Version 2.3.0 w/ support for Translator 3.3.2 (#39)

* Version 2.3.0 w/ support for Translator 3.3.2 Update the translator to the latest one in the 3.x line. This required code changes, as the Translator classes have been refactored. * Add xpp3 library to support UCUM operations
cqframework · Dec 1, 2023 · 7dbd46c · 7dbd46c
1 parent b5ff2fd
commit 7dbd46c
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Showing 6 changed files with 91 additions and 55 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -19,4 +19,4 @@ EXPOSE 8080
 
 # execute it
 # CMD ["mvn", "exec:java"]
-CMD ["java", "-jar", "target/cqlTranslationServer-2.2.0.jar", "-d"]
+CMD ["java", "-jar", "target/cqlTranslationServer-2.3.0.jar", "-d"]
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ Build:
 
 Execute via the command line:
 
-    java -jar target/cqlTranslationServer-2.2.0.jar
+    java -jar target/cqlTranslationServer-2.3.0.jar
 
 _NOTE: The cqlTranslationServer jar assumes that all dependency jars are located in a `libs` directory relative to the jar's location. If you move the jar from the `target` directory, you will need to move the `target/libs` directory as well. This project no longer produces an "uber-jar", as the CQL-to-ELM classes do not function properly when repackaged into a single jar file._
 
@@ -18,6 +18,7 @@ CQL Translation Service versions prior to version 2.0.0 always mirrored the CQL
 
 | CQL Translation Service | CQL Tools                               |
 |-------------------------|-----------------------------------------|
+| 2.3.0                   | 3.3.2                                   |
 | 2.2.0                   | 2.11.0                                  |
 | 2.1.0                   | 2.10.0                                  |
 | 2.0.0                   | 2.7.0                                   |

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
   <groupId>org.mitre.bonnie</groupId>
   <artifactId>cqlTranslationServer</artifactId>
   <packaging>jar</packaging>
-  <version>2.2.0</version>
+  <version>2.3.0</version>
   <name>cqlTranslationServer</name>
 
   <repositories>
@@ -112,6 +112,15 @@
       <artifactId>commons-cli</artifactId>
       <version>1.6.0</version>
     </dependency>
+    <!--
+      We now need to supply our own xpp3 implementation. Use the same one as is used here:
+      https://github.com/cqframework/clinical_quality_language/blob/master/Src/java/buildSrc/src/main/groovy/cql.fhir-conventions.gradle
+    -->
+    <dependency>
+      <groupId>org.ogce</groupId>
+      <artifactId>xpp3</artifactId>
+      <version>1.1.6</version>
+    </dependency>
   </dependencies>
 
   <build>
@@ -175,7 +184,7 @@
   </build>
 
   <properties>
-    <cql.version>2.11.0</cql.version>
+    <cql.version>3.3.2</cql.version>
     <jersey.version>2.41</jersey.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
   </properties>

diff --git a/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationResource.java b/src/main/java/org/mitre/bonnie/cqlTranslationServer/TranslationResource.java
@@ -19,16 +19,15 @@
 import javax.ws.rs.core.Response.ResponseBuilder;
 import javax.ws.rs.core.Response.Status;
 import javax.ws.rs.core.UriInfo;
-import org.cqframework.cql.cql2elm.CqlCompilerException;
+
+import org.cqframework.cql.cql2elm.CqlCompilerOptions;
 import org.cqframework.cql.cql2elm.CqlTranslator;
-import org.cqframework.cql.cql2elm.CqlTranslatorOptions.Options;
 import org.cqframework.cql.cql2elm.LibraryBuilder;
+import org.cqframework.cql.cql2elm.CqlCompilerOptions.Options;
 import org.cqframework.cql.cql2elm.LibraryManager;
 import org.cqframework.cql.cql2elm.ModelManager;
+import org.cqframework.cql.cql2elm.CqlCompilerException.ErrorSeverity;
 import org.cqframework.cql.cql2elm.quick.FhirLibrarySourceProvider;
-import org.fhir.ucum.UcumEssenceService;
-import org.fhir.ucum.UcumException;
-import org.fhir.ucum.UcumService;
 import org.glassfish.jersey.media.multipart.FormDataBodyPart;
 import org.glassfish.jersey.media.multipart.FormDataMultiPart;
 
@@ -69,34 +68,36 @@ public class TranslationResource {
             Options.EnableResultTypes)
     );
   }};
-  private final ModelManager modelManager;
-  private final LibraryManager libraryManager;
-
-  public TranslationResource() {
-    this.modelManager = new ModelManager();
-    this.libraryManager = new LibraryManager(modelManager);
-    // FHIR library source provider is always needed for FHIR and harmless for other models
-    libraryManager.getLibrarySourceLoader().registerProvider(new FhirLibrarySourceProvider());
-  }
 
   @POST
   @Consumes(CQL_TEXT_TYPE)
   @Produces(ELM_XML_TYPE)
   public Response cqlToElmXml(File cql, @Context UriInfo info) {
-    CqlTranslator translator = getTranslator(cql, info.getQueryParameters());
-    ResponseBuilder resp = getResponse(translator);
-    resp = resp.entity(translator.toXml()).type(ELM_XML_TYPE);
-    return resp.build();
+    try {
+      LibraryManager libraryManager = this.getLibraryManager(info.getQueryParameters());
+      CqlTranslator translator = CqlTranslator.fromFile(cql, libraryManager);
+      ResponseBuilder resp = getResponse(translator);
+      resp = resp.entity(translator.toXml()).type(ELM_XML_TYPE);
+      return resp.build();
+    } catch (IOException e) {
+      throw new TranslationFailureException("Unable to read request");
+    }
+
   }
 
   @POST
   @Consumes(CQL_TEXT_TYPE)
   @Produces(ELM_JSON_TYPE)
   public Response cqlToElmJson(File cql, @Context UriInfo info) {
-    CqlTranslator translator = getTranslator(cql, info.getQueryParameters());
-    ResponseBuilder resp = getResponse(translator);
-    resp = resp.entity(translator.toJson()).type(ELM_JSON_TYPE);
-    return resp.build();
+    try {
+      LibraryManager libraryManager = this.getLibraryManager(info.getQueryParameters());
+      CqlTranslator translator = CqlTranslator.fromFile(cql, libraryManager);
+      ResponseBuilder resp = getResponse(translator);
+      resp = resp.entity(translator.toJson()).type(ELM_JSON_TYPE);
+      return resp.build();
+    } catch (IOException e) {
+      throw new TranslationFailureException("Unable to read request");
+    }
   }
 
   @POST
@@ -110,12 +111,12 @@ public Response cqlPackageToElmPackage(
     // Jersey doesn't support parsing multiple value headers by comma, so we need to do it
 	  // for ourselves. See https://github.com/jersey/jersey/issues/2436
     try {
-      MultipartLibrarySourceProvider lsp = new MultipartLibrarySourceProvider(pkg);
-      libraryManager.getLibrarySourceLoader().registerProvider(lsp);
+      LibraryManager libraryManager = this.getLibraryManager(info.getQueryParameters());
+      libraryManager.getLibrarySourceLoader().registerProvider(new MultipartLibrarySourceProvider(pkg));
       FormDataMultiPart translatedPkg = new FormDataMultiPart();
       for (String fieldId: pkg.getFields().keySet()) {
         for (FormDataBodyPart part: pkg.getFields(fieldId)) {
-          CqlTranslator translator = getTranslator(part.getEntityAs(File.class), info.getQueryParameters());
+          CqlTranslator translator = CqlTranslator.fromFile(part.getEntityAs(File.class), libraryManager);
           for( String format : targetFormats ) {
             for( String subformat : format.split(",") ) {
               MediaType targetFormat = MediaType.valueOf( subformat );
@@ -134,37 +135,24 @@ public Response cqlPackageToElmPackage(
       return resp.build();
     } catch (IOException ex) {
       throw new TranslationFailureException("Unable to read request");
-    } finally {
-      // Clear the package-based source provider then add back the FHIR library source provider
-      libraryManager.getLibrarySourceLoader().clearProviders();
-      libraryManager.getLibrarySourceLoader().registerProvider(new FhirLibrarySourceProvider());
     }
   }
 
-  private CqlTranslator getTranslator(File cql, MultivaluedMap<String, String> params) {
-    try {
-      UcumService ucumService = null;
-      LibraryBuilder.SignatureLevel signatureLevel = LibraryBuilder.SignatureLevel.None;
-      List<Options> optionsList = new ArrayList<>();
-      for (String key: params.keySet()) {
-        if (PARAMS_TO_OPTIONS_MAP.containsKey(key) && Boolean.parseBoolean(params.getFirst(key))) {
-          optionsList.addAll(PARAMS_TO_OPTIONS_MAP.get(key));
-        } else if (key.equals("validate-units") && Boolean.parseBoolean(params.getFirst(key))) {
-          try {
-            ucumService = new UcumEssenceService(UcumEssenceService.class.getResourceAsStream("/ucum-essence.xml"));
-          } catch (UcumException e) {
-            throw new TranslationFailureException("Cannot load UCUM service to validate units");
-          }
-        } else if (key.equals("signatures")) {
-          signatureLevel = LibraryBuilder.SignatureLevel.valueOf(params.getFirst("signatures"));
-        }
+  private LibraryManager getLibraryManager(MultivaluedMap<String, String> params) {
+    LibraryBuilder.SignatureLevel signatureLevel = LibraryBuilder.SignatureLevel.None;
+    List<Options> optionsList = new ArrayList<>();
+    for (String key: params.keySet()) {
+      if (PARAMS_TO_OPTIONS_MAP.containsKey(key) && Boolean.parseBoolean(params.getFirst(key))) {
+        optionsList.addAll(PARAMS_TO_OPTIONS_MAP.get(key));
+      } else if (key.equals("signatures")) {
+        signatureLevel = LibraryBuilder.SignatureLevel.valueOf(params.getFirst("signatures"));
       }
-      Options[] options = optionsList.toArray(new Options[optionsList.size()]);
-      return CqlTranslator.fromFile(cql, modelManager, libraryManager, ucumService, CqlCompilerException.ErrorSeverity.Info,
-              signatureLevel, options);
-    } catch (IOException e) {
-      throw new TranslationFailureException("Unable to read request");
     }
+    Options[] options = optionsList.toArray(new Options[optionsList.size()]);
+    LibraryManager libraryManager = new LibraryManager(new ModelManager(), new CqlCompilerOptions(ErrorSeverity.Info, signatureLevel, options));
+    // FHIR library source provider is always needed for FHIR and harmless for other models
+    libraryManager.getLibrarySourceLoader().registerProvider(new FhirLibrarySourceProvider());
+    return libraryManager;
   }
 
   private ResponseBuilder getResponse(CqlTranslator translator) {

diff --git a/src/test/java/org/mitre/bonnie/cqlTranslationServer/TranslationResourceTest.java b/src/test/java/org/mitre/bonnie/cqlTranslationServer/TranslationResourceTest.java
@@ -365,6 +365,23 @@ public void testMultipartRequestAsJsonAndXml() throws Exception {
     }
   }
 
+  @Test
+  public void testLibraryThatNeedsUCUM() {
+    File file = new File(TranslationResourceTest.class.getResource("NeedsUCUM.cql").getFile());
+    Response resp = target.path("translator").queryParam("signatures", "All").request(TranslationResource.ELM_JSON_TYPE).post(Entity.entity(file, TranslationResource.CQL_TEXT_TYPE));
+    assertEquals(Status.OK.getStatusCode(), resp.getStatus());
+    assertEquals(TranslationResource.ELM_JSON_TYPE, resp.getMediaType().toString());
+    assertTrue(resp.hasEntity());
+    JsonReader reader = Json.createReader(new StringReader(resp.readEntity(String.class)));
+    JsonObject obj = reader.readObject();
+    JsonObject library = obj.getJsonObject("library");
+    JsonArray annotations = library.getJsonArray("annotation");
+    assertEquals(1, annotations.size());
+    JsonObject identifier = library.getJsonObject("identifier");
+    assertEquals("NeedsUCUM", identifier.getString("id"));
+    assertEquals("0.0.1", identifier.getString("version"));
+  }
+
   private Document parseAndValidateXml( BodyPart input, String expectedId, String expectedVersion, int expectedErrors ) throws Exception {
       Document doc = parseXml(input.getEntityAs(String.class));
       String errorCount = applyXPath(doc, "count(/elm:library/elm:annotation[@errorType='syntax'])");

diff --git a/src/test/resources/org/mitre/bonnie/cqlTranslationServer/NeedsUCUM.cql b/src/test/resources/org/mitre/bonnie/cqlTranslationServer/NeedsUCUM.cql
@@ -0,0 +1,21 @@
+library NeedsUCUM version '0.0.1'
+
+using FHIR version '4.0.1'
+
+include FHIRHelpers version '4.0.1'
+
+valueset "test-vs": 'http://example.com/test-vs'
+
+context Patient
+
+define "Query ExpressionRef with Value Comparison":
+  ("Simple Observation Query".value as Quantity) > 9 '%'
+
+define "Simple Observation Query":
+    Last([Observation: "test-vs"] O
+      where O.status in {'final', 'amended', 'corrected'})
+
+define "Has Elevated Value With Where":
+    Last([Observation: "test-vs"] O
+      where O.status in {'final', 'amended', 'corrected'}
+      and (O.value as Quantity) > 9 '%')