fix for 1.4.0 problems

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/ToolingExtensions.java

@@ -234,6 +234,14 @@ public class ToolingExtensions {
     }
   }
 
+  public static void addUriExtension(Element e, String url, String uri) {
+    Extension ex = getExtension(e, url);
+    if (ex != null)
+      ex.setValue(new UriType(uri));
+    else
+      e.getExtension().add(Factory.newExtension(url, new UriType(uri), true));   
+  }
+
   public static void addBooleanExtension(Element e, String url, boolean content) {
     Extension ex = getExtension(e, url);
     if (ex != null)

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

@@ -2459,7 +2459,7 @@ public class ProfileUtilities extends TranslatingUtilities {
 
       if (derived.hasIsSummaryElement()) {
         if (!Base.compareDeep(derived.getIsSummaryElement(), base.getIsSummaryElement(), false)) {
-          if (base.hasIsSummary())
+          if (base.hasIsSummary() && !context.getVersion().equals("1.4.0")) // work around a known issue with some 1.4.0 cosntraints
             throw new Error(context.formatMessage(I18nConstants.ERROR_IN_PROFILE__AT__BASE_ISSUMMARY___DERIVED_ISSUMMARY__, pn, derived.getPath(), base.getIsSummaryElement().asStringValue(), derived.getIsSummaryElement().asStringValue()));
           base.setIsSummaryElement(derived.getIsSummaryElement().copy());
         } else if (trimDifferential)

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

@@ -21,6 +21,7 @@ package org.hl7.fhir.r5.context;
  */
 
 import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -41,6 +42,8 @@ import org.hl7.fhir.exceptions.TerminologyServiceException;
 import org.hl7.fhir.r5.conformance.ProfileUtilities;
 import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory;
 import org.hl7.fhir.r5.context.TerminologyCache.CacheToken;
+import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.BooleanType;
 import org.hl7.fhir.r5.model.CapabilityStatement;
 import org.hl7.fhir.r5.model.CodeSystem;
@@ -50,6 +53,7 @@ import org.hl7.fhir.r5.model.CodeableConcept;
 import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.ConceptMap;
 import org.hl7.fhir.r5.model.Constants;
+import org.hl7.fhir.r5.model.ElementDefinition;
 import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
 import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
 import org.hl7.fhir.r5.model.ImplementationGuide;
@@ -67,6 +71,7 @@ import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.SearchParameter;
 import org.hl7.fhir.r5.model.StringType;
 import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.r5.model.StructureMap;
 import org.hl7.fhir.r5.model.TerminologyCapabilities;
 import org.hl7.fhir.r5.model.TerminologyCapabilities.TerminologyCapabilitiesCodeSystemComponent;
@@ -126,6 +131,8 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   }
 
   private Object lock = new Object(); // used as a lock for the data that follows
+  protected String version;
+
   
   private Map<String, Map<String, Resource>> allResourcesById = new HashMap<String, Map<String, Resource>>();
   // all maps are to the full URI
@@ -236,9 +243,13 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
           }
           throw new DefinitionException(formatMessage(I18nConstants.DUPLICATE_RESOURCE_, url));
         }
-        if (r instanceof StructureDefinition)
+        if (r instanceof StructureDefinition) {
-          structures.see((StructureDefinition) m);
+          StructureDefinition sd = (StructureDefinition) m;
-        else if (r instanceof ValueSet)
+          if ("1.4.0".equals(version)) {
+            fixOldSD(sd);
+          }
+          structures.see(sd);
+        } else if (r instanceof ValueSet)
           valueSets.see((ValueSet) m);
         else if (r instanceof CodeSystem)
           codeSystems.see((CodeSystem) m);
@@ -264,6 +275,21 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     }
   }
 
+  public void fixOldSD(StructureDefinition sd) {
+    if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT && sd.getType().equals("Extension") && sd.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
+      sd.setSnapshot(null);
+    }
+    for (ElementDefinition ed : sd.getDifferential().getElement()) {
+      if (ed.getPath().equals("Extension.url") || ed.getPath().endsWith(".extension.url") ) {
+        ed.setMin(1);
+        ed.getBase().setMin(1);
+      }
+      if ("extension".equals(ed.getSliceName())) {
+        ed.setSliceName(null);
+      }
+    }
+  }
+
   /*
    *  Compare business versions, returning "true" if the candidate newer version is in fact newer than the oldVersion
    *  Comparison will work for strictly numeric versions as well as multi-level versions separated by ., -, _, : or space
@@ -1277,4 +1303,29 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   public Map<String, byte[]> getBinaries() {
     return binaries;
   }
+  
+  public void finishLoading() {
+    for (StructureDefinition sd : listStructures()) {
+      try {
+        if (sd.getSnapshot().isEmpty()) { 
+          generateSnapshot(sd);
+//          new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "snapshot", tail(sd.getUrl())+".xml")), sd);
+        }
+      } catch (Exception e) {
+//        System.out.println("Unable to generate snapshot for "+tail(sd.getUrl()) +" from "+tail(sd.getBaseDefinition())+" because "+e.getMessage());
+      }
+
+    }  
+  }
+
+
+  protected String tail(String url) {
+  if (Utilities.noString(url)) {
+    return "noname";
+  }
+  if (url.contains("/")) {
+    return url.substring(url.lastIndexOf("/")+1);
+  }
+  return url;
+}
 }

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

@@ -101,7 +101,6 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
   }
 
 	private Questionnaire questionnaire;
-  private String version;
   private String revision;
   private String date;
   private IValidatorFactory validatorFactory;
@@ -179,6 +178,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     res.setAllowLoadingDuplicates(true);
     res.version = pi.getNpm().get("version").getAsString();
     res.loadFromPackage(pi, loader, filter);
+    res.finishLoading();
     return res;
   }
 
@@ -540,15 +540,6 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     return result;
   }
 
-  private String tail(String url) {
-    if (Utilities.noString(url)) {
-      return "noname";
-    }
-    if (url.contains("/")) {
-      return url.substring(url.lastIndexOf("/")+1);
-    }
-    return url;
-  }
 
   public void loadBinariesFromFolder(String folder) throws FileNotFoundException, Exception {
     for (String n : new File(folder).list()) {