Merge pull request #111 from cqframework/fix-110-add-library-generati…

…on-to-refresh

#110: Add library stub generation to the library refresh process.

src/main/java/org/opencds/cqf/tooling/processor/CqlProcessor.java

@@ -30,12 +30,19 @@ public class CqlProcessor {
      * information about a cql file
      */
     public class CqlSourceFileInformation {
+        private VersionedIdentifier identifier;
         private byte[] elm;
         private byte[] jsonElm;
         private List<ValidationMessage> errors = new ArrayList<>();
         private List<RelatedArtifact> relatedArtifacts = new ArrayList<>();
         private List<DataRequirement> dataRequirements = new ArrayList<>();
         private List<ParameterDefinition> parameters = new ArrayList<>();
+        public VersionedIdentifier getIdentifier() {
+            return identifier;
+        }
+        public void setIdentifier(VersionedIdentifier identifier) {
+            this.identifier = identifier;
+        }
         public byte[] getElm() {
             return elm;
         }
@@ -168,6 +175,14 @@ public CqlSourceFileInformation getFileInformation(String filename) {
         return this.fileMap.remove(filename);
     }
 
+    public Collection<CqlSourceFileInformation> getAllFileInformation() {
+        if (fileMap == null) {
+            throw new IllegalStateException("CQL File map is not available, execute has not been called");
+        }
+
+        return this.fileMap.values();
+    }
+
     /**
      * Called at the end after all getFileInformation have been called
      * return any errors that didn't have any particular home, and also
@@ -306,6 +321,7 @@ private void translateFile(ModelManager modelManager, LibraryManager libraryMana
                 // convert to base64 bytes
                 // NOTE: Publication tooling requires XML content
                 result.setElm(translator.toXml().getBytes());
+                result.setIdentifier(translator.toELM().getIdentifier());
                 if (options.getFormats().contains(CqlTranslator.Format.JSON)) {
                     result.setJsonElm(translator.toJson().getBytes());
                 }

src/main/java/org/opencds/cqf/tooling/processor/LibraryProcessor.java

@@ -57,7 +57,6 @@ public static List<String> refreshIgLibraryContent(BaseProcessor parentContext,
         params.fhirContext = fhirContext;
         params.encoding = outputEncoding;
         params.versioned = versioned;
-        params.libraryPath = libraryPath;
         return libraryProcessor.refreshLibraryContent(params);
     }
 
@@ -164,6 +163,30 @@ protected List<Library> refreshGeneratedContent(List<Library> sourceLibraries) {
 
         cqlProcessor.execute();
 
+        // For each CQL file, ensure that there is a Library resource with a matching name and version
+        for (CqlProcessor.CqlSourceFileInformation fileInfo : cqlProcessor.getAllFileInformation()) {
+            if (fileInfo.getIdentifier() != null && fileInfo.getIdentifier().getId() != null && !fileInfo.getIdentifier().getId().equals("")) {
+                Library existingLibrary = null;
+                for (Library sourceLibrary : sourceLibraries) {
+                    if (fileInfo.getIdentifier().getId().equals(sourceLibrary.getName())
+                            && (fileInfo.getIdentifier().getVersion() == null || fileInfo.getIdentifier().getVersion().equals(sourceLibrary.getVersion()))
+                    ) {
+                        existingLibrary = sourceLibrary;
+                        break;
+                    }
+                }
+
+                if (existingLibrary == null) {
+                    Library newLibrary = new Library();
+                    newLibrary.setName(fileInfo.getIdentifier().getId());
+                    newLibrary.setVersion(fileInfo.getIdentifier().getVersion());
+                    newLibrary.setUrl(String.format("%s/Library/%s", (newLibrary.getName().equals("FHIRHelpers") ? "http://hl7.org/fhir" : canonicalBase), fileInfo.getIdentifier().getId()));
+                    newLibrary.setId(LibraryProcessor.getId(newLibrary.getName()) + (versioned ? "-" + newLibrary.getVersion() : ""));
+                    sourceLibraries.add(newLibrary);
+                }
+            }
+        }
+
         List<Library> resources = new ArrayList<Library>();
         for (Library library : sourceLibraries) {
             resources.add(refreshGeneratedContent(library));

src/main/java/org/opencds/cqf/tooling/processor/MeasureProcessor.java

@@ -107,6 +107,7 @@ public static void bundleMeasures(ArrayList<String> refreshedLibraryNames, Strin
                     if (path.endsWith(refreshedLibraryFileName))
                     {
                         measureSourcePath = path;
+                        break;
                     }
                 }
 

src/main/java/org/opencds/cqf/tooling/processor/R4LibraryProcessor.java

@@ -43,7 +43,7 @@ public class R4LibraryProcessor extends LibraryProcessor {
     /*
     Refresh all library resources in the given libraryPath
      */
-    protected List<String> refreshLibraries(String libraryPath) {
+    protected List<String> refreshLibraries(String libraryPath, Encoding encoding) {
         File file = new File(libraryPath);
         Map<String, String> fileMap = new HashMap<String, String>();
         List<org.hl7.fhir.r5.model.Library> libraries = new ArrayList<>();
@@ -76,10 +76,19 @@ protected List<String> refreshLibraries(String libraryPath) {
         List<String> refreshedLibraryNames = new ArrayList<String>();
         List<org.hl7.fhir.r5.model.Library> refreshedLibraries = super.refreshGeneratedContent(libraries);
         for (org.hl7.fhir.r5.model.Library refreshedLibrary : refreshedLibraries) {
-            String filePath = fileMap.get(refreshedLibrary.getId());
             Library library = (Library) VersionConvertor_40_50.convertResource(refreshedLibrary);
+            String filePath = null;
+            Encoding fileEncoding = null;            
+            if (fileMap.containsKey(refreshedLibrary.getId()))
+            {
+                filePath = fileMap.get(refreshedLibrary.getId());
+                fileEncoding = IOUtils.getEncoding(filePath);
+            } else {
+                filePath = libraryPath;
+                fileEncoding = encoding;
+            }    
             cqfmHelper.ensureToolingExtensionAndDevice(library, fhirContext);
-            IOUtils.writeResource(library, filePath, IOUtils.getEncoding(filePath), fhirContext);
+            IOUtils.writeResource(library, filePath, fileEncoding, fhirContext);
             refreshedLibraryNames.add(refreshedLibrary.getName());
         }
 
@@ -102,7 +111,7 @@ public List<String> refreshLibraryContent(RefreshLibraryParameters params) {
         encoding = params.encoding;
         versioned = params.versioned;
 
-        return refreshLibraries(libraryPath);
+        return refreshLibraries(libraryPath, encoding);
 
         /*
         CqlTranslator translator = getTranslator(cqlContentPath);