Translator supports namespaces

Src/java/cqf-fhir/src/main/java/org/cqframework/fhir/utilities/IGContext.java

@@ -16,8 +16,24 @@
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
+import org.slf4j.LoggerFactory;
 
 public class IGContext {
+    private static class DefaultLogger implements ILoggingService {
+        private final org.slf4j.Logger log = LoggerFactory.getLogger(IGContext.class);
+
+        public void logMessage(String s) {
+            log.warn(s);
+        }
+
+        public void logDebugMessage(LogCategory logCategory, String s) {
+            log.debug("{}: {}", logCategory, s);
+        }
+
+        public boolean isDebugLogging() {
+            return log.isDebugEnabled();
+        }
+    }
 
     private ILoggingService logger;
 
@@ -69,6 +85,10 @@ public IGContext(ILoggingService logger) {
         this.logger = logger;
     }
 
+    public IGContext() {
+        this.logger = new DefaultLogger();
+    }
+
     public void initializeFromIg(String rootDir, String igPath, String fhirVersion) {
         this.rootDir = rootDir;
 

Src/java/cql-to-elm-cli/build.gradle

@@ -9,6 +9,8 @@ application {
 
 dependencies {
     implementation project(':cql-to-elm')
+    implementation project(':cqf-fhir')
+    implementation project(':cqf-fhir-npm')
     implementation project(':quick')
     implementation project(':qdm')
     implementation project(':model-jaxb')
@@ -17,6 +19,7 @@ dependencies {
     implementation 'org.slf4j:slf4j-simple:2.0.13'
     implementation 'org.glassfish.jaxb:jaxb-runtime:4.0.5'
     implementation 'org.eclipse.persistence:org.eclipse.persistence.moxy:4.0.2'
+    implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-r5"
     testImplementation project(':model-jaxb')
     testImplementation project(':elm-jaxb')
 }

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

@@ -19,8 +19,14 @@
 import org.cqframework.cql.cql2elm.*;
 import org.cqframework.cql.cql2elm.quick.FhirLibrarySourceProvider;
 import org.cqframework.cql.elm.tracking.TrackBack;
+import org.cqframework.fhir.npm.LibraryLoader;
+import org.cqframework.fhir.npm.NpmLibrarySourceProvider;
+import org.cqframework.fhir.npm.NpmPackageManager;
+import org.cqframework.fhir.utilities.IGContext;
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.cql.model.ModelInfoProvider;
+import org.hl7.cql.model.NamespaceInfo;
+import org.hl7.cql.model.NamespaceManager;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
 import org.hl7.elm_modelinfo.r1.serializing.ModelInfoReaderFactory;
 
@@ -54,6 +60,7 @@ private static void writeELM(
             Path outPath,
             org.cqframework.cql.cql2elm.CqlTranslator.Format format,
             ModelInfoProvider modelProvider,
+            IGContext igContext,
             CqlCompilerOptions options)
             throws IOException {
 
@@ -77,7 +84,28 @@ private static void writeELM(
                 .registerModelInfoProvider(new DefaultModelInfoProvider(inPath.getParent()), true);
         libraryManager.getLibrarySourceLoader().registerProvider(new DefaultLibrarySourceProvider(inPath.getParent()));
         libraryManager.getLibrarySourceLoader().registerProvider(new FhirLibrarySourceProvider());
-        org.cqframework.cql.cql2elm.CqlTranslator translator = fromFile(inPath.toFile(), libraryManager);
+
+        NamespaceManager namespaceManager = libraryManager.getNamespaceManager();
+        NamespaceInfo namespaceInfo = null;
+        if (igContext != null) {
+            NpmPackageManager pm = new NpmPackageManager(igContext.getSourceIg());
+            pm.getNpmList().forEach(npm -> {
+                NamespaceInfo newNamespace = new NamespaceInfo(npm.id(), npm.canonical());
+                namespaceManager.ensureNamespaceRegistered(newNamespace);
+            });
+            LibraryLoader reader = new LibraryLoader(igContext.getFhirVersion());
+            NpmLibrarySourceProvider sp = new NpmLibrarySourceProvider(pm.getNpmList(), reader, pm);
+            libraryManager.getLibrarySourceLoader().registerProvider(sp);
+
+            String packageId = igContext.getPackageId();
+            String canonicalBase = igContext.getCanonicalBase();
+
+            if (packageId != null && !packageId.isEmpty() && canonicalBase != null && !canonicalBase.isEmpty()) {
+                namespaceInfo = new NamespaceInfo(packageId, canonicalBase);
+            }
+        }
+
+        CqlTranslator translator = fromFile(namespaceInfo, inPath.toFile(), libraryManager);
         libraryManager.getLibrarySourceLoader().clearProviders();
 
         if (!translator.getErrors().isEmpty()) {
@@ -135,6 +163,10 @@ public static void main(String[] args) throws IOException, InterruptedException
                 .ofType(org.cqframework.cql.cql2elm.CqlTranslator.Format.class)
                 .defaultsTo(org.cqframework.cql.cql2elm.CqlTranslator.Format.XML)
                 .describedAs("The target format for the output");
+        OptionSpec<File> rootDir = parser.accepts("root-dir")
+                .withOptionalArg()
+                .ofType(File.class)
+                .describedAs("Root directory of a FHIR IG project, used to resolve CQL namespaces");
         OptionSpec disableDefaultModelInfoLoad = parser.accepts("disable-default-modelinfo-load");
         OptionSpec verify = parser.accepts("verify");
         OptionSpec optimization = parser.accepts("date-range-optimization");
@@ -231,6 +263,12 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IO
                 throw new IllegalArgumentException("input and output file must be different!");
             }
 
+            IGContext igContext = null;
+            if (options.has(rootDir)) {
+                igContext = new IGContext();
+                igContext.initializeFromIni(options.valueOf("root-dir") + File.separator + "ig.ini");
+            }
+
             ModelInfoProvider modelProvider = null;
             if (options.has(model)) {
                 final File modelFile = options.valueOf(model);
@@ -245,6 +283,7 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IO
                     out,
                     outputFormat,
                     modelProvider,
+                    igContext,
                     new CqlCompilerOptions(
                             options.has(optimization),
                             options.has(debug) || options.has(annotations),