Merge pull request #895 from hapifhir/gg-202208-r5-build-issues

R5 related fixes

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

@@ -3721,14 +3721,19 @@ public class ProfileUtilities extends TranslatingUtilities {
               if (ref != null) {
                 String[] parts = ref.split("\\|");
                 if (parts[0].startsWith("http:") || parts[0].startsWith("https:")) {
-                  //            c.addPiece(checkForNoChange(t, gen.new Piece(parts[0], "<" + parts[1] + ">", t.getCode()))); Lloyd
+                  if (p.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT)) {
-                  c.addPiece(checkForNoChange(t, gen.new Piece(parts[0], parts[1], t.getWorkingCode())));
+                    String pp = p.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT);
+                    pp = pp.substring(pp.indexOf("."));
+                    c.addPiece(checkForNoChange(t, gen.new Piece(parts[0], parts[1]+pp, t.getWorkingCode())));
+                  } else {
+                    c.addPiece(checkForNoChange(t, gen.new Piece(parts[0], parts[1], t.getWorkingCode())));
+                  }
                 } else {
-                  //            c.addPiece(checkForNoChange(t, gen.new Piece((t.getProfile().startsWith(corePath)? corePath: "")+parts[0], "<" + parts[1] + ">", t.getCode())));
                   c.addPiece(checkForNoChange(t, gen.new Piece((p.getValue().startsWith(corePath+"StructureDefinition")? corePath: "")+parts[0], parts[1], t.getWorkingCode())));
                 }
-              } else
+              } else {
                 c.addPiece(checkForNoChange(t, gen.new Piece((p.getValue().startsWith(corePath)? corePath: "")+ref, t.getWorkingCode(), null)));
+              }
               if (!mustSupportMode && isMustSupport(p) && e.getMustSupport()) {
                 c.addPiece(gen.new Piece(null, " ", null));
                 c.addStyledText(translate("sd.table", "This profile must be supported"), "S", "white", "red", null, false);
@@ -5026,7 +5031,7 @@ public class ProfileUtilities extends TranslatingUtilities {
 
             Cell c = gen.new Cell();
             row.getCells().add(c);
-            c.addPiece(gen.new Piece((ed.getBase().getPath().equals(ed.getPath()) ? ref+ed.getPath() : (VersionUtilities.isThisOrLater("4.1", context.getVersion()) ? corePath+"types-definitions.html#"+ed.getBase().getPath() : corePath+"element-definitions.html#"+ed.getBase().getPath())), t.getName(), null));
+            c.addPiece(gen.new Piece((ed.getBase().getPath().equals(ed.getPath()) ? ref+ed.getPath() : (VersionUtilities.isR5Ver(context.getVersion()) ? corePath+"types-definitions.html#"+ed.getBase().getPath() : corePath+"element-definitions.html#"+ed.getBase().getPath())), t.getName(), null));
 
             c = gen.new Cell();
             row.getCells().add(c);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/CanonicalResourceManager.java

@@ -21,6 +21,7 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
 
   private final String[] INVALID_TERMINOLOGY_URLS = {
     "http://snomed.info/sct",
+    "http://dicom.nema.org/resources/ontology/DCM",
     "http://nucc.org/provider-taxonomy"
   };
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/RenderingContext.java

@@ -115,7 +115,7 @@ public class RenderingContext {
   private String tooCostlyNoteNotEmptyDependent;
   private List<String> codeSystemPropList = new ArrayList<>();
 
-  private ProfileUtilities profileUtilities;
+  private ProfileUtilities profileUtilitiesR;
   private String definitionsTarget;
   private String destDir;
   private boolean inlineGraphics;
@@ -152,7 +152,6 @@ public class RenderingContext {
     }
  // default to US locale - discussion here: https://github.com/hapifhir/org.hl7.fhir.core/issues/666
     this.locale = new Locale.Builder().setLanguageTag("en-US").build(); 
-    profileUtilities = new ProfileUtilities(worker, null, null);
   }
   public RenderingContext copy() {
     RenderingContext res = new RenderingContext(worker, markdown, terminologyServiceOptions, specificationLink, localPrefix, lang, mode);
@@ -174,7 +173,7 @@ public class RenderingContext {
     res.tooCostlyNoteNotEmptyDependent = tooCostlyNoteNotEmptyDependent;
     res.codeSystemPropList.addAll(codeSystemPropList);
 
-    res.profileUtilities = profileUtilities;
+    res.profileUtilitiesR = profileUtilitiesR;
     res.definitionsTarget = definitionsTarget;
     res.destDir = destDir;
     res.addGeneratedNarrativeHeader = addGeneratedNarrativeHeader;
@@ -204,7 +203,10 @@ public class RenderingContext {
   // -- 2. Markdown support -------------------------------------------------------
 
   public ProfileUtilities getProfileUtilities() {
-    return profileUtilities;
+    if (profileUtilitiesR == null) {
+      profileUtilitiesR = new ProfileUtilities(worker, null, null);
+    }
+    return profileUtilitiesR;
   }
 
   public IWorkerContext getWorker() {
@@ -331,7 +333,7 @@ public class RenderingContext {
   }
 
   public RenderingContext setProfileUtilities(ProfileUtilities profileUtilities) {
-    this.profileUtilities = profileUtilities;
+    this.profileUtilitiesR = profileUtilities;
     return this;
   }
 

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

@@ -8,24 +8,31 @@ import java.util.stream.Stream;
 
 import javax.xml.parsers.ParserConfigurationException;
 
+import org.apache.commons.lang3.NotImplementedException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
+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.elementmodel.Manager;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
 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.ElementDefinition.ElementDefinitionBindingComponent;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.renderers.RendererFactory;
 import org.hl7.fhir.r5.renderers.utils.ElementWrappers;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.ITypeParser;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
+import org.hl7.fhir.r5.test.NarrativeGenerationTests.TestProfileKnowledgeProvider;
 import org.hl7.fhir.r5.test.utils.CompareUtilities;
 import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.utilities.TerminologyServiceOptions;
 import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.hl7.fhir.utilities.xml.XMLUtil;
@@ -40,6 +47,64 @@ import org.xml.sax.SAXException;
 
 public class NarrativeGenerationTests {
 
+  public class TestProfileKnowledgeProvider implements ProfileKnowledgeProvider {
+
+    private IWorkerContext context;
+
+    public TestProfileKnowledgeProvider(IWorkerContext context) {
+      this.context = context;
+    }
+
+    @Override
+    public boolean isDatatype(String typeSimple) {
+      throw new NotImplementedException();      
+    }
+
+    @Override
+    public boolean isResource(String typeSimple) {
+      throw new NotImplementedException();      
+    }
+
+    @Override
+    public boolean hasLinkFor(String typeSimple) {
+      throw new NotImplementedException();      
+    }
+
+    @Override
+    public String getLinkFor(String corePath, String typeSimple) {
+      throw new NotImplementedException();      
+    }
+
+    @Override
+    public BindingResolution resolveBinding(StructureDefinition def, ElementDefinitionBindingComponent binding, String path) throws FHIRException {
+      throw new NotImplementedException();      
+    }
+
+    @Override
+    public BindingResolution resolveBinding(StructureDefinition def, String url, String path) throws FHIRException {
+      throw new NotImplementedException();      
+    }
+
+    @Override
+    public String getLinkForProfile(StructureDefinition profile, String url) {
+      if ("http://hl7.org/fhir/StructureDefinition/Composition".equals(url)) {
+        return "http://hl7.org/fhir/composition.html|TestComposition";
+      }
+      throw new NotImplementedException();      
+    }
+
+    @Override
+    public boolean prependLinks() {
+      throw new NotImplementedException();      
+    }
+
+    @Override
+    public String getLinkForUrl(String corePath, String s) {
+      throw new NotImplementedException();      
+    }
+
+  }
+
   public class TestTypeParser implements ITypeParser {
 
     @Override
@@ -111,7 +176,7 @@ public class NarrativeGenerationTests {
   @MethodSource("data")
   public void test(String id, TestDetails test) throws Exception {
     RenderingContext rc = new RenderingContext(context, null, null, "http://hl7.org/fhir", "", null, ResourceRendererMode.END_USER);
-    rc.setDestDir("");
+    rc.setDestDir(Utilities.path("[tmp]", "narrative"));
     rc.setHeader(test.isHeader());
     rc.setDefinitionsTarget("test.html");
     rc.setTerminologyServiceOptions(TerminologyServiceOptions.defaults());
@@ -123,6 +188,7 @@ public class NarrativeGenerationTests {
     rc.setDateTimeFormatString("yyyy-MM-dd'T'HH:mm:ssZZZZZ"); 
     rc.setDateFormatString("yyyy-MM-dd"); 
     rc.setMode(test.technical ? ResourceRendererMode.TECHNICAL : ResourceRendererMode.END_USER);
+    rc.setProfileUtilities(new ProfileUtilities(rc.getContext(), null, new TestProfileKnowledgeProvider(rc.getContext())));
         
     
     Resource source;

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

@@ -558,5 +558,12 @@ public class VersionUtilities {
     return version != null && (version.startsWith("4.") || version.startsWith("5.") || "current".equals(version));
   }
 
+  public static boolean refersTo(String refVer, String v) {
+    if (v.length() > refVer.length()) {
+      v = v.substring(0, refVer.length());
+    }
+    return refVer.equals(v);
+  }
+
 
 }