Fix loading canonical resources so that duplicates with different versions is OK

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

@@ -111,6 +111,7 @@ import org.hl7.fhir.r5.terminologies.ValueSetCheckerSimple;
 import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
 import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
 import org.hl7.fhir.r5.terminologies.ValueSetExpanderSimple;
+import org.hl7.fhir.r5.utils.PackageHackerR5;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
 import org.hl7.fhir.utilities.OIDUtils;
@@ -121,6 +122,7 @@ import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.i18n.I18nBase;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
+import org.hl7.fhir.utilities.npm.PackageHacker;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
 import org.hl7.fhir.utilities.validation.ValidationOptions;
@@ -312,6 +314,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   
 
   public void registerResourceFromPackage(CanonicalResourceProxy r, PackageVersion packageInfo) throws FHIRException {
+    PackageHackerR5.fixLoadedResource(r, packageInfo);
     
     synchronized (lock) {
       if (r.getId() != null) {
@@ -326,13 +329,14 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
       }
 
       String url = r.getUrl();
-      if (!allowLoadingDuplicates && hasResource(r.getType(), url)) {
+      if (!allowLoadingDuplicates && hasResourceVersion(r.getType(), url, r.getVersion()) && !packageInfo.isHTO()) {
         // spcial workaround for known problems with existing packages
         if (Utilities.existsInList(url, "http://hl7.org/fhir/SearchParameter/example")) {
           return;
         }
-        throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, 
+        CanonicalResource ex = fetchResourceWithException(r.getType(), url);
-            fetchResourceWithException(r.getType(), url).fhirType()));
+        throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, r.getVersion(), ex.getVersion(),
+            ex.fhirType()));
       }
       switch(r.getType()) {
       case "StructureDefinition":
@@ -413,8 +417,9 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
           if (Utilities.existsInList(url, "http://hl7.org/fhir/SearchParameter/example")) {
             return;
           }
-          throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, 
+          CanonicalResource ex = (CanonicalResource) fetchResourceWithException(r.getClass(), url);
-              fetchResourceWithException(r.getClass(), url).fhirType()));
+          throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url, ((CanonicalResource) r).getVersion(), ex.getVersion(),
+              ex.fhirType()));
         }
         if (r instanceof StructureDefinition) {
           StructureDefinition sd = (StructureDefinition) m;
@@ -1364,15 +1369,15 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   }
   
   public <T extends Resource> T fetchResourceWithException(String cls, String uri) throws FHIRException {
-    return fetchResourceWithException(cls, uri, null);
+    return fetchResourceWithExceptionByVersion(cls, uri, null, null);
   }
   
   public <T extends Resource> T fetchResourceWithException(Class<T> class_, String uri, CanonicalResource source) throws FHIRException {
-    return fetchResourceWithException(class_, uri, null, source);
+    return fetchResourceWithExceptionByVersion(class_, uri, null, source);
   }
   
   @SuppressWarnings("unchecked")
-  public <T extends Resource> T fetchResourceWithException(Class<T> class_, String uri, String version, CanonicalResource source) throws FHIRException {
+  public <T extends Resource> T fetchResourceWithExceptionByVersion(Class<T> class_, String uri, String version, CanonicalResource source) throws FHIRException {
     if (uri == null) {
       return null;
     }
@@ -1382,9 +1387,13 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     }
     synchronized (lock) {
 
-      if (uri.contains("|")) {
+      if (version == null) {
-        version = uri.substring(uri.lastIndexOf("|")+1);
+        if (uri.contains("|")) {
-        uri = uri.substring(0, uri.lastIndexOf("|"));
+          version = uri.substring(uri.lastIndexOf("|")+1);
+          uri = uri.substring(0, uri.lastIndexOf("|"));
+        }
+      } else {
+        assert !uri.contains("|");
       }
       if (uri.contains("#")) {
         uri = uri.substring(0, uri.indexOf("#"));
@@ -1556,7 +1565,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   }
   
   @SuppressWarnings("unchecked")
-  public <T extends Resource> T fetchResourceWithException(String cls, String uri, CanonicalResource source) throws FHIRException {
+  public <T extends Resource> T fetchResourceWithExceptionByVersion(String cls, String uri, String version, CanonicalResource source) throws FHIRException {
     if (uri == null) {
       return null;
     }
@@ -1566,10 +1575,14 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     }
     synchronized (lock) {
 
-      String version = null;
+      if (version == null) {
-      if (uri.contains("|")) {
+        if (uri.contains("|")) {
-        version = uri.substring(uri.lastIndexOf("|")+1);
+          version = uri.substring(uri.lastIndexOf("|")+1);
-        uri = uri.substring(0, uri.lastIndexOf("|"));
+          uri = uri.substring(0, uri.lastIndexOf("|"));
+        }
+      } else {
+        boolean b = !uri.contains("|");
+        assert b;
       }
       if (uri.contains("#")) {
         uri = uri.substring(0, uri.indexOf("#"));
@@ -1728,7 +1741,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   
   public <T extends Resource> T fetchResource(Class<T> class_, String uri, String version) {
     try {
-      return fetchResourceWithException(class_, uri, version, null);
+      return fetchResourceWithExceptionByVersion(class_, uri, version, null);
     } catch (FHIRException e) {
       throw new Error(e);
     }
@@ -1751,6 +1764,22 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     }
   }
 
+  public <T extends Resource> boolean hasResourceVersion(Class<T> class_, String uri, String version) {
+    try {
+      return fetchResourceWithExceptionByVersion(class_, uri, version, null) != null;
+    } catch (Exception e) {
+      return false;
+    }
+  }
+
+  public <T extends Resource> boolean hasResourceVersion(String cls, String uri, String version) {
+    try {
+      return fetchResourceWithExceptionByVersion(cls, uri, version, null) != null;
+    } catch (Exception e) {
+      return false;
+    }
+  }
+
 
   public TranslationServices translator() {
     return translator;

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

@@ -87,6 +87,13 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
     public String toString() {
       return type+"/"+id+": "+url+"|"+version;
     }
+
+    public void hack(String url, String version) {
+      this.url = url;
+      this.version = version;
+      getResource().setUrl(url).setVersion(version);
+
+    }      
   }
 
   public class CanonicalListSorter implements Comparator<CanonicalResource> {

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

@@ -193,6 +193,10 @@ public interface IWorkerContext {
     public Date getDate() {
       return date;
     }
+    public boolean isHTO() {
+      boolean b = id.startsWith("hl7.terminology.r");
+      return b;
+    }
     
   }