Merge pull request #30 from MeasureAuthoringTool/MAT-4721_UpdateCqFra…

…mework

Mat 4721 update cq framework

pom.xml

@@ -14,7 +14,7 @@
   <description>Translates CQL to ELM for MADiE</description>
 
   <properties>
-    <cqframework.version>1.5.8</cqframework.version>
+    <cqframework.version>2.2.0</cqframework.version>
     <java.version>16</java.version>
     <mvn.checkstyle.file>madie-checkstyle.xml</mvn.checkstyle.file>
     <mvn.checkstyle.version>3.1.2</mvn.checkstyle.version>
@@ -23,6 +23,26 @@
   </properties>
 
   <dependencies>
+    <dependency>
+      <groupId>org.fhir</groupId>
+      <artifactId>ucum</artifactId>
+      <version>1.0.3</version>
+    </dependency>
+    <!-- JAXB API only -->
+
+    <dependency>
+      <groupId>org.eclipse.persistence</groupId>
+      <artifactId>org.eclipse.persistence.moxy</artifactId>
+      <version>2.6.8</version>
+    </dependency>
+
+    <!-- END JAXB API only -->
+
+    <dependency>
+      <groupId>org.jvnet.jaxb2_commons</groupId>
+      <artifactId>jaxb2-basics-runtime</artifactId>
+      <version>0.13.1</version>
+    </dependency>
 
     <dependency>
       <groupId>org.springframework.boot</groupId>
@@ -58,6 +78,12 @@
       <version>${cqframework.version}</version>
     </dependency>
 
+    <dependency>
+      <groupId>info.cqframework</groupId>
+      <artifactId>model-jaxb</artifactId>
+      <version>${cqframework.version}</version>
+    </dependency>
+
     <dependency>
       <groupId>info.cqframework</groupId>
       <artifactId>cql-to-elm</artifactId>
@@ -69,7 +95,11 @@
       <artifactId>elm</artifactId>
       <version>${cqframework.version}</version>
     </dependency>
-
+    <dependency>
+      <groupId>info.cqframework</groupId>
+      <artifactId>elm-jaxb</artifactId>
+      <version>${cqframework.version}</version>
+    </dependency>
     <dependency>
       <groupId>info.cqframework</groupId>
       <artifactId>quick</artifactId>
@@ -139,7 +169,6 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>
-      <version>3.12.0</version>
     </dependency>
 
     <dependency>
@@ -189,7 +218,6 @@
       <artifactId>spring-security-test</artifactId>
       <scope>test</scope>
     </dependency>
-
   </dependencies>
 
   <!--    Required to fetch artifacts from repositories other than maven central -->

src/main/java/gov/cms/mat/cql_elm_translation/config/logging/InterceptorConfig.java

@@ -9,7 +9,6 @@
 
 /** Class creates the interceptors used in header processing */
 @Configuration
-@Slf4j
 public class InterceptorConfig implements WebMvcConfigurer {
 
   /**

src/main/java/gov/cms/mat/cql_elm_translation/controllers/MatMeasureController.java

@@ -21,7 +21,9 @@
 
 @RestController
 @RequestMapping(path = "/mat/translator")
-@Tag(name = "Transfer-Translator", description = "API for translating MAT transferred measure CQL to ELM.")
+@Tag(
+    name = "Transfer-Translator",
+    description = "API for translating MAT transferred measure CQL to ELM.")
 @Slf4j
 @RequiredArgsConstructor
 public class MatMeasureController {

src/main/java/gov/cms/mat/cql_elm_translation/cql_translator/TranslationResource.java

@@ -1,7 +1,9 @@
 package gov.cms.mat.cql_elm_translation.cql_translator;
 
+import org.cqframework.cql.cql2elm.CqlCompilerException;
 import org.cqframework.cql.cql2elm.CqlTranslator;
-import org.cqframework.cql.cql2elm.CqlTranslatorException;
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
+
 import org.cqframework.cql.cql2elm.LibraryBuilder;
 import org.cqframework.cql.cql2elm.LibraryManager;
 import org.cqframework.cql.cql2elm.ModelManager;
@@ -22,44 +24,48 @@ public enum ModelType {
     QICore;
   }
 
-  private static final MultivaluedMap<String, CqlTranslator.Options> PARAMS_TO_OPTIONS_MAP =
+  private static final MultivaluedMap<String, CqlTranslatorOptions.Options> PARAMS_TO_OPTIONS_MAP =
       new MultivaluedHashMap<>() {
         {
-          putSingle("date-range-optimization", CqlTranslator.Options.EnableDateRangeOptimization);
-          putSingle("annotations", CqlTranslator.Options.EnableAnnotations);
-          putSingle("locators", CqlTranslator.Options.EnableLocators);
-          putSingle("result-types", CqlTranslator.Options.EnableResultTypes);
-          putSingle("detailed-errors", CqlTranslator.Options.EnableDetailedErrors);
-          putSingle("disable-list-traversal", CqlTranslator.Options.DisableListTraversal);
-          putSingle("disable-list-demotion", CqlTranslator.Options.DisableListDemotion);
-          putSingle("disable-list-promotion", CqlTranslator.Options.DisableListPromotion);
-          putSingle("enable-interval-demotion", CqlTranslator.Options.EnableIntervalDemotion);
-          putSingle("enable-interval-promotion", CqlTranslator.Options.EnableIntervalPromotion);
-          putSingle("disable-method-invocation", CqlTranslator.Options.DisableMethodInvocation);
-          putSingle("require-from-keyword", CqlTranslator.Options.RequireFromKeyword);
+          putSingle(
+              "date-range-optimization", CqlTranslatorOptions.Options.EnableDateRangeOptimization);
+          putSingle("annotations", CqlTranslatorOptions.Options.EnableAnnotations);
+          putSingle("locators", CqlTranslatorOptions.Options.EnableLocators);
+          putSingle("result-types", CqlTranslatorOptions.Options.EnableResultTypes);
+          putSingle("detailed-errors", CqlTranslatorOptions.Options.EnableDetailedErrors);
+          putSingle("disable-list-traversal", CqlTranslatorOptions.Options.DisableListTraversal);
+          putSingle("disable-list-demotion", CqlTranslatorOptions.Options.DisableListDemotion);
+          putSingle("disable-list-promotion", CqlTranslatorOptions.Options.DisableListPromotion);
+          putSingle(
+              "enable-interval-demotion", CqlTranslatorOptions.Options.EnableIntervalDemotion);
+          putSingle(
+              "enable-interval-promotion", CqlTranslatorOptions.Options.EnableIntervalPromotion);
+          putSingle(
+              "disable-method-invocation", CqlTranslatorOptions.Options.DisableMethodInvocation);
+          putSingle("require-from-keyword", CqlTranslatorOptions.Options.RequireFromKeyword);
 
           // Todo Do we even use these consolidated options ?
           put(
               "strict",
               Arrays.asList(
-                  CqlTranslator.Options.DisableListTraversal,
-                  CqlTranslator.Options.DisableListDemotion,
-                  CqlTranslator.Options.DisableListPromotion,
-                  CqlTranslator.Options.DisableMethodInvocation));
+                  CqlTranslatorOptions.Options.DisableListTraversal,
+                  CqlTranslatorOptions.Options.DisableListDemotion,
+                  CqlTranslatorOptions.Options.DisableListPromotion,
+                  CqlTranslatorOptions.Options.DisableMethodInvocation));
           put(
               "debug",
               Arrays.asList(
-                  CqlTranslator.Options.EnableAnnotations,
-                  CqlTranslator.Options.EnableLocators,
-                  CqlTranslator.Options.EnableResultTypes));
+                  CqlTranslatorOptions.Options.EnableAnnotations,
+                  CqlTranslatorOptions.Options.EnableLocators,
+                  CqlTranslatorOptions.Options.EnableResultTypes));
           put(
               "mat",
               Arrays.asList(
-                  CqlTranslator.Options.EnableAnnotations,
-                  CqlTranslator.Options.EnableLocators,
-                  CqlTranslator.Options.DisableListDemotion,
-                  CqlTranslator.Options.DisableListPromotion,
-                  CqlTranslator.Options.DisableMethodInvocation));
+                  CqlTranslatorOptions.Options.EnableAnnotations,
+                  CqlTranslatorOptions.Options.EnableLocators,
+                  CqlTranslatorOptions.Options.DisableListDemotion,
+                  CqlTranslatorOptions.Options.DisableListPromotion,
+                  CqlTranslatorOptions.Options.DisableMethodInvocation));
         }
       };
 
@@ -91,7 +97,7 @@ public CqlTranslator buildTranslator(
     try {
       UcumService ucumService = null;
       LibraryBuilder.SignatureLevel signatureLevel = LibraryBuilder.SignatureLevel.None;
-      List<CqlTranslator.Options> optionsList = new ArrayList<>();
+      List<CqlTranslatorOptions.Options> optionsList = new ArrayList<>();
 
       for (String key : params.keySet()) {
         if (PARAMS_TO_OPTIONS_MAP.containsKey(key) && Boolean.parseBoolean(params.getFirst(key))) {
@@ -103,7 +109,8 @@ public CqlTranslator buildTranslator(
         }
       }
 
-      CqlTranslator.Options[] options = optionsList.toArray(new CqlTranslator.Options[0]);
+      CqlTranslatorOptions.Options[] options =
+          optionsList.toArray(new CqlTranslatorOptions.Options[0]);
 
       libraryManager.getLibrarySourceLoader().registerProvider(new MadieLibrarySourceProvider());
 
@@ -112,7 +119,7 @@ public CqlTranslator buildTranslator(
           modelManager,
           libraryManager,
           ucumService,
-          CqlTranslatorException.ErrorSeverity.Error,
+          CqlCompilerException.ErrorSeverity.Error,
           signatureLevel,
           options);
 

src/main/java/gov/cms/mat/cql_elm_translation/service/CqlConversionService.java

@@ -13,7 +13,7 @@
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
 import org.cqframework.cql.cql2elm.CqlTranslator;
-import org.cqframework.cql.cql2elm.CqlTranslatorException;
+import org.cqframework.cql.cql2elm.CqlCompilerException;
 import org.springframework.stereotype.Service;
 import java.util.List;
 
@@ -36,7 +36,7 @@ public CqlConversionPayload processCqlDataWithErrors(RequestData requestData) {
     // Gets the translator results
     CqlTranslator cqlTranslator = processCqlData(requestData);
 
-    List<CqlTranslatorException> cqlTranslatorExceptions =
+    List<CqlCompilerException> cqlTranslatorExceptions =
         processErrors(
             requestData.getCqlData(), requestData.isShowWarnings(), cqlTranslator.getExceptions());
 
@@ -61,18 +61,18 @@ public CqlTranslator processCqlData(RequestData requestData) {
         .buildTranslator(requestData.getCqlDataInputStream(), requestData.createMap());
   }
 
-  private List<CqlTranslatorException> processErrors(
-      String cqlData, boolean showWarnings, List<CqlTranslatorException> cqlTranslatorExceptions) {
+  private List<CqlCompilerException> processErrors(
+      String cqlData, boolean showWarnings, List<CqlCompilerException> cqlTranslatorExceptions) {
     logErrors(cqlTranslatorExceptions);
     return new CqlTranslatorExceptionFilter(cqlData, showWarnings, cqlTranslatorExceptions)
         .filter();
   }
 
-  private void logErrors(List<CqlTranslatorException> exceptions) {
+  private void logErrors(List<CqlCompilerException> exceptions) {
     exceptions.forEach(e -> log.debug(formatMessage(e)));
   }
 
-  private String formatMessage(CqlTranslatorException e) {
+  private String formatMessage(CqlCompilerException e) {
     return String.format(
         LOG_MESSAGE_TEMPLATE,
         e.getSeverity() != null ? e.getSeverity().name() : null,

src/main/java/gov/cms/mat/cql_elm_translation/service/filters/CqlTranslatorExceptionFilter.java

@@ -4,7 +4,7 @@
 import lombok.Getter;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.collections4.CollectionUtils;
-import org.cqframework.cql.cql2elm.CqlTranslatorException;
+import org.cqframework.cql.cql2elm.CqlCompilerException;
 import org.hl7.elm.r1.VersionedIdentifier;
 
 import java.util.Collections;
@@ -15,10 +15,10 @@
 public class CqlTranslatorExceptionFilter implements CqlLibraryFinder {
   @Getter private final String cqlData;
   private final boolean showWarnings;
-  private final List<CqlTranslatorException> cqlTranslatorExceptions;
+  private final List<CqlCompilerException> cqlTranslatorExceptions;
 
   public CqlTranslatorExceptionFilter(
-      String cqlData, boolean showWarnings, List<CqlTranslatorException> cqlTranslatorExceptions) {
+      String cqlData, boolean showWarnings, List<CqlCompilerException> cqlTranslatorExceptions) {
     this.cqlData = cqlData;
     this.showWarnings = showWarnings;
     this.cqlTranslatorExceptions = cqlTranslatorExceptions;
@@ -29,12 +29,12 @@ public CqlTranslatorExceptionFilter(
    * Then the cqlTranslatorExceptions are filtered out if they are not pointed to the
    * parent library. ( reason: unknown )
    * */
-  public List<CqlTranslatorException> filter() {
+  public List<CqlCompilerException> filter() {
     if (CollectionUtils.isEmpty(cqlTranslatorExceptions)) {
       log.debug("No CQL Errors found");
       return Collections.emptyList();
     } else {
-      List<CqlTranslatorException> filteredCqlTranslatorExceptions = filterOutWarnings();
+      List<CqlCompilerException> filteredCqlTranslatorExceptions = filterOutWarnings();
 
       if (filteredCqlTranslatorExceptions.isEmpty()) {
         return Collections.emptyList();
@@ -44,27 +44,27 @@ public List<CqlTranslatorException> filter() {
     }
   }
 
-  private List<CqlTranslatorException> filterOutWarnings() {
+  private List<CqlCompilerException> filterOutWarnings() {
     if (showWarnings) {
       return cqlTranslatorExceptions;
     } else {
       return cqlTranslatorExceptions.stream().filter(this::isError).collect(Collectors.toList());
     }
   }
 
-  private boolean isError(CqlTranslatorException cqlTranslatorException) {
+  private boolean isError(CqlCompilerException cqlTranslatorException) {
     return cqlTranslatorException != null
         && cqlTranslatorException.getSeverity() != null
-        && cqlTranslatorException.getSeverity() == CqlTranslatorException.ErrorSeverity.Error;
+        && cqlTranslatorException.getSeverity() == CqlCompilerException.ErrorSeverity.Error;
   }
 
   /*
    * Few exceptions from CqlTranslator doesn't have a library.version, so they are removed.
    * This filter also removes if there are any errors caught by translator in any of the
    * included libraries
    * */
-  private List<CqlTranslatorException> filterByLibrary(
-      List<CqlTranslatorException> filteredCqlTranslatorExceptions) {
+  private List<CqlCompilerException> filterByLibrary(
+      List<CqlCompilerException> filteredCqlTranslatorExceptions) {
     var libraryProperties = parseLibrary();
 
     return filteredCqlTranslatorExceptions.stream()
@@ -73,7 +73,7 @@ private List<CqlTranslatorException> filterByLibrary(
   }
 
   private boolean filterOutInclude(
-      CqlTranslatorException cqlTranslatorException, LibraryProperties libraryProperties) {
+      CqlCompilerException cqlTranslatorException, LibraryProperties libraryProperties) {
     if (cqlTranslatorException.getLocator() == null
         || cqlTranslatorException.getLocator().getLibrary() == null) {
       return false;
@@ -85,6 +85,10 @@ private boolean filterOutInclude(
   }
 
   private boolean isPointingToSameLibrary(LibraryProperties p, VersionedIdentifier v) {
-    return p.getName().equals(v.getId()) && p.getVersion().equals(v.getVersion());
+    log.debug(v.toString());
+    String id = v.getId();
+    String version = v.getVersion();
+
+    return p.getName().equals(id) && p.getVersion().equals(version);
   }
 }

src/main/java/gov/cms/mat/cql_elm_translation/service/support/CqlExceptionErrorProcessor.java

@@ -6,7 +6,7 @@
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.cqframework.cql.cql2elm.CqlTranslatorException;
+import org.cqframework.cql.cql2elm.CqlCompilerException;
 import org.cqframework.cql.elm.tracking.TrackBack;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -16,14 +16,14 @@ public class CqlExceptionErrorProcessor {
 
   private static final ObjectMapper mapper = new ObjectMapper();
 
-  private final List<CqlTranslatorException> cqlErrors;
+  private final List<CqlCompilerException> cqlErrors;
   private final String json;
 
   /**
    * Transforms CqlTranslatorException to MatCqlConversionException and prepend with
    * "errorExceptions" object to the translator.json
    */
-  public CqlExceptionErrorProcessor(List<CqlTranslatorException> cqlErrors, String json) {
+  public CqlExceptionErrorProcessor(List<CqlCompilerException> cqlErrors, String json) {
     this.cqlErrors = cqlErrors;
     this.json = json;
   }
@@ -55,7 +55,7 @@ private List<MatCqlConversionException> buildMatErrors() {
     return cqlErrors.stream().map(this::createDto).collect(Collectors.toList());
   }
 
-  private MatCqlConversionException createDto(CqlTranslatorException cqlException) {
+  private MatCqlConversionException createDto(CqlCompilerException cqlException) {
     MatCqlConversionException matCqlConversionException = buildMatError(cqlException);
 
     if (cqlException.getLocator() == null) {
@@ -67,7 +67,7 @@ private MatCqlConversionException createDto(CqlTranslatorException cqlException)
     return matCqlConversionException;
   }
 
-  private MatCqlConversionException buildMatError(CqlTranslatorException cqlTranslatorException) {
+  private MatCqlConversionException buildMatError(CqlCompilerException cqlTranslatorException) {
     MatCqlConversionException matCqlConversionException = new MatCqlConversionException();
     matCqlConversionException.setErrorSeverity(cqlTranslatorException.getSeverity().name());
     log.debug("buildMatError" + cqlTranslatorException.getMessage());