Merge pull request #1194 from hapifhir/gg-202303-r5-path-fixes

Gg 202303 r5 path fixes

RELEASE_NOTES.md

@@ -4,4 +4,9 @@
 
 ## Other code changes
 
-* no changes
+* Fix R5 path for spec in generated narratives
+* Hack to fix wrong R5 paths in generated narratives in extensions pack
+* Suppress Prism rendering if ttl source is too big
+* Fix up URLs in untouched elements when processing snapshots
+* Fix up URLs in binding.description when generating snapshots
+

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

@@ -725,6 +725,7 @@ public class ProfilePathProcessor {
     outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
     profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
     profileUtilities.updateConstraintSources(outcome, getSourceStructureDefinition().getUrl());
+    profileUtilities.updateURLs(url, webUrl, outcome);
     profileUtilities.markDerived(outcome);
     if (cursors.resultPathBase == null)
       cursors.resultPathBase = outcome.getPath();

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

@@ -1651,15 +1651,22 @@ public class ProfileUtilities extends TranslatingUtilities {
       }
       if (webUrl != null) {
         // also, must touch up the markdown
-        if (element.hasDefinition())
+        if (element.hasDefinition()) {
           element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
-        if (element.hasComment())
+        }
+        if (element.hasComment()) {
           element.setComment(processRelativeUrls(element.getComment(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
-        if (element.hasRequirements())
+        }
+        if (element.hasRequirements()) {
           element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
-        if (element.hasMeaningWhenMissing())
+        }
+        if (element.hasMeaningWhenMissing()) {
           element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
         }
+        if (element.hasBinding() && element.getBinding().hasDescription()) {
+          element.getBinding().setDescription(processRelativeUrls(element.getBinding().getDescription(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
+        }
+      }
     }
     return element;
   }
@@ -2335,6 +2342,7 @@ public class ProfileUtilities extends TranslatingUtilities {
     if (dest.hasPattern()) {
       checkTypeOk(dest, dest.getPattern().fhirType(), srcSD, "pattern");
     }
+    //updateURLs(url, webUrl, dest);
   }
 
   private void addMappings(List<ElementDefinitionMappingComponent> destination, List<ElementDefinitionMappingComponent> source) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/R5Hacker.java

@@ -4,6 +4,7 @@ import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.r5.model.ElementDefinition;
 import org.hl7.fhir.r5.model.Enumerations.BindingStrength;
+import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.r5.model.StructureDefinition;
 
 public class R5Hacker {
@@ -16,50 +17,22 @@ public class R5Hacker {
 
 
   private static void fixSD(StructureDefinition sd) {
-    if ("5.0.0-ballot".equals(sd.getVersion()) && "ElementDefinition".equals(sd.getType())) {
+    if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
       for (ElementDefinition ed : sd.getDifferential().getElement()) {
-        hackEDR5BallotError(ed);
+        fix(ed);
       }
       for (ElementDefinition ed : sd.getSnapshot().getElement()) {
-        hackEDR5BallotError(ed);
+        fix(ed);
       }
     }
-    if ("5.0.0-ballot".equals(sd.getVersion()) && "Base".equals(sd.getType())) {
-      for (ElementDefinition ed : sd.getDifferential().getElement()) {
-        hackBaseR5BallotError(ed);
-      }
-      for (ElementDefinition ed : sd.getSnapshot().getElement()) {
-        hackBaseR5BallotError(ed);
-      }
-    }
-    if ("5.0.0-ballot".equals(sd.getVersion()) && "Bundle".equals(sd.getType())) {
-      for (ElementDefinition ed : sd.getDifferential().getElement()) {
-        hackBundleR5BallotError(ed);
-      }
-      for (ElementDefinition ed : sd.getSnapshot().getElement()) {
-        hackBundleR5BallotError(ed);
-      }
-    }
-    if ("5.0.0-ballot".equals(sd.getVersion()) && "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaulttype".equals(sd.getUrl())) {
-      sd.getContextFirstRep().setExpression("ElementDefinition");
-    }
   }
 
 
-  private static void hackBaseR5BallotError(ElementDefinition ed) {
+  private static void fix(ElementDefinition ed) {
-    ed.getConstraint().clear(); 
+    if (ed.hasDefinition()) {
+      ed.setDefinition(ed.getDefinition().replace("http://hl7.org/fhir/5.0.0-snapshot3/", "http://hl7.org/fhir/R5/"));
     }
     
-  private static void hackBundleR5BallotError(ElementDefinition ed) {
-    if (ed.getPath().equals("Bundle.link.relation")) {
-      ToolingExtensions.removeExtension(ed.getBinding(), ToolingExtensions.EXT_BINDING_NAME);
-    }    
-  }
-
-  private static void hackEDR5BallotError(ElementDefinition ed) {
-    if (ed.getPath().equals("ElementDefinition.type.code")) {
-      ed.getBinding().setStrength(BindingStrength.EXTENSIBLE);
-    }    
   }
 
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java

@@ -598,7 +598,7 @@ public class VersionUtilities {
     case "3.0" : return "http://hl7.org/fhir/STU3";
     case "4.0" : return "http://hl7.org/fhir/R4";
     case "4.3" : return "http://hl7.org/fhir/R4B";
-    case "5.0" : return "http://hl7.org/fhir/5.0.0-snapshot3";
+    case "5.0" : return "http://hl7.org/fhir/R5";
     default:
       return "http://hl7.org/fhir";
     }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/turtle/Turtle.java

@@ -415,14 +415,14 @@ public class Turtle {
 		writer.close();
 	}
 
-  public String asHtml() throws Exception {
+  public String asHtml(boolean prism) throws Exception {
     StringBuilder b = new StringBuilder();
-    b.append("<pre class=\"rdf\" style=\"white-space: pre; overflow: hidden\"><code class=\"language-turtle\">\r\n");
+    b.append("<pre class=\"rdf\" style=\"white-space: pre; overflow: hidden\">"+(prism ? "<code class=\"language-turtle\">" : "")+"\r\n");
     commitPrefixes(b);
     for (Section s : sections) {
       commitSection(b, s);
     }
-    b.append("</code></pre>\r\n");
+    b.append((prism ? "</code>" : "")+"</pre>\r\n");
     b.append("\r\n");
     return b.toString();
   }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xml/XMLUtil.java

@@ -563,6 +563,15 @@ public class XMLUtil {
     child.setAttribute("value", text);    
   }
 
+  public static Element addTextTag(Document doc, Element element, String name, String text, int indent) {
+    Node node = doc.createTextNode("\n"+Utilities.padLeft("", ' ', indent));
+    element.appendChild(node);
+    Element child = doc.createElement(name);
+    element.appendChild(child);
+    child.appendChild(doc.createTextNode(text));
+    return child;
+  }
+
   public static void saveToFile(Element root, OutputStream stream) throws TransformerException {
     Transformer transformer = TransformerFactory.newInstance().newTransformer();
     Result output = new StreamResult(stream);

pom.xml

@@ -19,7 +19,7 @@
 
     <properties>
         <hapi_fhir_version>6.2.1</hapi_fhir_version>
-        <validator_test_case_version>1.2.24</validator_test_case_version>
+        <validator_test_case_version>1.2.25-SNAPSHOT</validator_test_case_version>
         <junit_jupiter_version>5.7.1</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
         <maven_surefire_version>3.0.0-M5</maven_surefire_version>