Handle secondary terminology server errors properly

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/client/FHIRToolingClient.java

@@ -439,7 +439,7 @@ public Bundle fetchFeed(String url) {
     try {
       feed = utils.issueGetFeedRequest(new URI(url), getPreferredResourceFormat());
     } catch (Exception e) {
-      handleException("An error has occurred while trying to retrieve history since last update", e);
+      handleException("An error has occurred while trying to read a bundle", e);
     }
     return feed;
   }

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/client/FHIRToolingClient.java

@@ -714,7 +714,7 @@ public Bundle fetchFeed(String url) {
     try {
       feed = utils.issueGetFeedRequest(new URI(url), getPreferredResourceFormat());
     } catch (Exception e) {
-      handleException("An error has occurred while trying to retrieve history since last update", e);
+      handleException("An error has occurred while trying to read a bundle", e);
     }
     return feed;
   }

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/client/FHIRToolingClient.java

@@ -413,7 +413,7 @@ public Bundle fetchFeed(String url) {
     try {
       feed = client.issueGetFeedRequest(new URI(url), getPreferredResourceFormat());
     } catch (Exception e) {
-      handleException("An error has occurred while trying to retrieve history since last update", e);
+      handleException("An error has occurred while trying to read a bundle", e);
     }
     return feed;
   }

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/FHIRToolingClient.java

@@ -383,7 +383,7 @@ public Bundle fetchFeed(String url) {
     try {
       feed = client.issueGetFeedRequest(new URI(url), withVer(getPreferredResourceFormat(), "4.0"), timeoutLong);
     } catch (Exception e) {
-      handleException(0, "An error has occurred while trying to retrieve history since last update", e);
+      handleException(0, "An error has occurred while trying to read a bundle", e);
     }
     return feed;
   }

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/network/FhirRequestBuilder.java

@@ -20,6 +20,7 @@
 import org.hl7.fhir.r4.utils.client.ResourceFormat;
 import org.hl7.fhir.utilities.MimeType;
 import org.hl7.fhir.utilities.ToolingClientLogger;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.http.*;
 import org.hl7.fhir.utilities.xhtml.XhtmlUtils;
 
@@ -179,7 +180,11 @@ protected <T extends Resource> T unmarshalReference(HTTPResult response, String
     boolean ok = code >= 200 && code < 300;
     if (response.getContent() == null) {
       if (!ok) {
-        throw new EFhirClientException(response.getMessage());
+        if (Utilities.noString(response.getMessage())) {
+          throw new EFhirClientException(response.getMessagefromCode());
+        } else {
+          throw new EFhirClientException(response.getMessage());
+        }
       } else {
         return null;
       }

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/client/FHIRToolingClient.java

@@ -399,7 +399,7 @@ public Bundle fetchFeed(String url) {
     try {
       feed = client.issueGetFeedRequest(new URI(url), getPreferredResourceFormat());
     } catch (Exception e) {
-      handleException("An error has occurred while trying to retrieve history since last update", e);
+      handleException("An error has occurred while trying to read a bundle", e);
     }
     return feed;
   }

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/client/network/FhirRequestBuilder.java

@@ -18,6 +18,7 @@
 import org.hl7.fhir.r4b.utils.client.EFhirClientException;
 import org.hl7.fhir.r4b.utils.client.ResourceFormat;
 import org.hl7.fhir.utilities.ToolingClientLogger;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.http.*;
 import org.hl7.fhir.utilities.xhtml.XhtmlUtils;
 
@@ -174,7 +175,11 @@ protected <T extends Resource> T unmarshalReference(HTTPResult response, String
     boolean ok = code >= 200 && code < 300;
     if (response.getContent() == null) {
       if (!ok) {
-        throw new EFhirClientException(response.getMessage());
+        if (Utilities.noString(response.getMessage())) {
+          throw new EFhirClientException(response.getMessagefromCode());
+        } else {
+          throw new EFhirClientException(response.getMessage());
+        }
       } else {
         return null;
       }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java

@@ -794,6 +794,19 @@ public void generateSnapshot(StructureDefinition base, StructureDefinition deriv
           }
         }
 
+        for (int i = 0; i < derived.getSnapshot().getElement().size(); i++) {
+          ElementDefinition ed = derived.getSnapshot().getElement().get(i);
+          if (ed.getType().size() > 1) {
+            List<TypeRefComponent> toRemove = new ArrayList<ElementDefinition.TypeRefComponent>();
+            for (TypeRefComponent tr : ed.getType()) {
+              ElementDefinition typeSlice = findTypeSlice(derived.getSnapshot().getElement(), i, ed.getPath(), tr.getWorkingCode());
+              if (typeSlice != null && typeSlice.prohibited()) {
+                toRemove.add(tr);
+              }
+            }
+            ed.getType().removeAll(toRemove);
+          }
+        }
         if (derived.getKind() != StructureDefinitionKind.LOGICAL && !derived.getSnapshot().getElementFirstRep().getType().isEmpty())
           throw new Error(context.formatMessage(I18nConstants.TYPE_ON_FIRST_SNAPSHOT_ELEMENT_FOR__IN__FROM_, derived.getSnapshot().getElementFirstRep().getPath(), derived.getUrl(), base.getUrl()));
         mappingDetails.update();
@@ -992,6 +1005,34 @@ public void generateSnapshot(StructureDefinition base, StructureDefinition deriv
   }
 
 
+  private ElementDefinition findTypeSlice(List<ElementDefinition> list, int i, String path, String typeCode) {
+    for (int j = i+1; j < list.size(); j++) {
+      ElementDefinition ed = list.get(j);
+      if (pathMatches(path, ed) && typeMatches(ed, typeCode)) {
+        return ed;
+      }
+    }
+    return null;
+  }
+
+  private boolean pathMatches(String path, ElementDefinition ed) {
+    String p = ed.getPath();
+    if (path.equals(p)) {
+      return true;
+    }
+    if (path.endsWith("[x]")) { // it should
+      path = path.substring(0, path.length()-3);
+      if (p.startsWith(path) && p.length() > path.length() && !p.substring(path.length()).contains(".")) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  private boolean typeMatches(ElementDefinition ed, String typeCode) {
+    return ed.getType().size() == 1 && typeCode.equals(ed.getTypeFirstRep().getWorkingCode());
+  }
+
   private void checkTypeParameters(StructureDefinition base, StructureDefinition derived) {
     String bt = ToolingExtensions.readStringExtension(base, ToolingExtensions.EXT_TYPE_PARAMETER);
     if (!derived.hasExtension(ToolingExtensions.EXT_TYPE_PARAMETER)) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java

@@ -237,7 +237,6 @@ public int compare(T arg1, T arg2) {
   private Object lock = new Object(); // used as a lock for the data that follows
   protected String version; // although the internal resources are all R5, the version of FHIR they describe may not be 
 
-  protected final TerminologyClientManager terminologyClientManager = new TerminologyClientManager(new TerminologyClientR5.TerminologyClientR5Factory(), UUID.randomUUID().toString());
   private boolean minimalMemory = false;
 
   private Map<String, Map<String, ResourceProxy>> allResourcesById = new HashMap<String, Map<String, ResourceProxy>>();
@@ -279,6 +278,7 @@ public int compare(T arg1, T arg2) {
   protected boolean noTerminologyServer;
   private int expandCodesLimit = 1000;
   protected org.hl7.fhir.r5.context.ILoggingService logger = new SystemOutLoggingService();
+  protected final TerminologyClientManager terminologyClientManager = new TerminologyClientManager(new TerminologyClientR5.TerminologyClientR5Factory(), UUID.randomUUID().toString(), logger);
   protected Parameters expParameters;
   private Map<String, PackageInformation> packages = new HashMap<>();
 
@@ -2031,6 +2031,7 @@ public void setCanRunWithoutTerminology(boolean canRunWithoutTerminology) {
 
   public void setLogger(@Nonnull org.hl7.fhir.r5.context.ILoggingService logger) {
     this.logger = logger;
+    getTxClientManager().setLogger(logger);
   }
 
   public Parameters getExpansionParameters() {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientManager.java

@@ -15,6 +15,7 @@
 
 import org.hl7.fhir.exceptions.TerminologyServiceException;
 import org.hl7.fhir.r5.context.CanonicalResourceManager;
+import org.hl7.fhir.r5.context.ILoggingService;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r5.model.CodeSystem;
@@ -27,6 +28,7 @@
 import org.hl7.fhir.r5.terminologies.ValueSetUtilities;
 import org.hl7.fhir.r5.terminologies.client.TerminologyClientContext.TerminologyClientContextUseType;
 import org.hl7.fhir.r5.terminologies.client.TerminologyClientManager.ServerOptionList;
+import org.hl7.fhir.r5.terminologies.client.TerminologyClientR5.TerminologyClientR5Factory;
 import org.hl7.fhir.r5.terminologies.utilities.TerminologyCache;
 import org.hl7.fhir.r5.terminologies.utilities.TerminologyCache.SourcedCodeSystem;
 import org.hl7.fhir.r5.terminologies.utilities.TerminologyCache.SourcedValueSet;
@@ -86,11 +88,14 @@ public interface ITerminologyClientFactory {
   }
 
   public class InternalLogEvent {
+    private boolean error;
     private String message;
     private String server;
     private String vs;
     private String systems;
     private String choices;
+    private String context;
+    private String request;
     protected InternalLogEvent(String message, String server, String vs, String systems, String choices) {
       super();
       this.message = message;
@@ -99,9 +104,12 @@ protected InternalLogEvent(String message, String server, String vs, String syst
       this.systems = systems;
       this.choices = choices;
     }
-    protected InternalLogEvent(String message) {
+    protected InternalLogEvent(String message, String ctxt, String request) {
       super();
+      error = true;
       this.message = message;
+      this.context = ctxt;
+      this.request = request;
     }
     public String getMessage() {
       return message;
@@ -118,7 +126,15 @@ public String getChoices() {
     public String getServer() {
       return server;
     }
-
+    public boolean isError() {
+      return error;
+    }
+    public String getContext() {
+      return context;
+    }
+    public String getRequest() {
+      return request;
+    }
   }
 
   public static final String UNRESOLVED_VALUESET = "--unknown--";
@@ -142,10 +158,13 @@ public String getServer() {
 
   private boolean useEcosystem;
 
-  public TerminologyClientManager(ITerminologyClientFactory factory, String cacheId) {
+  private ILoggingService logger;
+
+  public TerminologyClientManager(ITerminologyClientFactory factory, String cacheId, ILoggingService logger) {
     super();
     this.factory = factory;
     this.cacheId = cacheId;
+    this.logger = logger;
   }
 
   public String getCacheId() {
@@ -346,11 +365,11 @@ private ServerOptionList decideWhichServer(String url) {
       }
       return ret;
     } catch (Exception e) {
-      String msg = "Error resolving system "+url+": "+e.getMessage()+" ("+request+")";
+      String msg = "Error resolving system "+url+": "+e.getMessage();
       if (!hasMessage(msg)) {
-        internalLog.add(new InternalLogEvent(msg));
+        internalLog.add(new InternalLogEvent(msg, url, request));
       }
-      if (!monitorServiceURL.contains("tx.fhir.org")) {
+      if (logger.isDebugLogging()) {
         e.printStackTrace();
       }
     }
@@ -571,12 +590,13 @@ public SourcedValueSet findValueSetOnServer(String canonical) {
       ValueSet vs = (ValueSet) client.getClient().read("ValueSet", rid);
       return new SourcedValueSet(server, vs);
     } catch (Exception e) {
-      e.printStackTrace();
-      String msg = "Error resolving valueSet "+canonical+": "+e.getMessage()+" ("+request+")";
+      String msg = "Error resolving valueSet "+canonical+": "+e.getMessage();
       if (!hasMessage(msg)) {
-        internalLog.add(new InternalLogEvent(msg));
+        internalLog.add(new InternalLogEvent(msg, canonical, request));
+      }
+      if (logger.isDebugLogging()) {
+        e.printStackTrace();
       }
-      e.printStackTrace();
       return null;
     }
   }
@@ -651,12 +671,13 @@ public SourcedCodeSystem findCodeSystemOnServer(String canonical) {
       CodeSystem vs = (CodeSystem) client.getClient().read("CodeSystem", rid);
       return new SourcedCodeSystem(server, vs);
     } catch (Exception e) {
-      e.printStackTrace();
-      String msg = "Error resolving valueSet "+canonical+": "+e.getMessage()+" ("+request+")";
+      String msg = "Error resolving CodeSystem "+canonical+": "+e.getMessage();
       if (!hasMessage(msg)) {
-        internalLog.add(new InternalLogEvent(msg));
+        internalLog.add(new InternalLogEvent(msg, canonical, request));
+      }
+      if (logger.isDebugLogging()) {
+        e.printStackTrace();
       }
-      e.printStackTrace();
       return null;
     }
   }
@@ -673,4 +694,14 @@ public boolean supportsSystem(String system) throws IOException {
   public List<InternalLogEvent> getInternalLog() {
     return internalLog;
   }
+
+  public ILoggingService getLogger() {
+    return logger;
+  }
+
+  public void setLogger(ILoggingService logger) {
+    this.logger = logger;
+  }
+
+
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/CompareUtilities.java

@@ -112,6 +112,7 @@ private String presentExpected(String expected) {
         case "$url$": return "\"A URL\"";
         case "$token$": return "\"A Token\"";
         case "$version$": return variables.containsKey("version") ? variables.get("version") : "(anything)";
+        case "$semver$": return "A semver"; 
         default: return "Unhandled template: "+expected;
         }
       }
@@ -558,6 +559,7 @@ private boolean matches(String actualJsonString, String expectedJsonString) {
         case "$id$": return actualJsonString.matches("[A-Za-z0-9\\-\\.]{1,64}");
         case "$url$": return actualJsonString.matches("(https?://|www\\.)[-a-zA-Z0-9+&@#/%?=~_|!:.;]*[-a-zA-Z0-9+&@#/%=~_|]");
         case "$token$": return actualJsonString.matches("[0-9a-zA-Z_][0-9a-zA-Z_\\.\\-]*");
+        case "$semver$": return actualJsonString.matches("^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$");
         case "$version$": return matchesVariable(actualJsonString, "version");
         default: 
           throw new Error("Unhandled template: "+expectedJsonString);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/FHIRToolingClient.java

@@ -441,7 +441,7 @@ public Bundle fetchFeed(String url) {
     try {
       feed = client.issueGetFeedRequest(new URI(url), getPreferredResourceFormat());
     } catch (Exception e) {
-      handleException(0, "An error has occurred while trying to retrieve history since last update", e);
+      handleException(0, "An error has occurred while trying to read a bundle", e);
     }
     return feed;
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/network/FhirRequestBuilder.java

@@ -19,6 +19,7 @@
 import org.hl7.fhir.r5.utils.client.ResourceFormat;
 import org.hl7.fhir.utilities.MimeType;
 import org.hl7.fhir.utilities.ToolingClientLogger;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.http.*;
 import org.hl7.fhir.utilities.xhtml.XhtmlUtils;
 
@@ -162,7 +163,11 @@ protected <T extends Resource> T unmarshalReference(HTTPResult response, String
     boolean ok = code >= 200 && code < 300;
     if (response.getContent() == null) {
       if (!ok) {
-        throw new EFhirClientException(code, response.getMessage());
+        if (Utilities.noString(response.getMessage())) {
+          throw new EFhirClientException(code, response.getMessagefromCode());
+        } else {
+          throw new EFhirClientException(code, response.getMessage());
+        }
       } else {
         return null;
       }