator = createTranslator("OpioidCDS/cql/OpioidCDSCommon.cql", cqlTranslatorOptions);
-            Library elmLibrary = translator.toELM();
+            translator.toELM();
             assertTrue(translator.getErrors().isEmpty());
             cacheLibrary(translator.getTranslatedLibrary());
             DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
@@ -157,7 +182,7 @@ public void TestLibraryDataRequirements() {
         try {
 //            CqlTranslator translator = createTranslator("/ecqm/resources/library-EXM506-2.2.000.json", cqlTranslatorOptions);
             CqlTranslator translator = createTranslator("CompositeMeasures/cql/BCSComponent.cql", cqlTranslatorOptions);
-            Library elmLibrary = translator.toELM();
+            translator.toELM();
             assertTrue(translator.getErrors().isEmpty());
             cacheLibrary(translator.getTranslatedLibrary());
             DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
@@ -225,7 +250,7 @@ private CqlTranslatorOptions getTranslatorOptions() {
 
     private CqlTranslator setupDataRequirementsAnalysis(String fileName, CqlTranslatorOptions cqlTranslatorOptions) throws IOException {
         CqlTranslator translator = createTranslator(fileName, cqlTranslatorOptions);
-        Library elmLibrary = translator.toELM();
+        translator.toELM();
         assertTrue(translator.getErrors().isEmpty());
         cacheLibrary(translator.getTranslatedLibrary());
         return translator;
@@ -879,13 +904,9 @@ public static CqlTranslator createTranslator(NamespaceInfo namespaceInfo, String
 
     public static CqlTranslator createTranslator(NamespaceInfo namespaceInfo, String testFileName, CqlTranslatorOptions options) throws IOException {
         File translationTestFile = new File(DataRequirementsProcessorTest.class.getResource(testFileName).getFile());
-        if(null != translationTestFile) {
-            reset();
-            setup(translationTestFile.getParent());
-            CqlTranslator translator = CqlTranslator.fromFile(namespaceInfo, translationTestFile, getModelManager(), getLibraryManager(), getUcumService(), options);
-            return translator;
-
-        }
-        return null;
+        reset();
+        setup(translationTestFile.getParent());
+        CqlTranslator translator = CqlTranslator.fromFile(namespaceInfo, translationTestFile, getModelManager(), getLibraryManager(), getUcumService(), options);
+        return translator;
     }
 }