Merge pull request #139 from ahdis/oe_343

changes for version 3.4.3
ahdis · Sep 20, 2023 · 5e2c42b · 5e2c42b
2 parents 04b7536 + c13e1c4
commit 5e2c42b
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Showing 16 changed files with 6,856 additions and 154 deletions.
diff --git a/matchbox-engine/src/main/java/ch/ahdis/matchbox/engine/cli/MatchboxService.java b/matchbox-engine/src/main/java/ch/ahdis/matchbox/engine/cli/MatchboxService.java
@@ -407,6 +407,7 @@ public String initializeValidator(CliContext cliContext, String definitions, Tim
       validator.setLanguage(cliContext.getLang());
       validator.setLocale(cliContext.getLocale());
       validator.setSnomedExtension(cliContext.getSnomedCTCode());
+      validator.setDisplayWarnings(cliContext.isDisplayWarnings());
       validator.setAssumeValidRestReferences(cliContext.isAssumeValidRestReferences());
       validator.setShowMessagesFromReferences(cliContext.isShowMessagesFromReferences());
       validator.setDoImplicitFHIRPathStringConversion(cliContext.isDoImplicitFHIRPathStringConversion());

diff --git a/...engine/src/main/java/ch/ahdis/matchbox/mappinglanguage/MatchboxStructureMapUtilities.java b/...engine/src/main/java/ch/ahdis/matchbox/mappinglanguage/MatchboxStructureMapUtilities.java
@@ -117,8 +117,7 @@ public Base translate(TransformContext context, StructureMap map, Base source, S
 			ConceptMap cmap = null;
 			if (conceptMapUrl.startsWith("#")) {
 				for (Resource r : map.getContained()) {
-//				if (r instanceof ConceptMap && r.getId().equals(conceptMapUrl)) { FIXME: looks like a simpleworkercontext issue
-					if (r instanceof ConceptMap && r.getId().equals(conceptMapUrl.substring(1))) {
+					if (r instanceof ConceptMap && (r.getId().equals(conceptMapUrl.substring(1)) || r.getId().equals(conceptMapUrl))) {
 						cmap = (ConceptMap) r;
 						su = map.getUrl() + "#" + conceptMapUrl;
 					}

diff --git a/matchbox-engine/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java b/matchbox-engine/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
@@ -116,6 +116,9 @@ public interface IPackageProvider {
 	private boolean suppressErrors;
 	private boolean minimalMemory;
 
+	private final static String VER_XVER_PROVIDED = "0.0.13";
+
+
 
 	public FilesystemPackageCacheManager(boolean userMode) throws IOException {
 		init(userMode ? FilesystemPackageCacheMode.USER : FilesystemPackageCacheMode.SYSTEM);
@@ -293,16 +296,27 @@ private void listSpecs(Map<String, String> specList, PackageServer server) throw
 
 	protected InputStreamWithSrc loadFromPackageServer(String id, String version) {
 
-  	// matchbox-engine PATCH, we do not want to load from a package server for hl7.fhir.xver-extension :
-  	if (CommonPackages.ID_XVER.equals(id)) {
-      version = "0.0.13";
+  		// matchbox-engine PATCH, we do not want to load from a package server for hl7.fhir.xver-extension :
+  		if (CommonPackages.ID_XVER.equals(id)) {
+			ourLog.info("loading " +id+ " form classpath");
+		    version = VER_XVER_PROVIDED;
 			InputStream stream = getClass().getResourceAsStream("/"+id+"#"+version+".tgz");
 			if (stream==null) {
 				ourLog.error("Unable to find/resolve/read from classpath (we dont' want go to the package server) for :" + id+"#"+version+".tgz");
 				throw new FHIRException("Unable to find/resolve/read from classpath (we dont' want go to the package server) for :" + id+"#"+version+".tgz");
 			}
 			return new InputStreamWithSrc(stream, "http://fhir.org/packages/hl7.fhir.xver-extensions", version);
-  	}
+  		}
+
+	  	if ("hl7.fhir.r5.core".equals(id)) {
+			ourLog.info("loading hl7.fhir.r5.core form classpath");
+			InputStream stream = getClass().getResourceAsStream("/"+id+".tgz");
+			if (stream==null) {
+				ourLog.error("Unable to find/resolve/read from classpath (we dont' want go to the package server) for :" + id+"#"+version+".tgz");
+				throw new FHIRException("Unable to find/resolve/read from classpath (we dont' want go to the package server) for :" + id+"#"+version+".tgz");
+			}
+			return new InputStreamWithSrc(stream, "https://hl7.org/fhir/R5/hl7.fhir.r5.core.tgz", version);
+	  	}
 
 		InputStreamWithSrc retVal = super.loadFromPackageServer(id, version);
 		if (retVal != null) {
@@ -464,7 +478,7 @@ public NpmPackage loadPackageFromCacheOnly(String id, String version) throws IOE
 	public NpmPackage addPackageToCache(String id, String version, InputStream packageTgzInputStream, String sourceDesc) throws IOException {
   	// matchbox-engine PATCH, we do not want to load from a package server for hl7.fhir.xver-extension :
   	if (CommonPackages.ID_XVER.equals(id)) {
-  		version = "0.0.13";
+  		version = VER_XVER_PROVIDED;
       NpmPackage npm = NpmPackage.fromPackage(packageTgzInputStream, sourceDesc, true);
       return npm;
   	}
@@ -586,6 +600,23 @@ public void listAllIds(Map<String, String> specList) throws IOException {
 	@Override
 	public NpmPackage loadPackage(String id, String version) throws FHIRException, IOException {
 		//ok, try to resolve locally
+
+		if (CommonPackages.ID_XVER.equals(id)) {
+	  		version = VER_XVER_PROVIDED;
+			InputStreamWithSrc packageTgzInputStream = this.loadFromPackageServer(id, version);
+    	  	NpmPackage npm = NpmPackage.fromPackage(packageTgzInputStream.stream);
+			// org.hl7.fhir.exceptions.FHIRException: Unknown FHIRVersion code '0.0.13'
+			// https://github.com/ahdis/matchbox/issues/135 
+			npm.getNpm().set("version", "4.0");
+		    return npm;
+  		}
+
+		if ("hl7.fhir.r5.core".equals(id)) {
+			InputStreamWithSrc packageTgzInputStream = this.loadFromPackageServer(id, version);
+    	  	NpmPackage npm = NpmPackage.fromPackage(packageTgzInputStream.stream);
+		    return npm;
+  		}
+
 		if (!Utilities.noString(version) && version.startsWith("file:")) {
 			return loadPackageFromFile(id, version.substring(5));
 		}