Merge pull request #747 from hapifhir/gg-202202-rendering

Gg 202202 rendering

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/utg/UTGCaseSensitivePopulator.java

@@ -0,0 +1,105 @@
+package org.hl7.fhir.convertors.misc.utg;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.time.LocalDate;
+import java.time.ZoneId;
+import java.util.Calendar;
+import java.util.Date;
+
+import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.r4.formats.IParser;
+import org.hl7.fhir.r4.formats.IParser.OutputStyle;
+import org.hl7.fhir.r4.formats.JsonParser;
+import org.hl7.fhir.r4.formats.XmlParser;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleType;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
+import org.hl7.fhir.r4.model.Period;
+import org.hl7.fhir.r4.model.Provenance;
+import org.hl7.fhir.r4.model.Provenance.ProvenanceAgentComponent;
+import org.hl7.fhir.r4.model.Resource;
+import org.hl7.fhir.utilities.Utilities;
+
+public class UTGCaseSensitivePopulator {
+
+  public static void main(String[] args) throws FileNotFoundException, IOException {
+    new UTGCaseSensitivePopulator().process(new File(args[0]));
+
+  }
+
+  private void process(File root) throws FileNotFoundException, IOException {
+    Bundle bundle = new Bundle();
+    bundle.setType(BundleType.COLLECTION);
+    bundle.setId("hxutg1-1-0-12");
+    
+    scanFolders(root, bundle);
+    new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(root.getAbsolutePath(), "input", "sourceOfTruth", "history", "utgrel1hx-1-0-12.json")), bundle);
+    System.out.println("Done");
+  }
+
+  private void scanFolders(File folder, Bundle bundle) throws FileNotFoundException, IOException {
+    Calendar today = Calendar.getInstance();
+    Date dt = today.getTime();
+    today.set(Calendar.HOUR_OF_DAY, 0);
+    Date d = today.getTime();
+    System.out.println("Scan "+folder.getAbsolutePath());
+        
+    for (File f : folder.listFiles()) {
+      if (f.isDirectory() && !f.getName().equals("retired")) {
+        scanFolders(f, bundle);
+      } else if (f.getName().endsWith(".xml")) {
+        processFile(f, bundle, new XmlParser(), d, dt);
+      } else if (f.getName().endsWith(".json")) {
+        processFile(f, bundle, new JsonParser(), d, dt);
+      }
+    }
+    
+  }
+
+  private void processFile(File f, Bundle bundle, IParser parser, Date d, Date dt) {
+    try {
+      Resource r = parser.parse(new FileInputStream(f));
+      if (r instanceof CodeSystem) {
+        if (processCodeSystem((CodeSystem) r, bundle, d, dt)) {
+          parser.setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f), r);
+        }
+      }
+    } catch (Exception e) {
+    }
+    
+  }
+
+  private boolean processCodeSystem(CodeSystem cs, Bundle bundle, Date d, Date dt) {
+    if (cs.hasCaseSensitive()) {
+      return false;
+    }
+    if (!cs.getUrl().startsWith("http://terminology.hl7.org") || cs.getContent() == CodeSystemContentMode.NOTPRESENT) {
+      return false;
+    }
+    cs.setCaseSensitive(true);
+    Provenance p = new Provenance();
+    p.setId("cs-286-"+cs.getId());
+    p.addTarget().setReference("CodeSystem/"+cs.getId());
+    p.setOccurred(new Period());
+    p.getOccurredPeriod().setEnd(d);
+    p.setRecorded(dt);
+    p.addReason().setText("Populate Missing caseSensitive property;UP-286").addCoding().setSystem("http://terminology.hl7.org/CodeSystem/v3-ActReason").setCode("METAMGT");
+    p.getActivity().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/v3-DataOperation").setCode("UPDATE");
+    ProvenanceAgentComponent agent = p.addAgent();
+    agent.getType().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/provenance-participant-type").setCode("author");
+    agent.getWho().setDisplay("Grahame Grieve");
+    agent = p.addAgent();
+    agent.getType().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/provenance-participant-type").setCode("custodian");
+    agent.getWho().setDisplay("Vocabulary WG");
+    
+    bundle.addEntry().setFullUrl("http://terminology.hl7.org/fhir/Provenance/cs-286-"+cs.getId()).setResource(p);
+    
+    return true;
+  }
+
+}

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

@@ -553,8 +553,18 @@ public class ProfileUtilities extends TranslatingUtilities {
   }
 
   public List<ElementDefinition> getChildList(StructureDefinition structure, ElementDefinition element) {
+    if (element.hasContentReference()) {
+      ElementDefinition target = element;
+      for (ElementDefinition t : structure.getSnapshot().getElement()) {
+        if (t.getId().equals(element.getContentReference().substring(1))) {
+          target = t;
+        }
+      }      
+      return getChildList(structure, target.getPath(), target.getId(), false);
+    } else {
       return getChildList(structure, element.getPath(), element.getId(), false);
     }
+	}
 
   public void updateMaps(StructureDefinition base, StructureDefinition derived) throws DefinitionException {
     if (base == null)
@@ -2524,10 +2534,10 @@ public class ProfileUtilities extends TranslatingUtilities {
               // re-enabled 11-Feb 2022 GDG - we do want to do this. At least, $assemble in davinci-dtr, where the markdown comes from the SDC IG, and an SDC local reference must be changed to point to SDC. in this case, it's called when generating snapshots
               // added processRelatives parameter to deal with this (well, to try)
               if (processRelatives && webUrl != null) {
-                System.out.println("Making "+url+" relative to '"+webUrl+"'");
+//                System.out.println("Making "+url+" relative to '"+webUrl+"'");
                 b.append(webUrl);
               } else {
-                System.out.println("Not making "+url+" relative to '"+webUrl+"'");
+//                System.out.println("Not making "+url+" relative to '"+webUrl+"'");
               }
               i = i + 1;
             }
@@ -3680,7 +3690,7 @@ public class ProfileUtilities extends TranslatingUtilities {
   }
 
 
-  private String codeForAggregation(AggregationMode a) {
+  public static String codeForAggregation(AggregationMode a) {
     switch (a) {
     case BUNDLED : return "b";
     case CONTAINED : return "c";
@@ -3689,7 +3699,7 @@ public class ProfileUtilities extends TranslatingUtilities {
     }
   }
 
-  private String hintForAggregation(AggregationMode a) {
+  public static  String hintForAggregation(AggregationMode a) {
     if (a != null)
       return a.getDefinition();
     else 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/BundleRenderer.java

@@ -104,7 +104,7 @@ public class BundleRenderer extends ResourceRenderer {
               xn.para().b().tx("Exception generating narrative: "+e.getMessage());
             }
           }
-          root.blockquote().addChildren(xn);
+          root.blockquote().para().addChildren(xn);
         }
       }
     }
@@ -156,7 +156,7 @@ public class BundleRenderer extends ResourceRenderer {
         List<BaseWrapper> sections = section.children("section");
         for (BaseWrapper child : sections) {
           if (nested) {
-            addSection(x.blockquote(), child, level+1, true);
+            addSection(x.blockquote().para(), child, level+1, true);
           } else {
             addSection(x, child, level+1, true);
           }
@@ -241,7 +241,7 @@ public class BundleRenderer extends ResourceRenderer {
         List<SectionComponent> sections = section.getSection();
         for (SectionComponent child : sections) {
           if (nested) {
-            addSection(x.blockquote(), child, level+1, true);
+            addSection(x.blockquote().para(), child, level+1, true);
           } else {
             addSection(x, child, level+1, true);            
           }
@@ -300,7 +300,7 @@ public class BundleRenderer extends ResourceRenderer {
                 xn = makeExceptionXhtml(e, "generating narrative");
               }
             }
-            root.blockquote().getChildNodes().addAll(checkInternalLinks(b, xn.getChildNodes()));
+            root.blockquote().para().getChildNodes().addAll(checkInternalLinks(b, xn.getChildNodes()));
           }
         }
       }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/CodeSystemRenderer.java

@@ -51,7 +51,7 @@ public class CodeSystemRenderer extends TerminologyRenderer {
       h.addText(cs.hasTitle() ? cs.getTitle() : cs.getName());
       addMarkdown(x, cs.getDescription());
       if (cs.hasCopyright())
-        generateCopyright(x, cs);
+        generateCopyright(x, cs );
     }
 
     generateProperties(x, cs);
@@ -245,7 +245,7 @@ public class CodeSystemRenderer extends TerminologyRenderer {
       if (cs == null) {
         return false;
       }
-      return CodeSystemUtilities.hasCode(cs, code);
+      return code == null ? false : CodeSystemUtilities.hasCode(cs, code);
     }
     return false;
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/PatientRenderer.java

@@ -223,7 +223,7 @@ public class PatientRenderer extends ResourceRenderer {
 
   @Override
   public boolean render(XhtmlNode x, ResourceWrapper r) throws FHIRFormatError, DefinitionException, IOException {
-    describe(x, r);
+    describe(x.para(), r);
     return false;
   }
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/QuestionnaireResponseRenderer.java

@@ -168,11 +168,13 @@ public class QuestionnaireResponseRenderer extends ResourceRenderer {
     r.getCells().add(gen.new Cell(null, context.getDefinitionsTarget() == null ? "" : context.getDefinitionsTarget()+"#item."+linkId, linkId, null, null));
     r.getCells().add(gen.new Cell(null, null, text, null, null));
     r.getCells().add(gen.new Cell(null, null, null, null, null));
-    if (answers.size() == 0) {
+    if (answers == null ||  answers.size() == 0) {
       r.getCells().add(gen.new Cell(null, null, null, null, null));
+      if (items != null) {
         for (BaseWrapper si : items) {
           renderTreeItem(gen, r.getSubRows(), q, si);
         }
+      }
     } else if (answers.size() == 1) {
       BaseWrapper ans = answers.get(0);
       renderAnswer(gen, q, r, ans);

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlComposer.java

@@ -314,6 +314,9 @@ public class XhtmlComposer {
     else if (node.getNodeType() == NodeType.Element) {
       Element child = e.getOwnerDocument().createElementNS(XHTML_NS, node.getName());
       e.appendChild(child);
+      for (String n : node.getAttributes().keySet()) {
+        child.setAttribute(n,  node.getAttribute(n));
+      }
       for (XhtmlNode c : node.getChildNodes()) {
         appendChild(child, c);
       }