Merge pull request #104 from cqframework/fix-99-support-fhir-stu3

#99: Added support for FHIR STU3.

Examples/Zika/zika-virus-intervention-logic.cql

@@ -35,6 +35,7 @@ define "Pregnancy Conditions":
   [Condition: "Pregnancy"] C
     where C.clinicalStatus = 'active'
       and C.verificationStatus = 'confirmed'
+      // well, this is ugly....
       and Interval[C.onsetDateTime, C.abatementDateTime] includes Today()
 
 define "Is Patient Pregnant":
@@ -123,7 +124,7 @@ define "Has Possible Zika Exposure":
 define "Zika Symptom Onset":
   First(
     "Zika Symptoms" S
-      sort by S.onsetDateTime
+      sort by (S.onsetDateTime)
   ).onsetDateTime
 
 define "Time Since Symptom Onset":

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/CqlTranslator.java

@@ -204,6 +204,7 @@ private static void writeELM(Path inPath, Path outPath, Format format, boolean d
 
         LibraryManager libraryManager = new LibraryManager();
         libraryManager.getLibrarySourceLoader().registerProvider(new DefaultLibrarySourceProvider(inPath.getParent()));
+        libraryManager.getLibrarySourceLoader().registerProvider(new FhirLibrarySourceProvider());
         CqlTranslator translator = fromFile(inPath.toFile(), libraryManager, options.toArray(new Options[options.size()]));
         libraryManager.getLibrarySourceLoader().clearProviders();
 

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/DefaultLibrarySourceLoader.java

@@ -51,6 +51,11 @@ public InputStream getLibrarySource(VersionedIdentifier libraryIdentifier) {
             }
         }
 
+        if (source == null) {
+            throw new IllegalArgumentException(String.format("Could not load source for library %s, version %s.",
+                    libraryIdentifier.getId(), libraryIdentifier.getVersion()));
+        }
+
         return source;
     }
 }

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/DefaultLibrarySourceProvider.java

@@ -55,16 +55,21 @@ public boolean accept(File path, String name) {
                 }
             }
 
-            if (mostRecentFile == null) {
-                throw new IllegalArgumentException(String.format("Could not resolve most recent source library for library %s.", libraryIdentifier.getId()));
-            }
+            // Do not throw, allow the loader to throw, just report null
+            //if (mostRecentFile == null) {
+            //    throw new IllegalArgumentException(String.format("Could not resolve most recent source library for library %s.", libraryIdentifier.getId()));
+            //}
 
             libraryFile = mostRecentFile;
         }
         try {
-            return new FileInputStream(libraryFile);
+            if (libraryFile != null) {
+                return new FileInputStream(libraryFile);
+            }
         } catch (FileNotFoundException e) {
             throw new IllegalArgumentException(String.format("Could not load source for library %s.", libraryIdentifier.getId()), e);
         }
+
+        return null;
     }
 }

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/FhirLibrarySourceProvider.java

@@ -0,0 +1,16 @@
+package org.cqframework.cql.cql2elm;
+
+import org.hl7.elm.r1.VersionedIdentifier;
+
+import java.io.InputStream;
+
+/**
+ * Created by Bryn on 3/28/2017.
+ */
+public class FhirLibrarySourceProvider implements LibrarySourceProvider {
+    @Override
+    public InputStream getLibrarySource(VersionedIdentifier libraryIdentifier) {
+        return FhirLibrarySourceProvider.class.getResourceAsStream(String.format("/org/hl7/fhir/%s-%s.cql", libraryIdentifier.getId(),
+                libraryIdentifier.getVersion()));
+    }
+}

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/FhirModelInfoProvider.java

@@ -36,10 +36,14 @@ public ModelInfo load() {
                         ModelInfo.class);
 
             case "1.8":
-            case "":
                 return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-1.8.xml"),
                         ModelInfo.class);
 
+            case "3.0.0":
+            case "":
+                return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-3.0.0.xml"),
+                        ModelInfo.class);
+
             default:
                 throw new IllegalArgumentException(String.format("Unknown version %s of the FHIR model.", localVersion));
         }

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/ModelInfoLoader.java

@@ -24,6 +24,7 @@ public class ModelInfoLoader {
         registerModelInfoProvider(new VersionedIdentifier().withId("FHIR").withVersion("1.6"), new FhirModelInfoProvider().withVersion("1.6"));
         registerModelInfoProvider(new VersionedIdentifier().withId("FHIR").withVersion("1.4"), new FhirModelInfoProvider().withVersion("1.4"));
         registerModelInfoProvider(new VersionedIdentifier().withId("FHIR").withVersion("1.8"), new FhirModelInfoProvider().withVersion("1.8"));
+        registerModelInfoProvider(new VersionedIdentifier().withId("FHIR").withVersion("3.0.0"), new FhirModelInfoProvider().withVersion("3.0.0"));
     }
 
     public static ModelInfoProvider getModelInfoProvider(VersionedIdentifier modelIdentifier) {