Merge branch 'develop' into feature/MAT-7300-signature-level

pom.xml

@@ -267,7 +267,7 @@
     <dependency>
       <groupId>gov.cms.madie</groupId>
       <artifactId>madie-java-models</artifactId>
-      <version>0.6.30-SNAPSHOT</version>
+      <version>0.6.42-SNAPSHOT</version>
       <exclusions>
         <exclusion>
           <artifactId>jackson-core</artifactId>

src/main/java/gov/cms/mat/cql_elm_translation/utils/cql/parsing/Cql2ElmListener.java

@@ -164,12 +164,20 @@ public void enterCodesystemDefinition(cqlParser.CodesystemDefinitionContext ctx)
       CQLCodeSystem codeSystem = new CQLCodeSystem();
       codeSystem.setId(csDef.getId());
       codeSystem.setOID(csDef.getId());
+      codeSystem.setCodeSystemVersion(getParsedVersion(csDef.getVersion()));
       codeSystem.setCodeSystemName(csDef.getName());
 
       codeSystemMap.putIfAbsent(identifier, codeSystem);
     }
   }
 
+  private String getParsedVersion(String version) {
+    if (version != null && version.startsWith("urn:hl7:version:")) {
+      return version.substring("urn:hl7:version:".length());
+    }
+    return version;
+  }
+
   @Override
   public void enterQualifiedFunction(QualifiedFunctionContext ctx) {
     if (ctx.identifierOrFunctionIdentifier() != null
@@ -556,18 +564,29 @@ private Element resolve(String identifier, CompiledLibrary library) {
           currentContext, def.getPath() + "-" + def.getVersion() + "|" + def.getLocalIdentifier());
       libraryAccessor = def;
       try {
-        parseChildLibraries(def);
-        libraries.add(
-            CQLIncludeLibrary.builder()
-                .cqlLibraryName(def.getPath())
-                .aliasName(def.getLocalIdentifier())
-                .version(def.getVersion())
-                // TODO: should be taken from librarySetId
-                .id(def.getTrackerId().toString())
-                .setId(def.getTrackerId().toString())
-                .build());
+        var parsedLibrary =
+            libraries.stream()
+                .filter(
+                    l ->
+                        l.getCqlLibraryName().equalsIgnoreCase(def.getPath())
+                            && l.getVersion().equalsIgnoreCase(def.getVersion()))
+                .findFirst();
+        if (parsedLibrary.isEmpty()) {
+          parseChildLibraries(def);
+          libraries.add(
+              CQLIncludeLibrary.builder()
+                  .cqlLibraryName(def.getPath())
+                  .aliasName(def.getLocalIdentifier())
+                  .version(def.getVersion())
+                  // TODO: should be taken from librarySetId
+                  .id(def.getTrackerId().toString())
+                  .setId(def.getTrackerId().toString())
+                  .build());
+        }
       } catch (IOException e) {
-        e.printStackTrace();
+        log.error(
+            "IOException while parsing child library [{}] " + e.getMessage(),
+            def.getPath() + "-" + def.getVersion());
       }
     } else if (element instanceof CodeDef codeDef) {
       codes.add(formattedIdentifier);
@@ -578,6 +597,8 @@ private Element resolve(String identifier, CompiledLibrary library) {
               .codeName(codeDef.getDisplay())
               .codeSystemName(codeDef.getCodeSystem().getName())
               .codeSystemOID(cqlCodeSystem == null ? null : cqlCodeSystem.getOID())
+              .codeSystemVersion(
+                  cqlCodeSystem == null ? null : cqlCodeSystem.getCodeSystemVersion())
               .codeIdentifier(formattedIdentifier)
               .build();
       declaredCodes.add(declaredCode);

src/main/java/gov/cms/mat/cql_elm_translation/utils/cql/parsing/model/CQLGraph.java

@@ -9,6 +9,9 @@
 import java.util.Queue;
 import java.util.Set;
 
+import lombok.extern.slf4j.Slf4j;
+
+@Slf4j
 public class CQLGraph {
 
   private final Map<String, Set<String>> graph = new HashMap<>();
@@ -49,20 +52,32 @@ public boolean isPath(String source, String destination) {
 
     while (!queue.isEmpty()) {
       String currentNode = queue.remove();
-      List<String> adjacentVertices = new ArrayList<>(this.graph.get(currentNode));
-
-      for (String adjacentNode : adjacentVertices) {
-        // we've found the destination node that we were looking for, so return true.
-        if (adjacentNode.equals(destination)) {
-          return true;
-        }
 
-        // if it's not the destination node and the node hasn't been visited yet, add it to the
-        // queue to be visited.
-        if (!visited.contains(adjacentNode)) {
-          visited.add(adjacentNode);
-          queue.add(adjacentNode);
+      if (this.graph.get(currentNode) != null) {
+        List<String> adjacentVertices = new ArrayList<>(this.graph.get(currentNode));
+
+        for (String adjacentNode : adjacentVertices) {
+          // we've found the destination node that we were looking for, so return true.
+          if (adjacentNode.equals(destination)) {
+            return true;
+          }
+
+          // if it's not the destination node and the node hasn't been visited yet, add it to the
+          // queue to be visited.
+          if (!visited.contains(adjacentNode)) {
+            visited.add(adjacentNode);
+            queue.add(adjacentNode);
+          }
         }
+      } else {
+        log.error(
+            "source = "
+                + source
+                + " destination = "
+                + destination
+                + " this.graph.get currentNode: "
+                + currentNode
+                + " is null");
       }
     }
 

src/main/resources/application.yaml

@@ -1,7 +1,7 @@
 server:
   port: 8083
   servlet:
-    context-path: /api/fhir
+    context-path: /api/qdm
 
 spring:
   profiles: