fix concept map error #227

.vscode/launch.json

@@ -84,6 +84,15 @@
       "projectName": "matchbox-server",
       "vmArgs": "-Dspring.config.additional-location=file:/Users/oegger/Documents/github/matchbox/matchbox-server/target/test-classes/application-test-r5onr4.yaml",
       "cwd": "${workspaceFolder}/matchbox-server"
+    },
+    {
+      "type": "java",
+      "name": "Launch Matchbox-Server (alis)",
+      "request": "launch",
+      "mainClass": "ca.uhn.fhir.jpa.starter.Application",
+      "projectName": "matchbox-server",
+      "vmArgs": "-Dspring.config.additional-location=file:with-alis/application.yaml",
+      "cwd": "${workspaceFolder}/matchbox-server"
     },    {
       "type": "java",
       "name": "Launch Matchbox-Server",

docs/changelog.md

@@ -1,7 +1,8 @@
-2024/04/xx Release 3.8.3
+2024/04/29 Release 3.8.3
 
 - profile validation with different ig version issues, GUI & EVS Client [#225](https://github.com/ahdis/matchbox/issues/225)
 - improved the profile selection in the validation GUI
+- FML: Side effect exception when updating a StructureMap [#227](https://github.com/ahdis/matchbox/issues/227)
 
 2024/04/22 Release 3.8.2
 

matchbox-engine/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>matchbox</artifactId>
         <groupId>health.matchbox</groupId>
-        <version>3.8.2</version>
+        <version>3.8.3</version>
     </parent>
 
     <artifactId>matchbox-engine</artifactId>

matchbox-engine/src/main/java/ch/ahdis/matchbox/engine/MatchboxEngine.java

@@ -254,6 +254,7 @@ public MatchboxEngine getEngine() throws MatchboxEngineCreationException {
 			try { engine = new MatchboxEngine(this.fromNothing()); }
 			catch (final IOException e) { throw new MatchboxEngineCreationException(e); }
 			engine.setVersion(this.fhirVersion.toCode());
+			engine.getContext().setAllowLoadingDuplicates(false);
 			if (this.txServer == null) {
 				engine.getContext().setCanRunWithoutTerminology(true);
 				engine.getContext().setNoTerminologyServer(true);

matchbox-engine/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java

@@ -56,6 +56,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.TerminologyServiceException;
+import org.hl7.fhir.r5.comparison.VersionComparisonAnnotation;
 import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
 import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
 import org.hl7.fhir.r5.context.ILoggingService.LogCategory;
@@ -383,9 +384,16 @@ public void registerResourceFromPackage(CanonicalResourceProxy r, PackageInforma
 				if (Utilities.existsInList(url, "http://hl7.org/fhir/SearchParameter/example")) {
 					return;
 				}
+				// matchbox patch for duplicate resources, see https://github.com/ahdis/matchbox/issues/227
+				// org.hl7.fhir.r5.conformance.R5ExtensionsLoader.loadR5SpecialTypes(R5ExtensionsLoader.java:141)
 				CanonicalResource ex = fetchResourceWithException(r.getType(), url);
-				throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, r.getVersion(), ex.getVersion(),
-																		  ex.fhirType()));
+				if (laterVersion(r.getVersion(), ex.getVersion())) {
+					logger.logMessage("Note replacing old version: " + formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, r.getVersion(), ex.getVersion(), ex.fhirType()));
+					dropResource(ex);
+				} else {
+					logger.logMessage("Note keeping newer version: " + formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, r.getVersion(), ex.getVersion(), ex.fhirType()));
+					return;
+				}
 			}
 			switch(r.getType()) {
 				case "StructureDefinition":
@@ -508,9 +516,16 @@ public void cacheResourceFromPackage(Resource r, PackageInformation packageInfo)
 					if (Utilities.existsInList(url, "http://hl7.org/fhir/SearchParameter/example")) {
 						return;
 					}
-					CanonicalResource ex = (CanonicalResource) fetchResourceWithException(r.getClass(), url);
-					throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, ((CanonicalResource) r).getVersion(), ex.getVersion(),
-																			  ex.fhirType()));
+					// matchbox patch for duplicate resources, see https://github.com/ahdis/matchbox/issues/227
+					// org.hl7.fhir.r5.conformance.R5ExtensionsLoader.loadR5SpecialTypes(R5ExtensionsLoader.java:141)
+					CanonicalResource ex = fetchResourceWithException(m.fhirType(), url);
+					if (laterVersion(m.getVersion(), ex.getVersion())) {
+						logger.logMessage("Note replacing old version: " + formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, m.getVersion(), ex.getVersion(), ex.fhirType()));
+						dropResource(ex);
+					} else {
+						logger.logMessage("Note keeping newer version: " + formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, m.getVersion(), ex.getVersion(), ex.fhirType()));
+						return;
+					}
 				}
 				if (r instanceof StructureDefinition) {
 					StructureDefinition sd = (StructureDefinition) m;

matchbox-frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matchbox",
-  "version": "3.8.2",
+  "version": "3.8.3",
   "license": "MIT",
   "scripts": {
     "ng": "ng",

matchbox-server/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>matchbox</artifactId>
         <groupId>health.matchbox</groupId>
-        <version>3.8.2</version>
+        <version>3.8.3</version>
     </parent>
 
     <artifactId>matchbox-server</artifactId>

matchbox-server/src/main/java/ch/ahdis/matchbox/ConformancePackageResourceProvider.java

@@ -179,10 +179,12 @@ public ca.uhn.fhir.rest.api.server.IBundleProvider search(jakarta.servlet.http.H
 				if (theUrl != null) {
 					String url = theUrl.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue();
 					R5 r = matchboxEngine.getContext().fetchResource(classR5,url);
-					resources.add(r);
+					if (r != null)
+						resources.add(r);
 				} else {
 					resources.addAll(matchboxEngine.getContext().fetchResourcesByType(classR5));
 				}
+
 				switch (getFhirVersion(this.cliContext.getFhirVersion())) {
 					case "4.0.1": return new SimpleBundleProvider(
 						resources.stream().map(VersionConvertorFactory_40_50::convertResource).collect(Collectors.toList()));

matchbox-server/src/main/java/ch/ahdis/matchbox/IgLoaderFromJpaPackageCache.java

@@ -34,9 +34,11 @@
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_43_50;
+import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.IBaseBinary;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
+import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.r5.model.ImplementationGuide;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.utilities.ByteProvider;
@@ -104,6 +106,42 @@ public FhirContext getFhirContext(FhirVersionEnum theFhirVersion) {
 		return myVersionToContext.computeIfAbsent(theFhirVersion, v -> new FhirContext(v));
 	}
 
+	private void cleanModifierExtensions(org.hl7.fhir.r5.model.ConceptMap r) {
+		for ( org.hl7.fhir.r5.model.ConceptMap.ConceptMapGroupComponent  group :r.getGroup()) {
+			group.getElement().forEach(element -> {
+				element.getTarget().forEach(target -> {
+					target.getModifierExtension().clear();
+				});
+			});
+		}
+	}
+
+	private void cleanModifierExtensions(org.hl7.fhir.r5.model.StructureMap r) {
+		r.getContained().forEach(c -> {
+			if (c instanceof org.hl7.fhir.r5.model.ConceptMap) {
+				cleanModifierExtensions((org.hl7.fhir.r5.model.ConceptMap) c);
+			}
+		});
+	}
+
+	private void cleanModifierExtensions(org.hl7.fhir.r4.model.ConceptMap r) {
+		for ( ConceptMapGroupComponent group :r.getGroup()) {
+			group.getElement().forEach(element -> {
+				element.getTarget().forEach(target -> {
+					target.getModifierExtension().clear();
+				});
+			});
+		}
+	}
+
+	private void cleanModifierExtensions(org.hl7.fhir.r4.model.StructureMap r) {
+		r.getContained().forEach(c -> {
+			if (c instanceof org.hl7.fhir.r4.model.ConceptMap) {
+				cleanModifierExtensions((org.hl7.fhir.r4.model.ConceptMap) c);
+			}
+		});
+	}
+
 	private org.hl7.fhir.r5.model.Resource loadPackageEntity(NpmPackageVersionResourceEntity contents) {
 		try {
 			final var binary = MatchboxServerUtils.getBinaryFromId(contents.getResourceBinary().getId(), myDaoRegistry);
@@ -115,8 +153,12 @@ private org.hl7.fhir.r5.model.Resource loadPackageEntity(NpmPackageVersionResour
 				return VersionConvertorFactory_30_50
 						.convertResource(new org.hl7.fhir.dstu3.formats.JsonParser().parse(resourceContents));
 			case R4:
+				org.hl7.fhir.r4.model.Resource r = new org.hl7.fhir.r4.formats.JsonParser().parse(resourceContents);
+				if (r instanceof org.hl7.fhir.r4.model.StructureMap ) {
+					cleanModifierExtensions((org.hl7.fhir.r4.model.StructureMap) r);
+				}
 				return VersionConvertorFactory_40_50
-						.convertResource(new org.hl7.fhir.r4.formats.JsonParser().parse(resourceContents));
+						.convertResource(r);
 			case R4B:
 				return VersionConvertorFactory_43_50
 						.convertResource(new org.hl7.fhir.r4b.formats.JsonParser().parse(resourceContents));
@@ -224,7 +266,24 @@ public void loadIg(List<ImplementationGuide> igs, Map<String, ByteProvider> bina
 						Resource r = null;
 						try {
 							r = loadResourceByVersion(npm.fhirVersion(), TextFile.streamToBytes(pi.load("package", s)), s);
-							this.getContext().cacheResource(r);
+							// https://github.com/ahdis/matchbox/issues/227
+							if (r instanceof org.hl7.fhir.r5.model.StructureMap ) {
+								cleanModifierExtensions((org.hl7.fhir.r5.model.StructureMap) r);
+							}			
+							if (r instanceof org.hl7.fhir.r5.model.ConceptMap ) {
+								cleanModifierExtensions((org.hl7.fhir.r5.model.ConceptMap) r);
+							}			
+							if (r instanceof CanonicalResource) {
+								CanonicalResource m = (CanonicalResource) r;
+								String url = m.getUrl();
+								if (this.getContext().hasResource(r.getClass(), url)) {
+									log.error("Duplicate canonical resource: " + r.getClass().getName() + " from package " +pi.name() + "#" + pi.version() + " with url " + url);
+								} else {
+									this.getContext().cacheResource(r);
+								}
+							} else {
+								log.error("Resource is not a CanonicalResource: " + r.getClass().getName() + " from package " +pi.name() + "#" + pi.version());
+							}
 						} catch (FHIRException e) {
 							log.error(s, e);
 						} catch (IOException e) {

matchbox-server/with-alis/application.yaml

@@ -0,0 +1,33 @@
+server:
+  servlet:
+    context-path: /matchboxv3
+hapi:
+  fhir:
+    server_address: http://localhost:8080/matchboxv3/fhir
+    implementationguides:
+      fhir_r4_core:
+        name: hl7.fhir.r4.core
+        version: 4.0.1
+        url: classpath:/hl7.fhir.r4.core.tgz
+      fhir_terminology:
+        name: hl7.terminology
+        version: 5.4.0
+        url: classpath:/hl7.terminology#5.4.0.tgz
+      fhir_extensions:
+        name: hl7.fhir.uv.extensions.r4
+        version: 1.0.0
+        url: classpath:/hl7.fhir.uv.extensions.r4#1.0.0.tgz
+      hl7_fhir_uv_ips:
+        name: ch.fhir.ig.ch-alis
+        version: 0.2.0
+        url: file:/Users/oegger/Documents/github/ch-alis/output/package.tgz
+    staticLocation: file:/apps/
+matchbox:
+  fhir:
+    context:
+      fhirVersion: 4.0.1
+      txServer: http://tx.fhir.org
+      onlyOneEngine: true
+spring:
+  datasource:
+    url: "jdbc:h2:mem:test"

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>health.matchbox</groupId>
     <artifactId>matchbox</artifactId>
-    <version>3.8.2</version>
+    <version>3.8.3</version>
     <packaging>pom</packaging>
     <name>matchbox</name>
     <description>An open-source implementation to support testing and implementation of FHIR based solutions and map or