add narrative generation tests

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java

@@ -23,7 +23,9 @@ package org.hl7.fhir.r5.terminologies;
 
 import java.util.ArrayList;
 import java.util.Calendar;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
@@ -47,6 +49,90 @@ import org.hl7.fhir.utilities.Utilities;
 
 public class CodeSystemUtilities {
 
+  public static class CodeSystemNavigator {
+
+    private CodeSystem cs;
+    private boolean restructure;
+    private Set<String> processed = new HashSet<>();
+
+    public CodeSystemNavigator(CodeSystem cs) {
+      this.cs = cs;
+      restructure = hasExtraRelationships(cs.getConcept());
+    }
+
+    public boolean isRestructure() {
+      return restructure;
+    }
+
+    private boolean hasExtraRelationships(List<ConceptDefinitionComponent> concept) {
+      for (ConceptDefinitionComponent cd : concept) {
+        if (getSubsumedBy(cd) != null) {
+          return true;
+        }
+        for (ConceptDefinitionComponent cdc : cd.getConcept()) {
+          if (hasExtraRelationships(cdc.getConcept())) {
+            return true;
+          }
+        }
+      }
+      return false;
+    }
+
+    public List<ConceptDefinitionComponent> getConcepts(ConceptDefinitionComponent context) {
+      if (context == null) {
+        if (restructure) {
+          List<ConceptDefinitionComponent> res = new ArrayList<>();
+          for (ConceptDefinitionComponent cd : cs.getConcept()) {
+            if (getSubsumedBy(cd) == null) {
+              res.add(cd);
+              processed.add(cd.getCode());
+            }
+          }
+          return res;
+        } else {
+          return cs.getConcept();
+        }
+      } else {
+        if (restructure) {
+          List<ConceptDefinitionComponent> res = new ArrayList<>();
+          for (ConceptDefinitionComponent cd : context.getConcept()) {
+            res.add(cd);
+            processed.add(cd.getCode());
+          }
+          for (ConceptDefinitionComponent cd : cs.getConcept()) {
+            if (context.getCode().equals(getSubsumedBy(cd)) && !processed.contains(cd.getCode())) {
+              res.add(cd);
+              processed.add(cd.getCode());
+            }
+          }
+          return res;
+        } else {
+          return context.getConcept();
+        }
+      }
+    }
+
+    private String getSubsumedBy(ConceptDefinitionComponent cd) {
+      for (ConceptPropertyComponent cp : cd.getProperty()) {
+        if (cp.getCode().equals("subsumedBy")) {
+          return cp.getValue().primitiveValue();
+        }
+      }
+      return null;
+    }
+
+    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())) {
+          res.add(cd);
+        }
+      }
+      return res;
+    }
+  }
+
+
   public static boolean isNotSelectable(CodeSystem cs, ConceptDefinitionComponent def) {
     for (ConceptPropertyComponent p : def.getProperty()) {
       if (p.getCode().equals("notSelectable") && p.hasValue() && p.getValue() instanceof BooleanType) 

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

@@ -177,6 +177,7 @@ import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
 import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionParameterComponent;
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
+import org.hl7.fhir.r5.terminologies.CodeSystemUtilities.CodeSystemNavigator;
 import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
 import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
 import org.hl7.fhir.r5.utils.LiquidEngine.LiquidDocument;
@@ -317,6 +318,9 @@ public class NarrativeGenerator implements INarrativeGenerator {
     return res;
   }
 
+  public boolean generate(DomainResource r) throws EOperationOutcome, FHIRException, IOException {
+    return generate(null, r, new HashSet<>());
+  }
   public boolean generate(DomainResource r, Set<String> outputTracker) throws EOperationOutcome, FHIRException, IOException {
     return generate(null, r, outputTracker);
   }
@@ -2667,7 +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);
     }
@@ -2768,9 +2772,10 @@ public class NarrativeGenerator implements INarrativeGenerator {
       version = version || conceptsHaveVersion(c);
       hierarchy = hierarchy || c.hasConcept();
     }
+    CodeSystemNavigator csNav = new CodeSystemNavigator(cs);
     addMapHeaders(addTableHeaderRowStandard(t, hierarchy, display, true, commentS, version, deprecated, lang, properties), maps);
-    for (ConceptDefinitionComponent c : cs.getConcept()) {
+    for (ConceptDefinitionComponent c : csNav.getConcepts(null)) {
-      hasExtensions = addDefineRowToTable(t, c, 0, hierarchy, display, commentS, version, deprecated, maps, cs.getUrl(), cs, lang, properties) || hasExtensions;
+      hasExtensions = addDefineRowToTable(t, c, 0, hierarchy || csNav.isRestructure(), display, commentS, version, deprecated, maps, cs.getUrl(), cs, lang, properties, csNav) || hasExtensions;
     }
 //    if (langs.size() > 0) {
 //      Collections.sort(langs);
@@ -2799,10 +2804,19 @@ public class NarrativeGenerator implements INarrativeGenerator {
 
   private boolean showPropertyInTable(PropertyComponent cp) {
     if (cp.hasCode()) {
+      if (cp.hasExtension(ToolingExtensions.EXT_RENDERED_VALUE)) {
+        return true;
+      }
+      String uri = cp.getUri();
+      if (Utilities.noString(uri)){
+        return false;
+      }
+      if (uri.contains("#")) {
+        uri = uri.substring(0, uri.indexOf("#"));
+      }
       return 
-        Utilities.existsInList(cp.getUri(), "http://hl7.org/fhir/concept-properties") ||
+        Utilities.existsInList(uri, "http://hl7.org/fhir/concept-properties") ||
-        codeSystemPropList.contains(cp.getUri()) || 
+        codeSystemPropList.contains(uri);
-        cp.hasExtension(ToolingExtensions.EXT_RENDERED_VALUE);
     }
     return false;
   }
@@ -3449,7 +3463,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
     return "??Lang";
   }
  
-  private boolean addDefineRowToTable(XhtmlNode t, ConceptDefinitionComponent c, int i, boolean hasHierarchy, boolean hasDisplay, boolean comment, boolean version, boolean deprecated, List<UsedConceptMap> maps, String system, CodeSystem cs, String lang, List<PropertyComponent> properties) throws FHIRFormatError, DefinitionException, IOException {
+  private boolean addDefineRowToTable(XhtmlNode t, ConceptDefinitionComponent c, int i, boolean hasHierarchy, boolean hasDisplay, boolean comment, boolean version, boolean deprecated, List<UsedConceptMap> maps, String system, CodeSystem cs, String lang, List<PropertyComponent> properties, CodeSystemNavigator csNav) throws FHIRFormatError, DefinitionException, IOException {
     boolean hasExtensions = false;
     XhtmlNode tr = t.tr();
     XhtmlNode td = tr.td();
@@ -3618,16 +3632,16 @@ public class NarrativeGenerator implements INarrativeGenerator {
           td.i().tx("("+mapping.comp.getComment()+")");
       }
     }
-    for (String e : CodeSystemUtilities.getOtherChildren(cs, c)) {
+    for (ConceptDefinitionComponent cc : csNav.getOtherChildren(c)) {
       tr = t.tr();
       td = tr.td();
       String s = Utilities.padLeft("", '.', i*2);
       td.addText(s);
-      a = td.ah("#"+Utilities.nmtokenize(e));
+      a = td.ah("#"+Utilities.nmtokenize(cc.getCode()));
       a.addText(c.getCode());
     }
-    for (ConceptDefinitionComponent cc : c.getConcept()) {
+    for (ConceptDefinitionComponent cc : csNav.getConcepts(c)) {
-      hasExtensions = addDefineRowToTable(t, cc, i+1, hasHierarchy, hasDisplay, comment, version, deprecated, maps, system, cs, lang, properties) || hasExtensions;
+      hasExtensions = addDefineRowToTable(t, cc, i+1, hasHierarchy, hasDisplay, comment, version, deprecated, maps, system, cs, lang, properties, csNav) || hasExtensions;
     }
     return hasExtensions;
   }

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/AllR5Tests.java

@@ -15,6 +15,7 @@ import org.junit.runners.Suite.SuiteClasses;
     GraphQLEngineTests.class,
     LiquidEngineTests.class,
     FHIRPathTests.class,
+    NarrativeGenerationTests.class,
     NarrativeGeneratorTests.class,
     ShexGeneratorTests.class,
     BaseDateTimeTypeTest.class,

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java

@@ -0,0 +1,129 @@
+package org.hl7.fhir.r5.test;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.NotImplementedException;
+import org.hl7.fhir.exceptions.DefinitionException;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.exceptions.PathEngineException;
+import org.hl7.fhir.r5.conformance.ProfileUtilities;
+import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
+import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.SimpleWorkerContext;
+import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.formats.JsonParser;
+import org.hl7.fhir.r5.formats.XmlParser;
+import org.hl7.fhir.r5.model.Base;
+import org.hl7.fhir.r5.model.Coding;
+import org.hl7.fhir.r5.model.DomainResource;
+import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
+import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
+import org.hl7.fhir.r5.model.MetadataResource;
+import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
+import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
+import org.hl7.fhir.r5.model.TestScript;
+import org.hl7.fhir.r5.model.TestScript.AssertionResponseTypes;
+import org.hl7.fhir.r5.model.TestScript.SetupActionAssertComponent;
+import org.hl7.fhir.r5.model.TestScript.SetupActionOperationComponent;
+import org.hl7.fhir.r5.model.TestScript.TestActionComponent;
+import org.hl7.fhir.r5.model.TestScript.TestScriptFixtureComponent;
+import org.hl7.fhir.r5.model.TestScript.TestScriptTestComponent;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
+import org.hl7.fhir.r5.model.TypeDetails;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.utils.CodingUtilities;
+import org.hl7.fhir.r5.utils.EOperationOutcome;
+import org.hl7.fhir.r5.utils.FHIRPathEngine;
+import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
+import org.hl7.fhir.r5.utils.IResourceValidator;
+import org.hl7.fhir.r5.utils.NarrativeGenerator;
+import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.VersionUtilities;
+import org.hl7.fhir.utilities.cache.PackageCacheManager;
+import org.hl7.fhir.utilities.cache.ToolsVersion;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
+import org.hl7.fhir.utilities.xml.XMLUtil;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.xml.sax.SAXException;
+
+import ca.uhn.fhir.rest.api.Constants;
+import junit.framework.Assert;
+
+@RunWith(Parameterized.class)
+public class NarrativeGenerationTests {
+
+  public static class TestDetails {
+    private String id;
+
+    public TestDetails(Element test) {
+      super();
+      id = test.getAttribute("id");
+    }
+    public String getId() {
+      return id;
+    }
+  }
+
+  private static FHIRPathEngine fp;
+
+  @Parameters(name = "{index}: file {0}")
+  public static Iterable<Object[]> data() throws ParserConfigurationException, IOException, FHIRFormatError, SAXException {
+
+    Document tests = XMLUtil.parseToDom(TestingUtilities.loadTestResource("r5", "narrative", "manifest.xml"));
+    Element test = XMLUtil.getFirstChild(tests.getDocumentElement());
+    List<Object[]> objects = new ArrayList<Object[]>();
+    while (test != null && test.getNodeName().equals("test")) {
+      TestDetails t = new TestDetails(test);
+      objects.add(new Object[] {t.getId(), t});
+      test = XMLUtil.getNextSibling(test);
+    }
+    return objects;
+
+  }
+
+
+  private final TestDetails test;
+  private IWorkerContext context;
+  private List<ValidationMessage> messages;
+
+  public NarrativeGenerationTests(String id, TestDetails test) {
+    this.test = test;
+    this.context = TestingUtilities.context();
+  }
+
+  @SuppressWarnings("deprecation")
+  @Test
+  public void test() throws Exception {
+    NarrativeGenerator gen = new NarrativeGenerator("", "http://hl7.org/fhir", context);
+    IOUtils.copy(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId()+"-expected.xml"), new FileOutputStream(TestingUtilities.tempFile("narrative", test.getId()+"-expected.xml")));
+    DomainResource source = (DomainResource) new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId()+"-input.xml"));
+    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);
+    Assert.assertTrue("Output does not match expected", source.equalsDeep(target));
+  }
+
+}

pom.xml

@@ -17,7 +17,7 @@
 
     <properties>
         <hapi_fhir_version>4.1.0</hapi_fhir_version>
-        <validator_test_case_version>1.0.14-SNAPSHOT</validator_test_case_version>
+        <validator_test_case_version>1.0.15-SNAPSHOT</validator_test_case_version>
     </properties>
 
     <artifactId>org.hl7.fhir.core</artifactId>