Merge remote-tracking branch 'origin/master' into i18n

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

@@ -587,6 +587,13 @@ public class ProfileUtilities extends TranslatingUtilities {
         else
           messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url, msg, ValidationMessage.IssueSeverity.ERROR));
       }
+      // hack around a problem in R4 definitions (somewhere?)
+      for (ElementDefinition ed : derived.getSnapshot().getElement()) {
+        for (ElementDefinitionMappingComponent mm : ed.getMapping()) {
+          mm.setMap(mm.getMap().trim());
+          
+        }
+      }
       if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
         for (ElementDefinition ed : derived.getSnapshot().getElement()) {
           if (!ed.hasBase()) {
@@ -2492,16 +2499,19 @@ public class ProfileUtilities extends TranslatingUtilities {
             for (ElementDefinitionMappingComponent d : base.getMapping()) {
               found = found || (d.getIdentity().equals(s.getIdentity()) && d.getMap().equals(s.getMap()));
             }
-            if (!found)
+            if (!found) {
               base.getMapping().add(s);
             }
           }
-        else if (trimDifferential)
+        }
+        else if (trimDifferential) {
           derived.getMapping().clear();
-        else
+        } else { 
-          for (ElementDefinitionMappingComponent t : derived.getMapping())
+          for (ElementDefinitionMappingComponent t : derived.getMapping()) {
             t.setUserData(DERIVATION_EQUALS, true);
           }
+        }
+      }
       for (ElementDefinitionMappingComponent m : base.getMapping()) {
         if (m.hasMap()) {
           m.setMap(m.getMap().trim());
@@ -2511,9 +2521,10 @@ public class ProfileUtilities extends TranslatingUtilities {
       // todo: constraints are cumulative. there is no replacing
       for (ElementDefinitionConstraintComponent s : base.getConstraint()) { 
         s.setUserData(IS_DERIVED, true);
-        if (!s.hasSource())
+        if (!s.hasSource()) {
           s.setSource(srcSD.getUrl());
         }
+      }
       if (derived.hasConstraint()) {
         for (ElementDefinitionConstraintComponent s : derived.getConstraint()) {
           if (!base.hasConstraint(s.getKey())) {
@@ -2523,19 +2534,22 @@ public class ProfileUtilities extends TranslatingUtilities {
       	}
       }
       for (IdType id : derived.getCondition()) {
-        if (!base.hasCondition(id))
+        if (!base.hasCondition(id)) {
           base.getCondition().add(id);
         }
+      }
       
       // now, check that we still have a bindable type; if not, delete the binding - see task 8477
-      if (dest.hasBinding() && !hasBindableType(dest))
+      if (dest.hasBinding() && !hasBindableType(dest)) {
         dest.setBinding(null);
+      }
         
       // finally, we copy any extensions from source to dest
       for (Extension ex : derived.getExtension()) {
         StructureDefinition sd  = context.fetchResource(StructureDefinition.class, ex.getUrl());
-        if (sd == null || sd.getSnapshot() == null || sd.getSnapshot().getElementFirstRep().getMax().equals("1"))
+        if (sd == null || sd.getSnapshot() == null || sd.getSnapshot().getElementFirstRep().getMax().equals("1")) {
           ToolingExtensions.removeExtension(dest, ex.getUrl());
+        }
         dest.addExtension(ex.copy());
       }
     }
@@ -2624,18 +2638,21 @@ public class ProfileUtilities extends TranslatingUtilities {
 
   private boolean hasBindableType(ElementDefinition ed) {
     for (TypeRefComponent tr : ed.getType()) {
-      if (Utilities.existsInList(tr.getWorkingCode(), "Coding", "CodeableConcept", "Quantity", "uri", "string", "code"))
+      if (Utilities.existsInList(tr.getWorkingCode(), "Coding", "CodeableConcept", "Quantity", "uri", "string", "code")) {
         return true;
       }
+    }
     return false;
   }
 
 
   private boolean isLargerMax(String derived, String base) {
-    if ("*".equals(base))
+    if ("*".equals(base)) {
       return false;
-    if ("*".equals(derived))
+    }
+    if ("*".equals(derived)) {
       return true;
+    }
     return Integer.parseInt(derived) > Integer.parseInt(base);
   }
 
@@ -2647,22 +2664,26 @@ public class ProfileUtilities extends TranslatingUtilities {
 
   private boolean codesInExpansion(List<ValueSetExpansionContainsComponent> contains, ValueSetExpansionComponent expansion) {
     for (ValueSetExpansionContainsComponent cc : contains) {
-      if (!inExpansion(cc, expansion.getContains()))
+      if (!inExpansion(cc, expansion.getContains())) {
         return false;
-      if (!codesInExpansion(cc.getContains(), expansion))
+      }
+      if (!codesInExpansion(cc.getContains(), expansion)) {
         return false;
       }
+    }
     return true;
   }
 
 
   private boolean inExpansion(ValueSetExpansionContainsComponent cc, List<ValueSetExpansionContainsComponent> contains) {
     for (ValueSetExpansionContainsComponent cc1 : contains) {
-      if (cc.getSystem().equals(cc1.getSystem()) && cc.getCode().equals(cc1.getCode()))
+      if (cc.getSystem().equals(cc1.getSystem()) && cc.getCode().equals(cc1.getCode())) {
         return true;
-      if (inExpansion(cc,  cc1.getContains()))
+      }
+      if (inExpansion(cc,  cc1.getContains())) {
         return true;
       }
+    }
     return false;
   }
 
@@ -2709,33 +2730,38 @@ public class ProfileUtilities extends TranslatingUtilities {
 
   private int findEnd(List<ElementDefinition> list, ElementDefinition ed, int cursor) {
     String path = ed.getPath()+".";
-    while (cursor < list.size() && list.get(cursor).getPath().startsWith(path))
+    while (cursor < list.size() && list.get(cursor).getPath().startsWith(path)) {
       cursor++;
+    }
     return cursor;
   }
 
 
   private ElementDefinition getMatchInDerived(ElementDefinition ed, List<ElementDefinition> list) {
-    for (ElementDefinition t : list)
+    for (ElementDefinition t : list) {
-      if (t.getPath().equals(ed.getPath()))
+      if (t.getPath().equals(ed.getPath())) {
         return t;
+      }
+    }
     return null;
   }
 
   private ElementDefinition getMatchInDerived(ElementDefinition ed, List<ElementDefinition> list, int start, int end) {
     for (int i = start; i < end; i++) {
       ElementDefinition t = list.get(i);
-      if (t.getPath().equals(ed.getPath()))
+      if (t.getPath().equals(ed.getPath())) {
         return t;
       }
+    }
     return null;
   }
 
 
   private boolean isImmediateChild(ElementDefinition ed) {
     String p = ed.getPath();
-    if (!p.contains("."))
+    if (!p.contains(".")) {
       return false;
+    }
     p = p.substring(p.indexOf(".")+1);
     return !p.contains(".");
   }
@@ -3305,8 +3331,10 @@ public class ProfileUtilities extends TranslatingUtilities {
         s = "@"+s;
       String hint = "";
       hint = checkAdd(hint, (element.hasSliceName() ? translate("sd.table", "Slice")+" "+element.getSliceName() : ""));
+     if (hasDef && element.hasDefinition()) {
         hint = checkAdd(hint, (hasDef && element.hasSliceName() ? ": " : ""));
         hint = checkAdd(hint, !hasDef ? null : gt(element.getDefinitionElement()));
+      }
       Cell left = gen.new Cell(null, ref, s, hint, null);
       row.getCells().add(left);
       Cell gc = gen.new Cell();

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java

@@ -3476,10 +3476,10 @@ public class NarrativeGenerator implements INarrativeGenerator {
     return false;
   }
 
-  private void generateCopyright(XhtmlNode x, ValueSet vs) {
+  private void generateCopyright(XhtmlNode x, ValueSet vs) throws FHIRFormatError, DefinitionException, IOException {
     XhtmlNode p = x.para();
     p.b().tx("Copyright Statement:");
-    smartAddText(p, " " + vs.getCopyright());
+    addMarkdown(x, vs.getCopyright());
   }
 
   private XhtmlNode addTableHeaderRowStandard(XhtmlNode t, boolean hasHierarchy, boolean hasDisplay, boolean definitions, boolean comments, boolean version, boolean deprecated, String lang, List<PropertyComponent> properties) {
@@ -3887,10 +3887,13 @@ public class NarrativeGenerator implements INarrativeGenerator {
       if (vs.hasCopyrightElement())
         generateCopyright(x, vs);
     }
-    XhtmlNode p = x.para();
-    p.tx("This value set includes codes from the following code systems:");
-
     XhtmlNode ul = x.ul();
+    if (vs.getCompose().getInclude().size() == 1 && vs.getCompose().getExclude().size() == 0) {
+      hasExtensions = genInclude(rcontext, ul, vs.getCompose().getInclude().get(0), "Include", langs, maps) || hasExtensions;
+    } else {
+      XhtmlNode p = x.para();
+      p.tx("This value set includes codes based on the following rules:");
+
       XhtmlNode li;
       for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
         hasExtensions = genInclude(rcontext, ul, inc, "Include", langs, maps) || hasExtensions;
@@ -3898,6 +3901,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
       for (ConceptSetComponent exc : vs.getCompose().getExclude()) {
         hasExtensions = genInclude(rcontext, ul, exc, "Exclude", langs, maps) || hasExtensions;
       }
+    }
     
     // now, build observed languages
 
@@ -4000,6 +4004,10 @@ public class NarrativeGenerator implements INarrativeGenerator {
         if (inc.getConcept().size() > 0) {
           li.addText(type+" these codes as defined in ");
           addCsRef(inc, li, e);
+          if (inc.hasVersion()) {
+            li.addText(" version ");
+            li.code(inc.getVersion()); 
+          }
 
           XhtmlNode t = li.table("none");
           boolean hasComments = false;

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java

@@ -106,19 +106,15 @@ POSSIBILITY OF SUCH DAMAGE.
  *  
  * 1/ Initialize
  *    ValidationEngine validator = new ValidationEngine(src);
- *      - this must refer to the igpack.zip for the version of the spec against which you want to validate
+ *      - this must be the packageId of the relevant core specification
- *       it can be a url or a file reference. It can nominate the igpack.zip directly, 
+ *        for the version you want to validate against (e.g. hl7.fhir.r4.core)
- *       or it can name the container alone (e.g. just the spec URL).
- *       The validation engine does not cache igpack.zip. the user must manage that if desired 
  *
  *    validator.connectToTSServer(txServer);
  *      - this is optional; in the absence of a terminology service, snomed, loinc etc will not be validated
  *      
  *    validator.loadIg(src);
- *      - call this any number of times for the Implementation Guide(s) of interest. This is a reference
+ *      - call this any number of times for the Implementation Guide(s) of interest. 
- *        to the igpack.zip for the implementation guide - same rules as above
+ *      - See https://confluence.hl7.org/display/FHIR/Using+the+FHIR+Validator for documentation about the src parameter (-ig parameter)
- *        the version of the IGPack must match that of the spec 
- *        Alternatively it can point to a local folder that contains conformance resources.
  *         
  *    validator.loadQuestionnaire(src)
  *      - url or filename of a questionnaire to load. Any loaded questionnaires will be used while validating
@@ -136,7 +132,8 @@ POSSIBILITY OF SUCH DAMAGE.
  *        if the source is provided as byte[] or stream, you need to provide a format too, though you can 
  *        leave that as null, and the validator will guess
  * 
- * 3. Or, instead of validating, transform        
+ * 3. Or, instead of validating, transform (see documentation and use in Validator.java)
+ *         
  * @author Grahame Grieve
  *
  */
@@ -549,8 +546,10 @@ public class ValidationEngine implements IValidatorResourceFetcher {
   }
 
   private boolean isIgnoreFile(File ff) {
-    return Utilities.existsInList(ff.getName(), ".DS_Store") || Utilities.existsInList(Utilities.getFileExtension(ff.getName()).toLowerCase(), "md", "css", "js", "png", "gif", "jpg", "html", "tgz", "pack", "zip");
+    if (ff.getName().startsWith(".")|| ff.getAbsolutePath().contains(".git")){
-    
+      return true;
+    }
+    return Utilities.existsInList(Utilities.getFileExtension(ff.getName()).toLowerCase(), "md", "css", "js", "png", "gif", "jpg", "html", "tgz", "pack", "zip");
   }
 
   private Map<String, byte[]> loadPackage(InputStream stream, String name) throws Exception {