Merge branch 'develop' into MAT-7481_UpdateConfigValues

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/controllers/CqlToolsController.java

@@ -2,6 +2,7 @@
 
 import gov.cms.madie.models.dto.TranslatedLibrary;
 import gov.cms.madie.models.measure.Measure;
+import gov.cms.mat.cql_elm_translation.dto.CqlBuilderLookup;
 import gov.cms.mat.cql_elm_translation.dto.CqlLookupRequest;
 import gov.cms.mat.cql_elm_translation.dto.CqlLookups;
 import gov.cms.mat.cql_elm_translation.dto.SourceDataCriteria;
@@ -103,4 +104,14 @@ public ResponseEntity<CqlLookups> getCqlLookups(
         cqlParsingService.getCqlLookups(
             lookupRequest.getCql(), lookupRequest.getMeasureExpressions(), accessToken));
   }
+
+  @PutMapping(
+      value = "/cql-builder-lookups",
+      produces = MediaType.APPLICATION_JSON_VALUE,
+      consumes = MediaType.APPLICATION_JSON_VALUE)
+  public ResponseEntity<CqlBuilderLookup> getCqlBuilderLookups(
+      @RequestBody String cql, @RequestHeader("Authorization") String accessToken) {
+    log.info("Preparing CqlBuilder Lookups");
+    return ResponseEntity.ok(cqlParsingService.getCqlBuilderLookups(cql, accessToken));
+  }
 }

src/main/java/gov/cms/mat/cql_elm_translation/dto/CqlBuilderLookup.java

@@ -0,0 +1,23 @@
+package gov.cms.mat.cql_elm_translation.dto;
+
+import lombok.Builder;
+import lombok.Data;
+
+import java.util.Set;
+
+@Data
+@Builder
+public class CqlBuilderLookup {
+  private Set<Lookup> parameters;
+  private Set<Lookup> definitions;
+  private Set<Lookup> functions;
+  private Set<Lookup> fluentFunctions;
+
+  @Builder
+  public static class Lookup {
+    private String name;
+    private String libraryName;
+    private String libraryAlias;
+    private String logic;
+  }
+}

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

@@ -1,5 +1,6 @@
 package gov.cms.mat.cql_elm_translation.service;
 
+import gov.cms.mat.cql_elm_translation.dto.CqlBuilderLookup;
 import gov.cms.mat.cql_elm_translation.dto.CqlLookups;
 import gov.cms.mat.cql_elm_translation.dto.ElementLookup;
 import gov.cms.mat.cql_elm_translation.utils.cql.CQLTools;
@@ -45,13 +46,13 @@ public Set<CQLDefinition> getAllDefinitions(String cql, String accessToken) {
   }
 
   /**
-   * Parses the CQL and generates cql artifacts(including for the CQL of the included Libraries).
-   * refer CQL artifacts- gov.cms.mat.cql_elm_translation.dto.CQLLookups
+   * Parses the CQL and generates only used cql artifacts(including for the CQL of the included
+   * Libraries). refer CQL artifacts- gov.cms.mat.cql_elm_translation.dto.CQLLookups
    *
    * @param cql- measure cql
    * @param measureExpressions- set of cql definitions used in measure groups, SDEs & RAVs
    * @param accessToken Requesting User's Okta Bearer token
-   * @return CQLLookups
+   * @return CQLLookups -> building blocks for HQMF and Human Readable generation
    */
   public CqlLookups getCqlLookups(String cql, Set<String> measureExpressions, String accessToken) {
     if (StringUtils.isBlank(cql) || CollectionUtils.isEmpty(measureExpressions)) {
@@ -104,6 +105,78 @@ public CqlLookups getCqlLookups(String cql, Set<String> measureExpressions, Stri
         .build();
   }
 
+  /**
+   * Parses the CQL and collect all CQL building blocks irrespective of used or unused(including for
+   * the CQL of the included Libraries)
+   *
+   * @param cql- measure cql
+   * @param accessToken Requesting User's Okta Bearer token
+   * @return CqlBuilderLookup -> building blocks for CQL Definition UI builder
+   */
+  public CqlBuilderLookup getCqlBuilderLookups(String cql, String accessToken) {
+    if (StringUtils.isBlank(cql)) {
+      return null;
+    }
+
+    CQLTools cqlTools = parseCql(cql, accessToken, cqlLibraryService, null);
+    // all parameters
+    Set<CqlBuilderLookup.Lookup> parameters =
+        cqlTools.getAllParameters().stream().map(this::buildParameterLookup).collect(toSet());
+
+    // get all CQLDefinitions including functions
+    Set<CQLDefinition> allCqlDefinitions = buildCqlDefinitions(cqlTools);
+    // prepare lookups for definitions, functions and fluent functions from CQLDefinitions
+    Set<CqlBuilderLookup.Lookup> definitions = new HashSet<>();
+    Set<CqlBuilderLookup.Lookup> functions = new HashSet<>();
+    Set<CqlBuilderLookup.Lookup> fluentFunctions = new HashSet<>();
+    for (CQLDefinition cqlDefinition : allCqlDefinitions) {
+      CqlBuilderLookup.Lookup lookup =
+          buildCqlBuilderLookup(
+              cqlDefinition.getName(),
+              cqlDefinition.getLogic(),
+              cqlDefinition.getParentLibrary(),
+              cqlDefinition.getLibraryDisplayName());
+      if (cqlDefinition.isFunction()) {
+        if (StringUtils.startsWith(cqlDefinition.getLogic(), "define fluent function")) {
+          fluentFunctions.add(lookup);
+        } else {
+          functions.add(lookup);
+        }
+      } else {
+        definitions.add(lookup);
+      }
+    }
+    return CqlBuilderLookup.builder()
+        .parameters(parameters)
+        .definitions(definitions)
+        .functions(functions)
+        .fluentFunctions(fluentFunctions)
+        .build();
+  }
+
+  private CqlBuilderLookup.Lookup buildParameterLookup(CQLParameter parameter) {
+    String[] parts = parameter.getParameterName().split("\\|");
+    String name = parameter.getParameterName();
+    String libraryName = null;
+    String libraryAlias = null;
+    if (parts.length == 3) {
+      libraryName = parts[0].split("-")[0];
+      libraryAlias = parts[1];
+      name = parts[2];
+    }
+    return buildCqlBuilderLookup(name, parameter.getParameterLogic(), libraryName, libraryAlias);
+  }
+
+  private CqlBuilderLookup.Lookup buildCqlBuilderLookup(
+      String name, String logic, String libraryName, String libraryAlias) {
+    return CqlBuilderLookup.Lookup.builder()
+        .name(name)
+        .logic(logic)
+        .libraryName(libraryName)
+        .libraryAlias(libraryAlias)
+        .build();
+  }
+
   /**
    * Maps the references between CQL Definitions. In other words, which CQL Definitions and
    * Functions are called by which other CQL Definition.
@@ -328,13 +401,7 @@ private CQLDefinition buildCqlDefinition(DefinitionContent definitionContent) {
         definition.setLibraryVersion(libraryParts[1]);
       }
     }
-    // TODO could use a stronger comparator for determining if node is Definition or Function
-    definition.setFunction(definition.getDefinitionLogic().startsWith("define function"));
+    definition.setFunction(definitionContent.isFunction());
     return definition;
   }
-
-  public Map<String, Set<String>> getUsedFunctions(String cql, String accessToken) {
-    CQLTools cqlTools = parseCql(cql, accessToken, cqlLibraryService, null);
-    return cqlTools.getUsedFunctions();
-  }
 }

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

@@ -26,10 +26,6 @@ public class DataCriteriaService extends CqlTooling {
 
   private final CqlLibraryService cqlLibraryService;
 
-  public DataCriteria parseDataCriteriaFromCql(String cql, String accessToken) {
-    return parseCql(cql, accessToken, cqlLibraryService, null).getDataCriteria();
-  }
-
   public Set<SourceDataCriteria> getRelevantElements(Measure measure, String accessToken) {
     if (StringUtils.isBlank(measure.getCql())) {
       log.info("Data criteria not found as cql is blank");

src/main/java/gov/cms/mat/cql_elm_translation/utils/cql/CQLTools.java

@@ -84,6 +84,7 @@ public class CQLTools {
   private Set<String> usedCodeSystems = new HashSet<>();
   private DataCriteria dataCriteria = new DataCriteria();
   private Set<DefinitionContent> definitionContents = new HashSet<>();
+  private Set<CQLParameter> allParameters = new HashSet<>();
   private Map<String, Set<String>> callstack = new HashMap<>();
   private UsingProperties usingProperties;
 
@@ -140,6 +141,7 @@ public void generate() throws IOException {
     walker.walk(listener, tree);
 
     definitionContents.addAll(listener.getDefinitionContents());
+    allParameters.addAll(listener.getParameters());
     callstack = graph.getAdjacencyList();
 
     Set<CQLIncludeLibrary> librariesSet = new HashSet<>(listener.getLibraries());

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

@@ -163,12 +163,20 @@ 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
@@ -201,6 +209,14 @@ public void enterQualifiedIdentifierExpression(QualifiedIdentifierExpressionCont
     }
   }
 
+  @Override
+  public void enterLocalIdentifier(cqlParser.LocalIdentifierContext ctx) {
+    String identifier = parseString(ctx.identifier().getText());
+    if (shouldResolve(identifier)) {
+      resolve(identifier, getCurrentLibraryContext());
+    }
+  }
+
   @Override
   public void enterReferentialIdentifier(ReferentialIdentifierContext ctx) {
     String identifier = parseString(ctx.getText());
@@ -275,6 +291,7 @@ public void enterFunctionDefinition(@NotNull cqlParser.FunctionDefinitionContext
             .name(currentContext)
             .content(content)
             .functionArguments(functionArguments)
+            .function(true)
             .build());
     graph.addNode(currentContext);
   }
@@ -335,6 +352,9 @@ public void enterParameterDefinition(@NotNull cqlParser.ParameterDefinitionConte
     String identifier = parseString(ctx.identifier().getText());
     this.currentContext = libraryIdentifier + identifier;
     graph.addNode(currentContext);
+    if (shouldResolve(identifier)) {
+      resolve(identifier, getCurrentLibraryContext());
+    }
   }
 
   @Override
@@ -555,18 +575,29 @@ 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);
@@ -577,6 +608,8 @@ 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);
@@ -633,9 +666,6 @@ private void parseChildLibraries(IncludeDef def) throws IOException {
     cqlLexer lexer = new cqlLexer(CharStreams.fromStream(stream));
     CommonTokenStream tokens = new CommonTokenStream(lexer);
     cqlParser parser = new cqlParser(tokens);
-
-    //        CompiledLibrary childLibrary = this.translatedLibraryMap.get(def.getPath() + "-" +
-    // def.getVersion());
     CompiledLibrary childLibrary = this.translatedLibraryMap.get(def.getPath());
     Cql2ElmListener listener =
         new Cql2ElmListener(

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/java/gov/cms/mat/cql_elm_translation/utils/cql/parsing/model/DefinitionContent.java

@@ -11,4 +11,5 @@ public class DefinitionContent {
   private String name;
   private String content;
   private List<CQLFunctionArgument> functionArguments;
+  private boolean function;
 }

src/main/resources/application.yaml

@@ -1,8 +1,7 @@
 server:
   port: 8083
   servlet:
-    context-path: /api/fhir
-
+    context-path: /api/qdm
 spring:
   profiles:
     active: local
@@ -29,8 +28,8 @@ madie:
       cql:
         uri: /cql-libraries/cql
   translatorVersion:
-      currentVersion: ${CURRENT_TRANSLATOR_VERSION:3.3.2}
-      mostRecentVersion: ${MOST_RECENT_TRANSLATOR_VERSION:3.3.2}
+      currentVersion: ${CURRENT_TRANSLATOR_VERSION:3.11.0}
+      mostRecentVersion: ${MOST_RECENT_TRANSLATOR_VERSION:3.11.0}
 
 springdoc:
   swagger-ui: