Merge pull request #94 from ahdis/oe_321

README.md

@@ -132,3 +132,18 @@ kubectl cp matchbox-test-app-d684cf865 ./fhir.logdir/
 # MVN run unit tests
 
 mvn -Dtest=CapabilityStatementTests test
+
+# Making a release
+
+To make a release, a [tag](https://github.com/ahdis/matchbox/tags) has to be created (e.g. `v.3.2.1`) in GitHub.
+It will trigger two workflows:
+
+1. The [Docker workflow](https://github.com/ahdis/matchbox/blob/main/.github/workflows/googleregistry.yml), that 
+   builds a Docker container around `matchbox-server` and publishes it to the Google Artifact registry.
+2. The [Maven workflow](https://github.com/ahdis/matchbox/blob/main/.github/workflows/central_repository.yml), that 
+   builds the `matchbox-engine` JAR and publishes it to the Maven Central Repository. The version used is the one 
+   specified in the POM.
+
+If a pull request is merged to create the release, and that it modifies files in the `matchbox-frontend` module, the 
+tag should not be created before the [Angular workflow](https://github.com/ahdis/matchbox/blob/main/.github/workflows/angular_build.yml)
+has completed. Otherwise, the Docker container will not contain the updated GUI.

docs/changelog.md

@@ -1,3 +1,10 @@
+2023/04/05 Release 3.2.1
+
+- docker pull \
+   europe-west6-docker.pkg.dev/ahdis-ch/ahdis/matchbox:v3.2.1
+- reenable proxy support for downloading packages
+- update to core 5.6.116
+
 2023/03/06 Release 3.2.0
 
 - updated CDA core logical model 2.0 and added tests

docs/docker.md

@@ -3,7 +3,7 @@
 if you have the rights you can download Matchbox as a docker container:
 
 ```
-docker pull europe-west6-docker.pkg.dev/ahdis-ch/ahdis/matchbox:v3.2.0-SNAPSHOT
+docker pull europe-west6-docker.pkg.dev/ahdis-ch/ahdis/matchbox:v3.2.1
 ```
 
 ## Configurable base image:

matchbox-engine/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>matchbox</artifactId>
         <groupId>health.matchbox</groupId>
-        <version>3.2.0</version>
+        <version>3.2.1</version>
     </parent>
 
     <artifactId>matchbox-engine</artifactId>

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

@@ -425,14 +425,11 @@ public org.hl7.fhir.r4.model.StructureDefinition getStructureDefinition(String p
 	public org.hl7.fhir.r4.model.Resource getCanonicalResource(String canonical) {
 		org.hl7.fhir.r5.model.Resource fetched = this.getContext().fetchResource(null, canonical);
 		// allResourcesById is not package aware (???) so we need to fetch it again
-		// if (fetched!=null) {
-		// 	org.hl7.fhir.r5.model.Resource fetched2  = this.getContext().fetchResource(fetched.getClass(), canonical);
-		// 	if (fetched2 != null) {
-		// 		return VersionConvertorFactory_40_50.convertResource(fetched2);
-		// 	}
-		// }
-		if (fetched !=null) {
-			return VersionConvertorFactory_40_50.convertResource(fetched);
+		if (fetched!=null) {
+		 	org.hl7.fhir.r5.model.Resource fetched2  = this.getContext().fetchResource(fetched.getClass(), canonical);
+		 	if (fetched2 != null) {
+		 		return VersionConvertorFactory_40_50.convertResource(fetched2);
+		 	}
 		}
 		return null;
 	}

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

@@ -63,7 +63,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r5.model.CanonicalType;
 import org.hl7.fhir.r5.model.CapabilityStatement;
 import org.hl7.fhir.r5.model.CodeSystem;
-import org.hl7.fhir.r5.model.CodeSystem.CodeSystemContentMode;
+import org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode;
 import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
 import org.hl7.fhir.r5.model.CodeableConcept;
 import org.hl7.fhir.r5.model.Coding;
@@ -793,7 +793,10 @@ public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean h
     if (pIn == null) {
       throw new Error(formatMessage(I18nConstants.NO_PARAMETERS_PROVIDED_TO_EXPANDVS));
     }
-
+    if (vs.getUrl().equals("http://hl7.org/fhir/ValueSet/all-time-units") || vs.getUrl().equals("http://hl7.org/fhir/ValueSet/all-distance-units")) {
+      return new ValueSetExpansionOutcome("This value set is not expanded correctly at this time (will be fixed in a future version)", TerminologyServiceErrorClass.VALUESET_UNSUPPORTED);
+    }
+
     Parameters p = pIn.copy();
 
     if (vs.hasExpansion()) {
@@ -827,21 +830,26 @@ public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean h
 
     // ok, first we try to expand locally
     ValueSetExpanderSimple vse = constructValueSetExpanderSimple();
+    res = null;
     try {
       res = vse.expand(vs, p);
-      allErrors.addAll(vse.getAllErrors());
-      if (res.getValueset() != null) {
-        if (!res.getValueset().hasUrl()) {
-          throw new Error(formatMessage(I18nConstants.NO_URL_IN_EXPAND_VALUE_SET));
-        }
-        txCache.cacheExpansion(cacheToken, res, TerminologyCache.TRANSIENT);
-        return res;
-      }
     } catch (Exception e) {
       allErrors.addAll(vse.getAllErrors());
       e.printStackTrace();
+      res = new ValueSetExpansionOutcome(e.getMessage(), TerminologyServiceErrorClass.UNKNOWN);
     }
-
+    allErrors.addAll(vse.getAllErrors());
+    if (res.getValueset() != null) {
+      if (!res.getValueset().hasUrl()) {
+        throw new Error(formatMessage(I18nConstants.NO_URL_IN_EXPAND_VALUE_SET));
+      }
+      txCache.cacheExpansion(cacheToken, res, TerminologyCache.TRANSIENT);
+      return res;
+    }
+    if (res.getErrorClass() == TerminologyServiceErrorClass.INTERNAL_ERROR) { // this class is created specifically to say: don't consult the server
+      return new ValueSetExpansionOutcome(res.getError(), res.getErrorClass());
+    }
+
     // if that failed, we try to expand on the server
     if (addDependentResources(p, vs)) {
       p.addParameter().setName("cache-id").setValue(new StringType(cacheId));              
@@ -1208,7 +1216,7 @@ protected ValidationResult validateOnServer(ValueSet vs, Parameters pin, Validat
       if (isTxCaching && cacheId != null && vs.getUrl() != null && cached.contains(vs.getUrl()+"|"+vs.getVersion())) {
         pin.addParameter().setName("url").setValue(new UriType(vs.getUrl()+(vs.hasVersion() ? "|"+vs.getVersion() : "")));        
       } else if (options.getVsAsUrl()){
-        pin.addParameter().setName("url").setValue(new StringType(vs.getUrl()));
+        pin.addParameter().setName("url").setValue(new UriType(vs.getUrl()));
       } else {
         pin.addParameter().setName("valueSet").setResource(vs);
         if (vs.getUrl() != null) {
@@ -1367,7 +1375,7 @@ public void setExpansionProfile(Parameters expParameters) {
 
   @Override
   public boolean isNoTerminologyServer() {
-    return noTerminologyServer;
+    return noTerminologyServer || txClient == null;
   }
 
   public void setNoTerminologyServer(boolean noTerminologyServer) {
@@ -2152,6 +2160,14 @@ public StructureDefinition fetchTypeDefinition(String typeName) {
     }
   }
 
+  @Override
+  public List<StructureDefinition> fetchTypeDefinitions(String typeName) {
+    List<StructureDefinition> res = new ArrayList<>();
+    structures.listAll(res);
+    res.removeIf(sd -> !sd.getType().equals(typeName));
+    return res;
+  }
+
   public boolean isTlogging() {
     return tlogging;
   }
@@ -2174,63 +2190,63 @@ public String getLinkForUrl(String corePath, String url) {
     }
 
     if (codeSystems.has(url)) {
-      return codeSystems.get(url).getUserString("path");
+      return codeSystems.get(url).getWebPath();
     }
 
     if (valueSets.has(url)) {
-      return valueSets.get(url).getUserString("path");
+      return valueSets.get(url).getWebPath();
     }
 
     if (maps.has(url)) {
-      return maps.get(url).getUserString("path");
+      return maps.get(url).getWebPath();
     }
 
     if (transforms.has(url)) {
-      return transforms.get(url).getUserString("path");
+      return transforms.get(url).getWebPath();
     }
 
     if (actors.has(url)) {
-      return actors.get(url).getUserString("path");
+      return actors.get(url).getWebPath();
     }
 
     if (requirements.has(url)) {
-      return requirements.get(url).getUserString("path");
+      return requirements.get(url).getWebPath();
     }
 
     if (structures.has(url)) {
-      return structures.get(url).getUserString("path");
+      return structures.get(url).getWebPath();
     }
 
     if (guides.has(url)) {
-      return guides.get(url).getUserString("path");
+      return guides.get(url).getWebPath();
     }
 
     if (capstmts.has(url)) {
-      return capstmts.get(url).getUserString("path");
+      return capstmts.get(url).getWebPath();
     }
 
     if (measures.has(url)) {
-      return measures.get(url).getUserString("path");
+      return measures.get(url).getWebPath();
     }
 
     if (libraries.has(url)) {
-      return libraries.get(url).getUserString("path");
+      return libraries.get(url).getWebPath();
     }
 
     if (searchParameters.has(url)) {
-      return searchParameters.get(url).getUserString("path");
+      return searchParameters.get(url).getWebPath();
     }
 
     if (questionnaires.has(url)) {
-      return questionnaires.get(url).getUserString("path");
+      return questionnaires.get(url).getWebPath();
     }
 
     if (operations.has(url)) {
-      return operations.get(url).getUserString("path");
+      return operations.get(url).getWebPath();
     }
 
     if (plans.has(url)) {
-      return plans.get(url).getUserString("path");
+      return plans.get(url).getWebPath();
     }
 
     if (url.equals("http://loinc.org")) {
@@ -2401,4 +2417,4 @@ public PEBuilder getProfiledElementBuilder(PEElementPropertiesPolicy elementProp
     // TODO Auto-generated method stub
     return new PEBuilder(this, elementProps, fixedProps);
   }
-}
+}

matchbox-engine/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java

@@ -36,6 +36,7 @@
 import org.hl7.fhir.utilities.json.model.JsonElement;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
+import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.IPackageProvider;
 import org.hl7.fhir.utilities.npm.NpmPackage.NpmPackageFolder;
 import org.hl7.fhir.utilities.npm.PackageList.PackageListEntry;
 import org.slf4j.Logger;
@@ -87,6 +88,14 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 public class FilesystemPackageCacheManager extends BasePackageCacheManager implements IPackageCacheManager {
 
 
+  // When running in testing mode, some packages are provided from the test case repository rather than by the normal means
+  // the PackageProvider is responsible for this. if no package provider is defined, or it declines to handle the package, 
+  // then the normal means will be used
+  public interface IPackageProvider {
+    boolean handlesPackage(String id, String version);
+    InputStreamWithSrc provide(String id, String version) throws IOException;
+  }
+  private static IPackageProvider packageProvider;
 
   //  private static final String SECONDARY_SERVER = "http://local.fhir.org:8080/packages";
   public static final String PACKAGE_REGEX = "^[a-zA-Z][A-Za-z0-9\\_\\-]*(\\.[A-Za-z0-9\\_\\-]+)+$";
@@ -404,8 +413,9 @@ public NpmPackage addPackageToCache(String id, String version, InputStream packa
         throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + npm.name());
       }
     }
-    if (version == null)
+    if (version == null) {
       version = npm.version();
+    }
 
     String v = version;
     return new CacheLock(id + "#" + version).doWithLock(() -> {
@@ -555,7 +565,9 @@ public NpmPackage loadPackage(String id, String version) throws FHIRException, I
 
     // nup, don't have it locally (or it's expired)
     FilesystemPackageCacheManager.InputStreamWithSrc source;
-    if ("current".equals(version) || (version!= null && version.startsWith("current$"))) {
+    if (packageProvider != null && packageProvider.handlesPackage(id, version)) {
+      source = packageProvider.provide(id, version);
+    } else if ("current".equals(version) || (version!= null && version.startsWith("current$"))) {
       // special case - fetch from ci-build server
       source = loadFromCIBuild(id, version.startsWith("current$") ? version.substring(8) : null);
     } else {
@@ -1005,5 +1017,13 @@ public void setSuppressErrors(boolean suppressErrors) {
     this.suppressErrors = suppressErrors;
   }
 
+  public static IPackageProvider getPackageProvider() {
+    return packageProvider;
+  }
+
+  public static void setPackageProvider(IPackageProvider packageProvider) {
+    FilesystemPackageCacheManager.packageProvider = packageProvider;
+  }
+
 
 }

matchbox-frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matchboxv3",
-  "version": "3.2.0",
+  "version": "3.2.1",
   "license": "MIT",
   "scripts": {
     "ng": "ng",

matchbox-server/ig.http

@@ -1,7 +1,8 @@
 ###@host = http://localhost:8080/matchbox/fhir
 # @host = https://test.ahdis.ch/matchbox/fhir
 
-@host = http://ehealthsuisse.ihe-europe.net:8622/matchbox/fhir
+### @host = http://ehealthsuisse.ihe-europe.net:8622/matchbox/fhir
+@host = http://gazelle.ihe.net/matchbox/fhir
 
 ###
 GET {{host}}/metadata HTTP/1.1