Fixes for 3.0 release

cqframework · Nov 28, 2023 · 1b5ecad · 1b5ecad
1 parent 8b356fd
commit 1b5ecad
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Showing 20 changed files with 265 additions and 371 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,18 +5,17 @@
 
     <groupId>org.opencds.cqf</groupId>
     <artifactId>tooling-parent</artifactId>
-    <version>2.6.0-SNAPSHOT</version>
+    <version>3.0.0-SNAPSHOT</version>
 
     <packaging>pom</packaging>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
         <cql-engine.version>3.3.2</cql-engine.version>
-        <cql-evaluator.version>2.6.0</cql-evaluator.version>
         <cqframework.version>3.3.2</cqframework.version>
-        <hapi.version>6.8.0</hapi.version>
-        <core.version>6.0.22</core.version>
+        <hapi.version>6.8.5</hapi.version>
+        <core.version>6.0.22.2</core.version>
         <spring-boot.version>2.1.5.RELEASE</spring-boot.version>
     </properties>
 
@@ -106,28 +105,10 @@
 
     <dependencyManagement>
         <dependencies>
-            <dependency>
-                <groupId>info.cqframework</groupId>
-                <artifactId>evaluator.builder</artifactId>
-                <version>${cql-evaluator.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.opencds.cqf.cql</groupId>
-                <artifactId>evaluator.jaxb-deps</artifactId>
-                <version>${cql-evaluator.version}</version>
-                <type>pom</type>
-            </dependency>
             <dependency>
                 <groupId>info.cqframework</groupId>
                 <artifactId>engine</artifactId>
                 <version>${cql-engine.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <groupId>org.slf4j</groupId>
-                        <artifactId>slf4j-log4j12</artifactId>
-                    </exclusion>
-                </exclusions>
             </dependency>
             <dependency>
                 <groupId>info.cqframework</groupId>

diff --git a/tooling-cli/pom.xml b/tooling-cli/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>2.6.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
 
     <artifactId>tooling-cli</artifactId>
-    <version>2.6.0-SNAPSHOT</version>
+    <version>3.0.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <description>CQF Tooling CLI</description>
@@ -19,20 +19,18 @@
         <dependency>
             <groupId>org.opencds.cqf</groupId>
             <artifactId>tooling</artifactId>
-            <version>2.6.0-SNAPSHOT</version>
+            <version>3.0.0-SNAPSHOT</version>
         </dependency>
-
-        <dependency>
-            <groupId>org.opencds.cqf.cql</groupId>
-            <artifactId>evaluator.jaxb-deps</artifactId>
-            <type>pom</type>
-        </dependency>
-
         <dependency>
             <groupId>org.eclipse.persistence</groupId>
             <artifactId>org.eclipse.persistence.moxy</artifactId>
             <version>2.7.7</version>
         </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-simple</artifactId>
+            <version>2.0.5</version>
+        </dependency>
 
         <dependency>
             <groupId>org.reflections</groupId>

diff --git a/tooling/pom.xml b/tooling/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>2.6.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
     </parent>
 
     <artifactId>tooling</artifactId>
-    <version>2.6.0-SNAPSHOT</version>
+    <version>3.0.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <dependencies>
@@ -272,26 +272,12 @@
         </dependency>
 
         <!-- test dependencies -->
-        <dependency>
-            <groupId>org.opencds.cqf.cql</groupId>
-            <artifactId>evaluator.jaxb-deps</artifactId>
-            <version>${cql-evaluator.version}</version>
-            <type>pom</type>
-            <scope>test</scope>
-        </dependency>
-
         <dependency>
             <groupId>org.eclipse.persistence</groupId>
             <artifactId>org.eclipse.persistence.moxy</artifactId>
             <version>2.7.7</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.opencds.cqf.cql</groupId>
-            <artifactId>evaluator.builder</artifactId>
-            <version>${cql-evaluator.version}</version>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>info.cqframework</groupId>
             <artifactId>engine</artifactId>

diff --git a/...main/java/org/opencds/cqf/tooling/common/JarEnabledCustomThymeleafNarrativeGenerator.java b/...main/java/org/opencds/cqf/tooling/common/JarEnabledCustomThymeleafNarrativeGenerator.java
@@ -10,14 +10,14 @@
 import java.util.Collection;
 import java.util.List;
 
-import ca.uhn.fhir.narrative.BaseThymeleafNarrativeGenerator;
-import com.google.common.base.Charsets;
-
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
+import com.google.common.base.Charsets;
+
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.narrative.BaseThymeleafNarrativeGenerator;
 import ca.uhn.fhir.narrative2.NarrativeTemplateManifest;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 
@@ -28,9 +28,10 @@ public class JarEnabledCustomThymeleafNarrativeGenerator extends BaseThymeleafNa
 
     public JarEnabledCustomThymeleafNarrativeGenerator(String... thePropertyFile) {
 		super();
-		setPropertyFile(thePropertyFile);
+		var propFile = Arrays.asList(thePropertyFile);
+		this.myPropertyFile = propFile;
 		 try {
-			 manifest = forManifestFileLocation(getPropertyFile());
+			 this.manifest = forManifestFileLocation(propFile);
 		 } catch (IOException e) {
 			 throw new InternalErrorException(e);
 		 }
@@ -46,7 +47,7 @@ public boolean populateResourceNarrative(FhirContext theFhirContext, IBaseResour
 	protected NarrativeTemplateManifest getManifest() {
 		return this.manifest;
 	}
-    
+
     public static NarrativeTemplateManifest forManifestFileLocation(Collection<String> thePropertyFilePaths) throws IOException {
 		List<String> manifestFileContents = new ArrayList<>(thePropertyFilePaths.size());
 		for (String next : thePropertyFilePaths) {
@@ -56,7 +57,7 @@ public static NarrativeTemplateManifest forManifestFileLocation(Collection<Strin
 
         return NarrativeTemplateManifest.forManifestFileContents(manifestFileContents);
     }
-    
+
     static String loadResourceAlsoFromJar(String name) throws IOException {
 		if (name.startsWith("classpath:")) {
 			String cpName = name.substring("classpath:".length());

diff --git a/...ing/src/main/java/org/opencds/cqf/tooling/cql_generation/builder/VmrToFhirElmBuilder.java b/...ing/src/main/java/org/opencds/cqf/tooling/cql_generation/builder/VmrToFhirElmBuilder.java
@@ -38,6 +38,7 @@ public class VmrToFhirElmBuilder extends VmrToModelElmBuilder {
      * @param modelVersion modelVersion
      * @param decimalFormat decimalFormat
      */
+    @SuppressWarnings("this-escape")
     public VmrToFhirElmBuilder(String modelVersion, DecimalFormat decimalFormat) {
         super("FHIR", modelVersion, "http://hl7.org/FHIR", new FhirLibrarySourceProvider(), decimalFormat);
         IncludeDef includeHelper = of.createIncludeDef().withLocalIdentifier("FHIRHelpers").withPath("FHIRHelpers")
@@ -184,7 +185,7 @@ private Expression buildModelingB(LibraryBuilder libraryBuilder) {
         codeRefs.setResultType(new ListType(finalCodeRef.getResultType()));
 
         String filterPath = "status";
-        
+
         Retrieve retrieve = resolveRetrieve(libraryBuilder, resource, null, null, null);
         AliasedQuerySource source = of.createAliasedQuerySource().withAlias(retrieveAlias).withExpression(retrieve);
         source.setResultType(source.getExpression().getResultType());
@@ -200,7 +201,7 @@ private Expression buildModelingB(LibraryBuilder libraryBuilder) {
      * [MedicationAdministration] M return M.reasonCode // TODO: Work out the "include" capability
      *   union
      *   (
-     *     [MedicationAdministration] M 
+     *     [MedicationAdministration] M
      *       let reasonConditions: [Condition: id in (M.reasonReference R return GetTail(R.reference))]
      *       return reasonConditions.code
      *   )
@@ -535,7 +536,7 @@ private Expression buildWhereReturnPathQuery(AliasedQuerySource source, LibraryB
         Query query = resolveQuery(libraryBuilder, sources, elements);
 
         Expression right = query;
-        
+
         Expression where = libraryBuilder.resolveIn(left, right);
         return where;
     }
@@ -669,7 +670,7 @@ private Query letConditionReturnQuery(LibraryBuilder libraryBuilder, String reso
         Expression idList = of.createList().withElement(letQuery);
         idList.setResultType(new ListType(letQuery.getResultType()));
         Retrieve conditionRetrieve = resolveRetrieve(libraryBuilder, "Condition", idList, "in", "id");
-        
+
         LetClause let = of.createLetClause().withIdentifier("reasonConditions").withExpression(conditionRetrieve);
         let.setResultType(conditionRetrieve.getResultType());
         elements.add(let);

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/library/r4/LibraryGenerator.java b/tooling/src/main/java/org/opencds/cqf/tooling/library/r4/LibraryGenerator.java
@@ -23,6 +23,7 @@
 
 public class LibraryGenerator extends BaseLibraryGenerator<Library, NarrativeProvider> {
 
+    @SuppressWarnings("this-escape")
     public LibraryGenerator() {
         setNarrativeProvider(new NarrativeProvider());
         setFhirContext(FhirContext.forR4Cached());

diff --git a/...g/src/main/java/org/opencds/cqf/tooling/library/stu3/InMemoryLibraryResourceProvider.java b/...g/src/main/java/org/opencds/cqf/tooling/library/stu3/InMemoryLibraryResourceProvider.java
diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/library/stu3/LibraryGenerator.java b/tooling/src/main/java/org/opencds/cqf/tooling/library/stu3/LibraryGenerator.java
@@ -30,6 +30,7 @@ public class LibraryGenerator extends BaseLibraryGenerator<Library, NarrativePro
 
     private Map<String, IBaseResource> libraryMap = new HashMap<>();
 
+    @SuppressWarnings("this-escape")
     public LibraryGenerator() {
         setNarrativeProvider(new NarrativeProvider());
         setFhirContext(FhirContext.forDstu3Cached());
@@ -48,7 +49,7 @@ public void processLibrary(String id, CqlTranslator translator) {
         if (elm.getIncludes() != null && !elm.getIncludes().getDef().isEmpty()) {
             for (IncludeDef def : elm.getIncludes().getDef()) {
                 addRelatedArtifact(library, def);
-            }        
+            }
         }
 
         resolveDataRequirements(library, translator);

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/library/stu3/LibraryRefresher.java b/tooling/src/main/java/org/opencds/cqf/tooling/library/stu3/LibraryRefresher.java
@@ -29,6 +29,7 @@ public class LibraryRefresher extends BaseLibraryGenerator<Library, NarrativePro
 
     private Map<String, IBaseResource> libraryMap = new HashMap<>();
 
+    @SuppressWarnings("this-escape")
     public LibraryRefresher() {
         setNarrativeProvider(new NarrativeProvider());
         setFhirContext(FhirContext.forDstu3Cached());
@@ -43,7 +44,7 @@ public void processLibrary(String id, CqlTranslator translator) {
         if (elm.getIncludes() != null && !elm.getIncludes().getDef().isEmpty()) {
             for (IncludeDef def : elm.getIncludes().getDef()) {
                 addRelatedArtifact(generatedLibrary, def);
-            }        
+            }
         }
 
         resolveDataRequirements(generatedLibrary, translator);

diff --git a/.../src/main/java/org/opencds/cqf/tooling/measure/adapters/FhirServerMeasureTestAdapter.java b/.../src/main/java/org/opencds/cqf/tooling/measure/adapters/FhirServerMeasureTestAdapter.java
@@ -3,14 +3,14 @@
 import java.text.SimpleDateFormat;
 import java.util.Objects;
 
-import ca.uhn.fhir.parser.IParser;
 import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.opencds.cqf.tooling.utilities.HttpClientUtils;
+import org.opencds.cqf.tooling.utilities.LogUtils;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
-import org.opencds.cqf.tooling.utilities.HttpClientUtils;
-import org.opencds.cqf.tooling.utilities.LogUtils;
 
 public abstract class FhirServerMeasureTestAdapter extends MeasureTestAdapter {
 
@@ -60,7 +60,7 @@ private IMeasureReportAdapter parseEvaluatedResponse(String response) {
         IParser parser = fhirContext.newJsonParser();
         measureReport = parser.parseResource(response);
 
-        measureReportAdapter = this.getMeasureReportAdapter(measureReport);
+        measureReportAdapter = getMeasureReportAdapter(this.fhirContext, measureReport);
         return measureReportAdapter;
     }
 }