Updated translator to 3.3.2

brynrhodes · brynrhodes · commit 2685f461b64f · 2023-10-29T08:53:02.000-06:00
Added skip-packages option to refresh ig operation
Removed operation processing for narrative refresh operations and drools operation
NOTE: This is known not to compile at this point, I've removed all the code related to the narrative refresh and drools operations locally, and have published a release based on that local code. This is in anticipation of a reorganization of the tooling that moves different operations into different packages, so I'm committing the changes here that are released as 2.6.0 from my local compile.
diff --git a/pom.xml b/pom.xml
@@ -5,19 +5,18 @@
 
     <groupId>org.opencds.cqf</groupId>
     <artifactId>tooling-parent</artifactId>
-    <version>2.5.0</version>
-
+    <version>2.6.0</version>
 
     <packaging>pom</packaging>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <cql-engine.version>2.9.0</cql-engine.version>
+        <cql-engine.version>3.3.2</cql-engine.version>
         <cql-evaluator.version>2.6.0</cql-evaluator.version>
-        <cqframework.version>2.9.0</cqframework.version>
-        <hapi.version>6.0.1</hapi.version>
-        <core.version>5.6.36</core.version>
+        <cqframework.version>3.3.2</cqframework.version>
+        <hapi.version>6.8.0</hapi.version>
+        <core.version>6.0.22</core.version>
         <spring-boot.version>2.1.5.RELEASE</spring-boot.version>
         <log4j2-version>2.17.1</log4j2-version>
     </properties>
diff --git a/tooling-cli/pom.xml b/tooling-cli/pom.xml
@@ -6,12 +6,12 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>2.5.0</version>
+        <version>2.6.0</version>
     </parent>
 
     <groupId>org.opencds.cqf</groupId>
     <artifactId>tooling-cli</artifactId>
-    <version>2.5.0</version>
+    <version>2.6.0</version>
     <packaging>jar</packaging>
 
     <description>CQF Tooling CLI</description>
@@ -20,7 +20,7 @@
         <dependency>
             <groupId>org.opencds.cqf</groupId>
             <artifactId>tooling</artifactId>
-            <version>2.5.0</version>
+            <version>2.6.0</version>
             <!-- <packaging>jar</packaging> -->
         </dependency>
 
diff --git a/tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/OperationFactory.java b/tooling-cli/src/main/java/org/opencds/cqf/tooling/cli/OperationFactory.java
@@ -9,7 +9,6 @@
 import org.opencds.cqf.tooling.Operation;
 import org.opencds.cqf.tooling.acceleratorkit.DTProcessor;
 import org.opencds.cqf.tooling.acceleratorkit.Processor;
-import org.opencds.cqf.tooling.library.r4.LibraryGenerator;
 import org.opencds.cqf.tooling.measure.r4.RefreshR4MeasureOperation;
 import org.opencds.cqf.tooling.measure.stu3.RefreshStu3MeasureOperation;
 import org.opencds.cqf.tooling.modelinfo.StructureDefinitionToModelInfo;
@@ -54,22 +53,12 @@ static Operation createOperation(String operationName) {
                 return new EnsureExecutableValueSetOperation();
             case "ToJsonValueSetDb":
                 return new ToJsonValueSetDbOperation();
-            case "CqlToSTU3Library":
-                return new org.opencds.cqf.tooling.library.stu3.LibraryGenerator();
-            case "CqlToR4Library":
-                return new LibraryGenerator();
-            case "UpdateSTU3Cql":
-                return new org.opencds.cqf.tooling.library.stu3.LibraryGenerator();
-            case "UpdateR4Cql":
-                return new LibraryGenerator();
             case "JsonSchemaGenerator":
 //                return new SchemaGenerator();
             case "BundleIg":
                 return new IgBundler();
 //            case "PackageIG":
 //                return new PackageOperation();
-            case "GenerateCQLFromDrool":
-                return new GenerateCQLFromDroolOperation();
             case "VmrToFhir":
                 return new VmrToFhirOperation();
             case "RefreshIG":
diff --git a/tooling/pom.xml b/tooling/pom.xml
@@ -6,13 +6,13 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>2.5.0</version>
+        <version>2.6.0</version>
 
     </parent>
 
     <groupId>org.opencds.cqf</groupId>
     <artifactId>tooling</artifactId>
-    <version>2.5.0</version>
+    <version>2.6.0</version>
     <packaging>jar</packaging>
 
     <dependencies>
@@ -179,6 +179,7 @@
         </dependency>
 
         <!-- Narrative Generation -->
+<!--
         <dependency>
             <groupId>org.thymeleaf</groupId>
             <artifactId>thymeleaf</artifactId>
@@ -187,15 +188,16 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.13.4.1</version>
+            <version>2.15.2</version>
         </dependency>
         <dependency>
             <groupId>com.github.ben-manes.caffeine</groupId>
             <artifactId>caffeine</artifactId>
             <version>2.9.1</version>
         </dependency>
-
+-->
         <!-- https://mvnrepository.com/artifact/javax.activation/activation -->
+<!--
         <dependency>
             <groupId>javax.activation</groupId>
             <artifactId>activation</artifactId>
@@ -205,7 +207,7 @@
         <dependency>
             <groupId>com.fasterxml.jackson.module</groupId>
             <artifactId>jackson-module-jaxb-annotations</artifactId>
-            <version>2.13.2</version>
+            <version>2.14.2</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
@@ -225,7 +227,7 @@
             <artifactId>validation-api</artifactId>
             <version>2.0.1.Final</version>
         </dependency>
-
+-->
         <!--redirects apache commons-logging to slf4j -->
         <dependency>
             <groupId>org.slf4j</groupId>
@@ -278,6 +280,18 @@
             <version>${cql-evaluator.version}</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>info.cqframework</groupId>
+            <artifactId>model-jaxb</artifactId>
+            <version>${cql-engine.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>info.cqframework</groupId>
+            <artifactId>elm-jaxb</artifactId>
+            <version>${cql-engine.version}</version>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>info.cqframework</groupId>
             <artifactId>engine</artifactId>
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/measure/MeasureProcessor.java b/tooling/src/main/java/org/opencds/cqf/tooling/measure/MeasureProcessor.java
@@ -278,7 +278,7 @@ private Measure refreshGeneratedContent(Measure measure) {
             String libraryUrl = ResourceUtils.getPrimaryLibraryUrl(measure, fhirContext);
             VersionedIdentifier primaryLibraryIdentifier = CanonicalUtils.toVersionedIdentifier(libraryUrl);
             List<CqlCompilerException> errors = new ArrayList<CqlCompilerException>();
-            CompiledLibrary CompiledLibrary = libraryManager.resolveLibrary(primaryLibraryIdentifier, cqlTranslatorOptions, errors);
+            CompiledLibrary CompiledLibrary = libraryManager.resolveLibrary(primaryLibraryIdentifier, errors);
             boolean hasErrors = false;
             if (errors.size() > 0) {
                 for (CqlCompilerException e : errors) {
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/measure/MeasureRefreshProcessor.java b/tooling/src/main/java/org/opencds/cqf/tooling/measure/MeasureRefreshProcessor.java
@@ -47,7 +47,7 @@ public Measure refreshMeasure(Measure measureToUse, LibraryManager libraryManage
     private Library getModuleDefinitionLibrary(Measure measureToUse, LibraryManager libraryManager, CompiledLibrary CompiledLibrary, CqlTranslatorOptions options){
         Set<String> expressionList = getExpressions(measureToUse);
         DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
-        return dqReqTrans.gatherDataRequirements(libraryManager, CompiledLibrary, options, expressionList, true);
+        return dqReqTrans.gatherDataRequirements(libraryManager, CompiledLibrary, options.getCqlCompilerOptions(), expressionList, true);
     }
 
     private Set<String> getExpressions(Measure measureToUse) {
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/npm/NpmPackageManager.java b/tooling/src/main/java/org/opencds/cqf/tooling/npm/NpmPackageManager.java
@@ -85,7 +85,7 @@ public NpmPackageManager(ImplementationGuide sourceIg, String version) {
         try {
             // userMode indicates whether the packageCache is within the working directory
             // or in the user home
-            pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
+            pcm = new FilesystemPackageCacheManager(true);
         } catch (IOException e) {
             throw new NpmPackageManagerException("error creating the FilesystemPackageCacheManager", e);
         }
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/parameter/RefreshIGParameters.java b/tooling/src/main/java/org/opencds/cqf/tooling/parameter/RefreshIGParameters.java
@@ -9,6 +9,7 @@ public class RefreshIGParameters {
     public String rootDir;
     public String igPath;
     public IOUtils.Encoding outputEncoding;
+    public Boolean skipPackages;
     public Boolean includeELM;
     public Boolean includeDependencies;
     public Boolean includeTerminology;
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/processor/BaseProcessor.java b/tooling/src/main/java/org/opencds/cqf/tooling/processor/BaseProcessor.java
@@ -236,4 +236,9 @@ public void logMessage(String msg) {
     public void logDebugMessage(IWorkerContext.ILoggingService.LogCategory category, String msg) {
         logger.debug("Category: {} Message: {}", category.name(), msg);
     }
+
+    @Override
+    public boolean isDebugLogging() {
+        return false;
+    }
 }
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/processor/CqlProcessor.java b/tooling/src/main/java/org/opencds/cqf/tooling/processor/CqlProcessor.java
@@ -259,6 +259,9 @@ private void translateFolder(String folder) {
         // Construct FhirLibrarySourceProvider
         ModelManager modelManager = new ModelManager();
         LibraryManager libraryManager = new LibraryManager(modelManager);
+        if (options.getCqlCompilerOptions().getValidateUnits()) {
+            libraryManager.setUcumService(ucumService);
+        }
         if (packages != null) {
             modelManager.getModelInfoLoader().registerModelInfoProvider(new NpmModelInfoProvider(packages, reader, logger), true);
             libraryManager.getLibrarySourceLoader().registerProvider(new NpmLibrarySourceProvider(packages, reader, logger));
@@ -273,7 +276,7 @@ private void translateFolder(String folder) {
         boolean hadCqlFiles = false;
         for (File file : new File(folder).listFiles(getCqlFilenameFilter())) {
             hadCqlFiles = true;
-            translateFile(modelManager, libraryManager, file, options);
+            translateFile(libraryManager, file, options);
         }
 
         if (hadCqlFiles) {
@@ -339,16 +342,15 @@ public static ValidationMessage exceptionToValidationMessage(File file, CqlCompi
         }
     }
 
-    private void translateFile(ModelManager modelManager, LibraryManager libraryManager, File file, CqlTranslatorOptions options) {
+    private void translateFile(LibraryManager libraryManager, File file, CqlTranslatorOptions options) {
         logger.logMessage(String.format("Translating CQL source in file %s", file.toString()));
         CqlSourceFileInformation result = new CqlSourceFileInformation();
         fileMap.put(file.getAbsoluteFile().toString(), result);
 
         try {
 
             // translate toXML
-            CqlTranslator translator = CqlTranslator.fromFile(namespaceInfo, file, modelManager, libraryManager,
-                    options.getValidateUnits() ? ucumService : null, options);
+            CqlTranslator translator = CqlTranslator.fromFile(namespaceInfo, file, libraryManager);
 
             // record errors and warnings
             for (CqlCompilerException exception : translator.getExceptions()) {
@@ -376,13 +378,12 @@ private void translateFile(ModelManager modelManager, LibraryManager libraryMana
 
                     // Add the translated library to the library manager (NOTE: This should be a "cacheLibrary" call on the LibraryManager, available in 1.5.3+)
                     // Without this, the data requirements processor will try to load the current library, resulting in a re-translation
-                    CompiledLibrary CompiledLibrary = translator.getTranslatedLibrary();
-                    String libraryPath = NamespaceManager.getPath(CompiledLibrary.getIdentifier().getSystem(), CompiledLibrary.getIdentifier().getId());
-                    libraryManager.getCompiledLibraries().put(libraryPath, CompiledLibrary);
+                    CompiledLibrary compiledLibrary = translator.getTranslatedLibrary();
+                    libraryManager.getCompiledLibraries().put(compiledLibrary.getIdentifier(), compiledLibrary);
 
                     DataRequirementsProcessor drp = new DataRequirementsProcessor();
                     org.hl7.fhir.r5.model.Library requirementsLibrary =
-                            drp.gatherDataRequirements(libraryManager, translator.getTranslatedLibrary(), options, null, false);
+                            drp.gatherDataRequirements(libraryManager, translator.getTranslatedLibrary(), options.getCqlCompilerOptions(), null, false);
 
                     // TODO: Report context, requires 1.5 translator (ContextDef)
                     // NOTE: In STU3, only Patient context is supported
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/processor/IGProcessor.java b/tooling/src/main/java/org/opencds/cqf/tooling/processor/IGProcessor.java
@@ -34,6 +34,9 @@ public IGProcessor(IGBundleProcessor igBundleProcessor, LibraryProcessor library
     }
     //mega ig method
     public void publishIG(RefreshIGParameters params) {
+        if (params.skipPackages == null) {
+            params.skipPackages = false;
+        }
         requireNonNull(params.includeDependencies, "includeDependencies can not be null");
         requireNonNull(params.includeELM, "includeELM can not be null");
         requireNonNull(params.includePatientScenarios, "includePatientScenarios can not be null");
@@ -58,6 +61,7 @@ public void publishIG(RefreshIGParameters params) {
         }
 
         Encoding encoding = params.outputEncoding;
+        Boolean skipPackages = params.skipPackages;
         Boolean includeELM = params.includeELM;
         Boolean includeDependencies = params.includeDependencies;
         Boolean includeTerminology = params.includeTerminology;
@@ -98,8 +102,22 @@ public void publishIG(RefreshIGParameters params) {
         //Use case 3
         //package everything
         LogUtils.info("IGProcessor.publishIG - bundleIg");
-        igBundleProcessor.bundleIg(refreshedResourcesNames, rootDir, getBinaryPaths(), encoding, includeELM, includeDependencies, includeTerminology, includePatientScenarios,
-        versioned, addBundleTimestamp, fhirContext, fhirUri);
+        if (!skipPackages) {
+            igBundleProcessor.bundleIg(
+                    refreshedResourcesNames,
+                    rootDir,
+                    getBinaryPaths(),
+                    encoding,
+                    includeELM,
+                    includeDependencies,
+                    includeTerminology,
+                    includePatientScenarios,
+                    versioned,
+                    addBundleTimestamp,
+                    fhirContext,
+                    fhirUri
+            );
+        }
         //test everything
         //IGTestProcessor.testIg(IGTestParameters);
         //Publish?
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/processor/argument/RefreshIGArgumentProcessor.java b/tooling/src/main/java/org/opencds/cqf/tooling/processor/argument/RefreshIGArgumentProcessor.java
@@ -23,6 +23,8 @@ public class RefreshIGArgumentProcessor {
     public static final String[] ROOT_DIR_OPTIONS = {"root-dir"};
     public static final String[] IG_PATH_OPTIONS = {"ip", "ig-path"};
     public static final String[] IG_OUTPUT_ENCODING = {"e", "encoding"};
+
+    public static final String[] SKIP_PACKAGES_OPTIONS = {"s", "skip-packages"};
     public static final String[] INCLUDE_ELM_OPTIONS = {"elm", "include-elm"};
     public static final String[] INCLUDE_DEPENDENCY_LIBRARY_OPTIONS = {"d", "include-dependencies"};
     public static final String[] INCLUDE_TERMINOLOGY_OPTIONS = {"t", "include-terminology"};
@@ -70,6 +72,7 @@ public OptionParser build() {
         OptionSpec<String> fhirUri = fhirUriBuilder.withOptionalArg().describedAs("uri of fhir server");  
 
         parser.acceptsAll(asList(OPERATION_OPTIONS),"The operation to run.");
+        parser.acceptsAll(asList(SKIP_PACKAGES_OPTIONS), "Specifies whether to skip packages building.");
         parser.acceptsAll(asList(INCLUDE_ELM_OPTIONS),"If omitted ELM will not be produced or packaged.");
         parser.acceptsAll(asList(INCLUDE_DEPENDENCY_LIBRARY_OPTIONS),"If omitted only the primary CQL library will be packaged.");
         parser.acceptsAll(asList(INCLUDE_TERMINOLOGY_OPTIONS),"If omitted terminology will not be packaged.");
@@ -107,6 +110,7 @@ public RefreshIGParameters parseAndConvert(String[] args) {
         if (igEncoding != null) {
             outputEncodingEnum = Encoding.parse(igEncoding.toLowerCase());
         }
+        Boolean skipPackages = options.has(SKIP_PACKAGES_OPTIONS[0]);
         Boolean includeELM = options.has(INCLUDE_ELM_OPTIONS[0]);  
         Boolean includeDependencies = options.has(INCLUDE_DEPENDENCY_LIBRARY_OPTIONS[0]);
         Boolean includeTerminology = options.has(INCLUDE_TERMINOLOGY_OPTIONS[0]);
@@ -152,6 +156,7 @@ public RefreshIGParameters parseAndConvert(String[] args) {
         ip.rootDir = rootDir;
         ip.igPath = igPath;
         ip.outputEncoding = outputEncodingEnum;
+        ip.skipPackages = skipPackages;
         ip.includeELM = includeELM;
         ip.includeDependencies = includeDependencies;
         ip.includeTerminology = includeTerminology;
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/utilities/IOUtils.java b/tooling/src/main/java/org/opencds/cqf/tooling/utilities/IOUtils.java
@@ -520,11 +520,7 @@ public static CqlTranslator translate(String cqlContentPath, ModelManager modelM
             // options.add(CqlTranslatorOptions.Options.EnableDateRangeOptimization);
   
             translator =
-                    CqlTranslator.fromFile(
-                            cqlFile,
-                            modelManager,
-                            libraryManager,
-                            null, options);
+                    CqlTranslator.fromFile(cqlFile, libraryManager);
 
             if (translator.getErrors().size() > 0) {
                 //System.err.println("Translation failed due to errors:");
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/utilities/ResourceUtils.java b/tooling/src/main/java/org/opencds/cqf/tooling/utilities/ResourceUtils.java
@@ -387,8 +387,8 @@ public static CqlTranslatorOptions getTranslatorOptions(String folder) {
       }
       else {
           options = CqlTranslatorOptions.defaultOptions();
-          if (!options.getFormats().contains(CqlTranslator.Format.XML)) {
-              options.getFormats().add(CqlTranslator.Format.XML);
+          if (!options.getFormats().contains(CqlTranslatorOptions.Format.XML)) {
+              options.getFormats().add(CqlTranslatorOptions.Format.XML);
           }
           logger.debug("cql-options not found. Using default options.");
       }
diff --git a/tooling/src/test/java/org/opencds/cqf/tooling/npm/NpmPackageManagerTests.java b/tooling/src/test/java/org/opencds/cqf/tooling/npm/NpmPackageManagerTests.java
@@ -84,4 +84,9 @@ public void logMessage(String msg) {
     public void logDebugMessage(IWorkerContext.ILoggingService.LogCategory category, String msg) {
         logMessage(msg);
     }
+
+    @Override
+    public boolean isDebugLogging() {
+        return false;
+    }
 }
diff --git a/tooling/src/test/java/org/opencds/cqf/tooling/utilities/ECQMCreatorIT.java b/tooling/src/test/java/org/opencds/cqf/tooling/utilities/ECQMCreatorIT.java

Original file line number	Diff line number	Diff line change
`@@ -47,7 +47,7 @@ public Measure refreshMeasure(Measure measureToUse, LibraryManager libraryManage`
`47`	`47`	`private Library getModuleDefinitionLibrary(Measure measureToUse, LibraryManager libraryManager, CompiledLibrary CompiledLibrary, CqlTranslatorOptions options){`
`48`	`48`	`Set<String> expressionList = getExpressions(measureToUse);`
`49`	`49`	`DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();`
`50`		`- return dqReqTrans.gatherDataRequirements(libraryManager, CompiledLibrary, options, expressionList, true);`
	`50`	`+ return dqReqTrans.gatherDataRequirements(libraryManager, CompiledLibrary, options.getCqlCompilerOptions(), expressionList, true);`
`51`	`51`	`}`
`52`	`52`
`53`	`53`	`private Set<String> getExpressions(Measure measureToUse) {`
Original file line number	Diff line number	Diff line change
`@@ -85,7 +85,7 @@ public NpmPackageManager(ImplementationGuide sourceIg, String version) {`
`85`	`85`	`try {`
`86`	`86`	`// userMode indicates whether the packageCache is within the working directory`
`87`	`87`	`// or in the user home`
`88`		`- pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);`
	`88`	`+ pcm = new FilesystemPackageCacheManager(true);`
`89`	`89`	`} catch (IOException e) {`
`90`	`90`	`throw new NpmPackageManagerException("error creating the FilesystemPackageCacheManager", e);`
`91`	`91`	`}`
Original file line number	Diff line number	Diff line change
`@@ -236,4 +236,9 @@ public void logMessage(String msg) {`
`236`	`236`	`public void logDebugMessage(IWorkerContext.ILoggingService.LogCategory category, String msg) {`
`237`	`237`	`logger.debug("Category: {} Message: {}", category.name(), msg);`
`238`	`238`	`}`
	`239`	`+`
	`240`	`+ @Override`
	`241`	`+ public boolean isDebugLogging() {`
	`242`	`+ return false;`
	`243`	`+ }`
`239`	`244`	`}`