From aec4a6c58ae5cd4c7ba1b11057913d4b772d39dd Mon Sep 17 00:00:00 2001
From: Grahame Grieve <grahameg@gmail.com>
Date: Wed, 11 Dec 2019 21:39:21 +1100
Subject: [PATCH] fix code system rendering

---
 .../java/org/hl7/fhir/r5/model/CodeSystem.java |  4 ++++
 .../r5/terminologies/CodeSystemUtilities.java  | 18 +++++++++++-------
 .../hl7/fhir/r5/utils/NarrativeGenerator.java  |  2 +-
 .../fhir/r5/test/NarrativeGenerationTests.java |  1 +
 4 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeSystem.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeSystem.java
index 039ffb8d0..5c1854484 100644
--- a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeSystem.java
+++ b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeSystem.java
@@ -2080,6 +2080,10 @@ public class CodeSystem extends MetadataResource {
 
   }
 
+   @Override
+   public String toString() {
+     return getCode()+": "+getDisplay();
+   }
   }
 
     @Block()
diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java
index e675fdc7e..2c28ac37d 100644
--- a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java
+++ b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java
@@ -66,7 +66,7 @@ public class CodeSystemUtilities {
 
     private boolean hasExtraRelationships(List<ConceptDefinitionComponent> concept) {
       for (ConceptDefinitionComponent cd : concept) {
-        if (getSubsumedBy(cd) != null) {
+        if (!getSubsumedBy(cd).isEmpty()) {
           return true;
         }
         for (ConceptDefinitionComponent cdc : cd.getConcept()) {
@@ -83,11 +83,12 @@ public class CodeSystemUtilities {
         if (restructure) {
           List<ConceptDefinitionComponent> res = new ArrayList<>();
           for (ConceptDefinitionComponent cd : cs.getConcept()) {
-            if (getSubsumedBy(cd) == null) {
+            if (getSubsumedBy(cd).isEmpty()) {
               res.add(cd);
               processed.add(cd.getCode());
             }
           }
+          System.out.println("children of (root): "+res);
           return res;
         } else {
           return cs.getConcept();
@@ -100,11 +101,12 @@ public class CodeSystemUtilities {
             processed.add(cd.getCode());
           }
           for (ConceptDefinitionComponent cd : cs.getConcept()) {
-            if (context.getCode().equals(getSubsumedBy(cd)) && !processed.contains(cd.getCode())) {
+            if (getSubsumedBy(cd).contains(context.getCode()) && !processed.contains(cd.getCode())) {
               res.add(cd);
               processed.add(cd.getCode());
             }
           }
+          System.out.println("children of "+context+": "+res);
           return res;
         } else {
           return context.getConcept();
@@ -112,22 +114,24 @@ public class CodeSystemUtilities {
       }
     }
 
-    private String getSubsumedBy(ConceptDefinitionComponent cd) {
+    private List<String> getSubsumedBy(ConceptDefinitionComponent cd) {
+      List<String> codes = new ArrayList<>();
       for (ConceptPropertyComponent cp : cd.getProperty()) {
         if (cp.getCode().equals("subsumedBy")) {
-          return cp.getValue().primitiveValue();
+          codes.add(cp.getValue().primitiveValue());
         }
       }
-      return null;
+      return codes;
     }
 
     public List<ConceptDefinitionComponent> getOtherChildren(ConceptDefinitionComponent context) {
       List<ConceptDefinitionComponent> res = new ArrayList<>();
       for (ConceptDefinitionComponent cd : cs.getConcept()) {
-        if (context.getCode().equals(getSubsumedBy(cd)) && processed.contains(cd.getCode())) {
+        if (getSubsumedBy(cd).contains(context.getCode()) && processed.contains(cd.getCode())) {
           res.add(cd);
         }
       }
+      System.out.println("non-children of "+context+": "+res);
       return res;
     }
   }
diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java
index e9d20433f..c6b65ac51 100644
--- a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java
+++ b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java
@@ -2671,7 +2671,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
     if (header) {
       XhtmlNode h = x.h2();
       h.addText(cs.hasTitle() ? cs.getTitle() : cs.getName());
- // ....     addMarkdown(x, cs.getDescription());
+      addMarkdown(x, cs.getDescription());
       if (cs.hasCopyright())
         generateCopyright(x, cs, lang);
     }
diff --git a/org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java b/org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java
index 5f0bd4d46..9b1de5c3d 100644
--- a/org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java
+++ b/org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java
@@ -123,6 +123,7 @@ public class NarrativeGenerationTests {
     DomainResource target = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId()+"-expected.xml"));
     gen.generate(source);
     new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(TestingUtilities.tempFile("narrative", test.getId()+"-actual.xml")), source);
+    source = (DomainResource) new XmlParser().parse(new FileInputStream(TestingUtilities.tempFile("narrative", test.getId()+"-actual.xml")));
     Assert.assertTrue("Output does not match expected", source.equalsDeep(target));
   }