Merge pull request #915 from hapifhir/gg-202209-r5-ballot

Gg 202209 r5 ballot

org.hl7.fhir.r4b/.classpath

@@ -19,7 +19,7 @@
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
@@ -29,5 +29,22 @@
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="src" path="target/generated-sources/annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="ignore_optional_problems" value="true"/>
+			<attribute name="m2e-apt" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="target/generated-test-sources/test-annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="ignore_optional_problems" value="true"/>
+			<attribute name="m2e-apt" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

org.hl7.fhir.r4b/.project

@@ -20,4 +20,15 @@
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 	</natures>
+	<filteredResources>
+		<filter>
+			<id>1662504185037</id>
+			<name></name>
+			<type>30</type>
+			<matcher>
+				<id>org.eclipse.core.resources.regexFilterMatcher</id>
+				<arguments>node_modules|.git|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>
+			</matcher>
+		</filter>
+	</filteredResources>
 </projectDescription>

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/renderers/ConceptMapRenderer.java

@@ -59,7 +59,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
       p.addText(Utilities.capitalize(cm.getStatus().toString())+" (not intended for production usage). ");
     else
       p.addText(Utilities.capitalize(cm.getStatus().toString())+". ");
-    p.tx("Published on "+(cm.hasDate() ? cm.getDateElement().toHumanDisplay() : "?ngen-10?")+" by "+cm.getPublisher());
+    p.tx("Published on "+(cm.hasDate() ? display(cm.getDateElement()) : "?ngen-10?")+" by "+cm.getPublisher());
     if (!cm.getContact().isEmpty()) {
       p.tx(" (");
       boolean firsti = true;
@@ -129,14 +129,28 @@ public class ConceptMapRenderer extends TerminologyRenderer {
         XhtmlNode tr = tbl.tr();
         tr.td().b().tx("Source Code");
         tr.td().b().tx("Relationship");
-        tr.td().b().tx("Destination Code");
+        tr.td().b().tx("Target Code");
         if (comment)
           tr.td().b().tx("Comment");
+        tr = tbl.tr();
+        XhtmlNode td = tr.td().colspan(comment ? "4" : "3");
+        td.tx("Mapping from ");
+        if (grp.hasSource()) {
+          renderCanonical(cm, td, grp.getSource());
+        } else {
+          td.code("unspecified code system");
+        }
+        td.tx(" to ");
+        if (grp.hasTarget()) {
+          renderCanonical(cm, td, grp.getTarget());
+        } else {
+          td.code("unspecified code system");
+        }
         for (SourceElementComponent ccl : grp.getElement()) {
           tr = tbl.tr();
-          XhtmlNode td = tr.td();
+          td = tr.td();
           td.addText(ccl.getCode());
-          display = getDisplayForConcept(systemFromCanonical(grp.getSource()), versionFromCanonical(grp.getSource()), ccl.getCode());
+          display = ccl.hasDisplay() ? ccl.getDisplay() : getDisplayForConcept(systemFromCanonical(grp.getSource()), versionFromCanonical(grp.getSource()), ccl.getCode());
           if (display != null && !isSameCodeAndDisplay(ccl.getCode(), display))
             td.tx(" ("+display+")");
           TargetElementComponent ccm = ccl.getTarget().get(0);
@@ -148,7 +162,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
           }
           td = tr.td();
           td.addText(ccm.getCode());
-          display = getDisplayForConcept(systemFromCanonical(grp.getTarget()), versionFromCanonical(grp.getTarget()), ccm.getCode());
+          display = ccm.hasDisplay() ? ccm.getDisplay() : getDisplayForConcept(systemFromCanonical(grp.getTarget()), versionFromCanonical(grp.getTarget()), ccm.getCode());
           if (display != null && !isSameCodeAndDisplay(ccm.getCode(), display))
             td.tx(" ("+display+")");
           if (comment)
@@ -174,7 +188,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
         if (hasRelationships) {
           tr.td().b().tx("Relationship");
         }
-        tr.td().colspan(Integer.toString(1+targets.size())).b().tx("Destination Concept Details");
+        tr.td().colspan(Integer.toString(1+targets.size())).b().tx("Target Concept Details");
         if (comment) {
           tr.td().b().tx("Comment");
         }
@@ -403,7 +417,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
     for (OtherElementComponent c : list) {
       if (s.equals(c.getProperty()))
         if (withSystem)
-          return c.getSystem()+" / "+c.getValue();
+          return /*c.getSystem()+" / "+*/c.getValue();
         else
           return c.getValue();
     }
@@ -412,8 +426,9 @@ public class ConceptMapRenderer extends TerminologyRenderer {
 
   private String getDisplay(List<OtherElementComponent> list, String s) {
     for (OtherElementComponent c : list) {
-      if (s.equals(c.getProperty()))
+      if (s.equals(c.getProperty())) {
-        return getDisplayForConcept(systemFromCanonical(c.getSystem()), versionFromCanonical(c.getSystem()), c.getValue());
+        // return getDisplayForConcept(systemFromCanonical(c.getSystem()), versionFromCanonical(c.getSystem()), c.getValue());
+      }
     }
     return null;
   }

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/renderers/QuestionnaireRenderer.java

@@ -713,7 +713,7 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
       XhtmlNode ans = item(ul, "Answers");
       if (!Utilities.noString(i.getAnswerValueSet()) && i.getAnswerValueSet().startsWith("#")) {
         ValueSet vs = (ValueSet) q.getContained(i.getAnswerValueSet().substring(1));
-        if (vs == null) {
+        if (vs == null || !vs.hasUserData("path")) {
           ans.tx(i.getAnswerValueSet());                    
         } else {
           ans.ah(vs.getUserString("path")).tx(vs.present());                              

org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/NarrativeGenerationTests.java

@@ -8,16 +8,21 @@ import java.util.stream.Stream;
 
 import javax.xml.parsers.ParserConfigurationException;
 
+import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.SystemUtils;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.r4b.conformance.ProfileUtilities;
+import org.hl7.fhir.r4b.conformance.ProfileUtilities.ProfileKnowledgeProvider;
 import org.hl7.fhir.r4b.context.IWorkerContext;
 import org.hl7.fhir.r4b.elementmodel.Manager;
 import org.hl7.fhir.r4b.elementmodel.Manager.FhirFormat;
 import org.hl7.fhir.r4b.formats.JsonParser;
 import org.hl7.fhir.r4b.formats.XmlParser;
 import org.hl7.fhir.r4b.model.Base;
+import org.hl7.fhir.r4b.model.ElementDefinition.ElementDefinitionBindingComponent;
 import org.hl7.fhir.r4b.model.Resource;
+import org.hl7.fhir.r4b.model.StructureDefinition;
 import org.hl7.fhir.r4b.renderers.RendererFactory;
 
 import org.hl7.fhir.r4b.renderers.utils.ElementWrappers;
@@ -28,6 +33,7 @@ import org.hl7.fhir.r4b.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;
@@ -42,6 +48,64 @@ 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
@@ -98,15 +162,7 @@ public class NarrativeGenerationTests {
     List<Arguments> objects = new ArrayList<>();
     while (test != null && test.getNodeName().equals("test")) {
       TestDetails t = new TestDetails(test);
-      if (t.getId().equals("sdc")) {
-        if (SystemUtils.OS_NAME.contains(WINDOWS)) {
       objects.add(Arguments.of(t.getId(), t));
-        } else {
-          System.out.println("sdc test not being adding because the current OS will not pass the test...");
-        }
-      } else {
-        objects.add(Arguments.of(t.getId(), t));
-      }
       test = XMLUtil.getNextSibling(test);
     }
     return objects.stream();
@@ -121,7 +177,7 @@ 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());
@@ -135,6 +191,7 @@ public class NarrativeGenerationTests {
     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;
@@ -145,7 +202,7 @@ public class NarrativeGenerationTests {
     }
     
     XhtmlNode x = RendererFactory.factory(source, rc).build(source);
-    String target = TextFile.streamToString(TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".html"));
+    String target = TextFile.streamToString(TestingUtilities.loadTestResourceStream("r4b", "narrative", test.getId() + ".html"));
     String output = HEADER+new XhtmlComposer(true, true).compose(x)+FOOTER;
     String tfn = TestingUtilities.tempFile("narrative", test.getId() + ".target.html");
     String ofn = TestingUtilities.tempFile("narrative", test.getId() + ".output.html");
@@ -155,7 +212,7 @@ public class NarrativeGenerationTests {
     Assertions.assertTrue(msg == null, "Output does not match expected: "+msg);
     
     if (test.isMeta()) {
-      org.hl7.fhir.r4b.elementmodel.Element e = Manager.parseSingle(context, TestingUtilities.loadTestResourceStream("r5", "narrative", test.getId() + ".xml"), FhirFormat.XML); 
+      org.hl7.fhir.r4b.elementmodel.Element e = Manager.parseSingle(context, TestingUtilities.loadTestResourceStream("r4b", "narrative", test.getId() + ".xml"), FhirFormat.XML); 
       x = RendererFactory.factory(source, rc).render(new ElementWrappers.ResourceWrapperMetaElement(rc, e));
 
       target = TextFile.streamToString(TestingUtilities.loadTestResourceStream("r4b", "narrative", test.getId() + "-meta.html"));

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java

@@ -310,12 +310,13 @@ public class XmlParser extends ParserBase {
             while (n.getNextSibling() != null && n.getNodeType() != Node.ELEMENT_NODE) {
               n = n.getNextSibling();
             }
-            while (n.getPreviousSibling() != null && n.getNodeType() != Node.ELEMENT_NODE) {
+            Node nt = n;
-              n = n.getPreviousSibling();
+            while (nt.getPreviousSibling() != null && nt.getNodeType() != Node.ELEMENT_NODE) {
+              nt = nt.getPreviousSibling();
             }
-            line = line(n);
+            line = line(nt);
-            col = col(n);
+            col = col(nt);
-            logError(line, col, path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.TEXT_SHOULD_NOT_BE_PRESENT, text), IssueSeverity.ERROR);
+            logError(line, col, path, IssueType.STRUCTURE, context.formatMessage(I18nConstants.TEXT_SHOULD_NOT_BE_PRESENT, Utilities.makeSingleLine(text)), IssueSeverity.ERROR);
           }
           n = n.getNextSibling();
         }

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

@@ -35,11 +35,12 @@ public class OperationDefinitionRenderer extends TerminologyRenderer {
   }
 
   public boolean render(XhtmlNode x, OperationDefinition opd) throws IOException, FHIRException, EOperationOutcome {
+    if (context.isHeader()) {
       x.h2().addText(opd.getName());
       x.para().addText(Utilities.capitalize(opd.getKind().toString())+": "+opd.getName());    
       x.para().tx("The official URL for this operation definition is: ");
       x.pre().tx(opd.getUrl());
-    addMarkdown(x, opd.getDescription());
+      addMarkdown(x, opd.getDescription());}
 
     if (opd.getSystem())
       x.para().tx("URL: [base]/$"+opd.getCode());

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

@@ -123,11 +123,13 @@ public class QuestionnaireBuilder {
   // we don't do the intensive parts of the work (save time)
   private Questionnaire prebuiltQuestionnaire;
   private ProfileUtilities profileUtilities;
+  private String rootPath;
 
-  public QuestionnaireBuilder(IWorkerContext context) {
+  public QuestionnaireBuilder(IWorkerContext context, String rootPath) {
     super();
     this.context = context;
     profileUtilities = new ProfileUtilities(context, null, null); 
+    this.rootPath = rootPath;
   }
 
   public Resource getReference() {
@@ -235,7 +237,8 @@ public class QuestionnaireBuilder {
       questionnaire.addItem(item);
       item.setLinkId("meta");
       item.getCode().addAll(profile.getKeyword());
-      questionnaire.setId(nextId("qs-"+profile.getType()));
+      questionnaire.setId(nextId("qgen-"+profile.getId()));
+      questionnaire.setUrl(Utilities.pathURL(rootPath, "Questionnaire", questionnaire.getId()));
     }
 
     if (response != null) {

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

@@ -15,7 +15,7 @@ public class QuestionnaireBuilderTester {
 //	private static final String TEST_DEST = Utilities.path("[tmp]", "questionnaires\\");
 
 	public static void main(String[] args) {
-		QuestionnaireBuilder b = new QuestionnaireBuilder(null);
+		QuestionnaireBuilder b = new QuestionnaireBuilder(null, "http://hl7.org/fhir/test");
 		for (String f : new File(TEST_PROFILE_DIR).list()) {
 			if (f.endsWith(".profile.xml") && !f.contains("type-")) {
 				System.out.println("process "+f);

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

@@ -1745,4 +1745,13 @@ public class Utilities {
     return Utilities.padLeft(Long.toString(i), ' ', len);
   }
 
+  public static Object makeSingleLine(String text) {
+    text = text.replace("\r", " ");
+    text = text.replace("\n", " ");
+    while (text.contains("  ")) {
+      text = text.replace("  ", " ");
+    }
+    return text;
+  }
+
 }

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/all-systems.cache

@@ -1551,3 +1551,11 @@ v: {
   "system" : "urn:ietf:bcp:47"
 }
 -------------------------------------------------------------------------------------
+{"code" : {
+  "code" : "[%payloadFormat%]"
+}, "url": "http://hl7.org/fhir/ValueSet/mimetypes", "version": "4.0.1", "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"true", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
+v: {
+  "severity" : "error",
+  "error" : "The code \"[%payloadFormat%]\" is not valid in the system urn:ietf:bcp:13; The code provided (urn:ietf:bcp:13#[%payloadFormat%]) is not valid in the value set 'Mime Types' (from http://tx.fhir.org/r4)"
+}
+-------------------------------------------------------------------------------------

pom.xml

@@ -19,7 +19,7 @@
 
     <properties>
         <hapi_fhir_version>5.4.0</hapi_fhir_version>
-        <validator_test_case_version>v1.1.105</validator_test_case_version>
+        <validator_test_case_version>1.1.106-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>