Merge pull request #287 from hapifhir/gg-work-202007

more fixes

RELEASE_NOTES.md

@@ -0,0 +1,4 @@
+* Batch validation of codes in value sets 
+* Fix path problem doing comparisons
+* Don't produce 2 columns for status for deprecated codes
+* Fix errors in StructureDefinition validation

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR2.java

@@ -35,8 +35,10 @@ import java.net.URISyntaxException;
 import java.util.Map;
 
 import org.hl7.fhir.convertors.VersionConvertor_10_50;
+import org.hl7.fhir.convertors.VersionConvertor_40_50;
 import org.hl7.fhir.dstu2.utils.client.FHIRToolingClient;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CapabilityStatement;
 import org.hl7.fhir.r5.model.Parameters;
 import org.hl7.fhir.r5.model.TerminologyCapabilities;
@@ -117,5 +119,10 @@ public class TerminologyClientR2 implements TerminologyClient {
     return client.getRetryCount();
   }
    
+  @Override
+  public Bundle validateBatch(Bundle batch) {
+    return (Bundle) VersionConvertor_10_50.convertResource(client.transaction((org.hl7.fhir.dstu2.model.Bundle) VersionConvertor_10_50.convertResource(batch)));
+  }
+
 
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java

@@ -35,8 +35,10 @@ import java.net.URISyntaxException;
 import java.util.Map;
 
 import org.hl7.fhir.convertors.VersionConvertor_30_50;
+import org.hl7.fhir.convertors.VersionConvertor_40_50;
 import org.hl7.fhir.dstu3.utils.client.FHIRToolingClient;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CapabilityStatement;
 import org.hl7.fhir.r5.model.Parameters;
 import org.hl7.fhir.r5.model.TerminologyCapabilities;
@@ -117,4 +119,10 @@ public class TerminologyClientR3 implements TerminologyClient {
     return client.getRetryCount();
   }
  
+  @Override
+  public Bundle validateBatch(Bundle batch) {
+    return (Bundle) VersionConvertor_30_50.convertResource(client.transaction((org.hl7.fhir.dstu3.model.Bundle) VersionConvertor_30_50.convertResource(batch, false)), false);
+  }
+
+
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR4.java

@@ -38,6 +38,7 @@ import org.hl7.fhir.convertors.VersionConvertor_40_50;
 import org.hl7.fhir.convertors.conv40_50.TerminologyCapabilities40_50;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
+import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CapabilityStatement;
 import org.hl7.fhir.r5.model.Parameters;
 import org.hl7.fhir.r5.model.TerminologyCapabilities;
@@ -118,4 +119,9 @@ public class TerminologyClientR4 implements TerminologyClient {
     return client.getRetryCount();
   }
  
+  @Override
+  public Bundle validateBatch(Bundle batch) {
+    return (Bundle) VersionConvertor_40_50.convertResource(client.transaction((org.hl7.fhir.r4.model.Bundle) VersionConvertor_40_50.convertResource(batch)));
+  }
+
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR5.java

@@ -35,6 +35,7 @@ import java.net.URISyntaxException;
 import java.util.Map;
 
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CapabilityStatement;
 import org.hl7.fhir.r5.model.CodeSystem;
 import org.hl7.fhir.r5.model.Parameters;
@@ -110,4 +111,9 @@ public class TerminologyClientR5 implements TerminologyClient {
     return client.getRetryCount();
   }
 
+  @Override
+  public Bundle validateBatch(Bundle batch) {
+    return client.transaction(batch);
+  }
+
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ComparisonRenderer.java

@@ -146,8 +146,8 @@ public class ComparisonRenderer implements IEvaluationContext {
     vars.put("concepts", new StringType(new XhtmlComposer(true).compose(cs.renderConcepts(comp, "", ""))));
     String cnt = processTemplate(template, "CodeSystem", vars);
     TextFile.stringToFile(cnt, file(comp.getId()+".html"));
-    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-union.json")), comp.getUnion());
-    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-intersection.json")), comp.getIntersection());
   }
 
   private String file(String name) throws IOException {
@@ -170,8 +170,8 @@ public class ComparisonRenderer implements IEvaluationContext {
     vars.put("expansion", new StringType(new XhtmlComposer(true).compose(cs.renderExpansion(comp, "", ""))));
     String cnt = processTemplate(template, "ValueSet", vars);
     TextFile.stringToFile(cnt, file(comp.getId()+".html"));
-    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-union.json")), comp.getUnion());
-    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-intersection.json")), comp.getIntersection());
   }
 
   private void renderProfile(String id, ProfileComparison comp) throws IOException {
@@ -189,8 +189,8 @@ public class ComparisonRenderer implements IEvaluationContext {
     vars.put("structure", new StringType(new XhtmlComposer(true).compose(cs.renderStructure(comp, "", "", "http://hl7.org/fhir"))));
     String cnt = processTemplate(template, "CodeSystem", vars);
     TextFile.stringToFile(cnt, file(comp.getId()+".html"));
-    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-union.json")), comp.getUnion());
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-union.json")), comp.getUnion());
-    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, "comparison", comp.getId() + "-intersection.json")), comp.getIntersection());
+    new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-intersection.json")), comp.getIntersection());
   }
 
   private String processTemplate(String template, String name, Map<String, Base> vars) {

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

@@ -2596,7 +2596,7 @@ public class ProfileUtilities extends TranslatingUtilities {
       if (derived.hasIsSummaryElement()) {
         if (!Base.compareDeep(derived.getIsSummaryElement(), base.getIsSummaryElement(), false)) {
           if (base.hasIsSummary() && !context.getVersion().equals("1.4.0")) // work around a known issue with some 1.4.0 cosntraints
-            throw new Error(context.formatMessage(I18nConstants.ERROR_IN_PROFILE__AT__BASE_ISSUMMARY___DERIVED_ISSUMMARY__, pn, derived.getPath(), base.getIsSummaryElement().asStringValue(), derived.getIsSummaryElement().asStringValue()));
+            throw new Error(context.formatMessage(I18nConstants.ERROR_IN_PROFILE__AT__BASE_ISSUMMARY___DERIVED_ISSUMMARY__, purl, derived.getPath(), base.getIsSummaryElement().asStringValue(), derived.getIsSummaryElement().asStringValue()));
           base.setIsSummaryElement(derived.getIsSummaryElement().copy());
         } else if (trimDifferential)
           derived.setIsSummaryElement(null);

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

@@ -55,6 +55,7 @@ import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
 import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory;
 import org.hl7.fhir.r5.context.TerminologyCache.CacheToken;
 import org.hl7.fhir.r5.model.BooleanType;
+import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.r5.model.CapabilityStatement;
 import org.hl7.fhir.r5.model.CodeSystem;
@@ -74,6 +75,7 @@ import org.hl7.fhir.r5.model.NamingSystem;
 import org.hl7.fhir.r5.model.NamingSystem.NamingSystemIdentifierType;
 import org.hl7.fhir.r5.model.NamingSystem.NamingSystemUniqueIdComponent;
 import org.hl7.fhir.r5.model.OperationDefinition;
+import org.hl7.fhir.r5.model.OperationOutcome;
 import org.hl7.fhir.r5.model.Parameters;
 import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
 import org.hl7.fhir.r5.model.PlanDefinition;
@@ -88,8 +90,12 @@ import org.hl7.fhir.r5.model.StructureMap;
 import org.hl7.fhir.r5.model.TerminologyCapabilities;
 import org.hl7.fhir.r5.model.TerminologyCapabilities.TerminologyCapabilitiesCodeSystemComponent;
 import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r5.model.Bundle.BundleType;
+import org.hl7.fhir.r5.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent;
+import org.hl7.fhir.r5.renderers.OperationOutcomeRenderer;
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
 import org.hl7.fhir.r5.terminologies.TerminologyClient;
 import org.hl7.fhir.r5.terminologies.ValueSetCheckerSimple;
@@ -111,6 +117,8 @@ import org.hl7.fhir.utilities.validation.ValidationOptions.ValueSetMode;
 
 import com.google.gson.JsonObject;
 
+import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
+
 public abstract class BaseWorkerContext extends I18nBase implements IWorkerContext{
 
   public class MetadataResourceVersionComparator<T extends CanonicalResource> implements Comparator<T> {
@@ -685,10 +693,103 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     return validateCode(options.guessSystem(), c, vs);
   }
 
+
+  @Override
+  public void validateCodeBatch(ValidationOptions options, List<? extends CodingValidationRequest> codes, ValueSet vs) {
+    if (options == null) {
+      options = ValidationOptions.defaults();
+    }
+    // 1st pass: what is in the cache? 
+    // 2nd pass: What can we do internally 
+    // 3rd pass: hit the server
+    for (CodingValidationRequest t : codes) {
+      t.setCacheToken(txCache != null ? txCache.generateValidationToken(options, t.getCoding(), vs) : null);
+      if (txCache != null) { 
+        t.setResult(txCache.getValidation(t.getCacheToken()));
+      }
+    }
+    if (options.isUseClient()) {
+      for (CodingValidationRequest t : codes) {
+        if (!t.hasResult()) {
+          try {
+            ValueSetCheckerSimple vsc = new ValueSetCheckerSimple(options, vs, this); 
+            ValidationResult res = vsc.validateCode(t.getCoding());
+            if (txCache != null)
+              txCache.cacheValidation(t.getCacheToken(), res, TerminologyCache.TRANSIENT);
+            t.setResult(res);
+          } catch (Exception e) {
+          }
+        }
+      }      
+    }  
+
+    for (CodingValidationRequest t : codes) {
+      if (!t.hasResult()) {
+        if (!options.isUseServer()) {
+         t.setResult(new ValidationResult(IssueSeverity.WARNING,formatMessage(I18nConstants.UNABLE_TO_VALIDATE_CODE_WITHOUT_USING_SERVER), TerminologyServiceErrorClass.BLOCKED_BY_OPTIONS));
+        } else if (unsupportedCodeSystems.contains(t.getCoding().getSystem())) {
+          t.setResult(new ValidationResult(IssueSeverity.ERROR,formatMessage(I18nConstants.TERMINOLOGY_TX_SYSTEM_NOTKNOWN, t.getCoding().getSystem()), TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED));      
+        } else if (noTerminologyServer) {
+          t.setResult(new ValidationResult(IssueSeverity.ERROR,formatMessage(I18nConstants.ERROR_VALIDATING_CODE_RUNNING_WITHOUT_TERMINOLOGY_SERVICES), TerminologyServiceErrorClass.NOSERVICE));
+        }
+      }
+    }
+    
+    if (expParameters == null)
+      throw new Error(formatMessage(I18nConstants.NO_EXPANSIONPROFILE_PROVIDED));
+    // for those that that failed, we try to validate on the server
+    Bundle batch = new Bundle();
+    batch.setType(BundleType.BATCH);
+    Set<String> systems = new HashSet<>();
+    for (CodingValidationRequest t : codes) {
+      if (!t.hasResult()) {
+        Parameters pIn = new Parameters();
+        pIn.addParameter().setName("coding").setValue(t.getCoding());
+        if (options.isGuessSystem())
+          pIn.addParameter().setName("implySystem").setValue(new BooleanType(true));
+        if (vs != null) {
+          pIn.addParameter().setName("valueSet").setResource(vs);
+        }
+        pIn.addParameter().setName("profile").setResource(expParameters);
+        setTerminologyOptions(options, pIn);
+        BundleEntryComponent be = batch.addEntry();
+        be.setResource(pIn);
+        be.getRequest().setMethod(HTTPVerb.POST);
+        be.getRequest().setUrl("ValueSet/$validate-code");
+        be.setUserData("source", t);
+        systems.add(t.getCoding().getSystem());
+      }
+    }
+    if (batch.getEntry().size() > 0) {
+      tlog("$batch validate for "+batch.getEntry().size()+" codes on systems "+systems.toString());
+      if (txClient == null) {
+        throw new FHIRException(formatMessage(I18nConstants.ATTEMPT_TO_USE_TERMINOLOGY_SERVER_WHEN_NO_TERMINOLOGY_SERVER_IS_AVAILABLE));
+      }
+      if (txLog != null) {
+        txLog.clearLastId();
+      }
+      Bundle resp = txClient.validateBatch(batch);
+      for (int i = 0; i < batch.getEntry().size(); i++) {
+        CodingValidationRequest t = (CodingValidationRequest) batch.getEntry().get(i).getUserData("source");
+        BundleEntryComponent r = resp.getEntry().get(i);
+        if (r.getResource() instanceof Parameters) {
+          t.setResult(processValidationResult((Parameters) r.getResource()));
+        } else {
+          t.setResult(new ValidationResult(IssueSeverity.ERROR, getResponseText(r.getResource())).setTxLink(txLog == null ? null : txLog.getLastId()));          
+        }
+      }
+    }    
+  }
+  
+  private String getResponseText(Resource resource) {
+    if (resource instanceof OperationOutcome) {
+      return OperationOutcomeRenderer.toString((OperationOutcome) resource);
+    }
+    return "Todo";
+  }
+
   @Override
   public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs) {
-    assert options != null;
-    
     if (options == null) {
       options = ValidationOptions.defaults();
     }
@@ -813,6 +914,10 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
       pOut = txClient.validateCS(pin);
     else
       pOut = txClient.validateVS(pin);
+    return processValidationResult(pOut);
+  }
+
+  public ValidationResult processValidationResult(Parameters pOut) {
     boolean ok = false;
     String message = "No Message returned";
     String display = null;
@@ -1622,4 +1727,5 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     return txClient;
   }
 
+
 }

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

@@ -44,6 +44,8 @@ import org.fhir.ucum.UcumService;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.TerminologyServiceException;
+import org.hl7.fhir.r5.context.IWorkerContext.CodingValidationRequest;
+import org.hl7.fhir.r5.context.TerminologyCache.CacheToken;
 import org.hl7.fhir.r5.formats.IParser;
 import org.hl7.fhir.r5.formats.ParserType;
 import org.hl7.fhir.r5.model.Bundle;
@@ -93,6 +95,53 @@ import com.google.gson.JsonSyntaxException;
  */
 public interface IWorkerContext {
 
+  public class CodingValidationRequest {
+    private Coding coding;
+    private ValidationResult result;
+    private CacheToken cacheToken;
+    
+    public CodingValidationRequest(Coding coding) {
+      super();
+      this.coding = coding;
+    }
+
+    public ValidationResult getResult() {
+      return result;
+    }
+
+    public void setResult(ValidationResult result) {
+      this.result = result;
+    }
+
+    public Coding getCoding() {
+      return coding;
+    }
+
+    public boolean hasResult() {
+      return result != null;
+    }
+
+    /**
+     * internal logic; external users of batch validation should ignore this property
+     * 
+     * @return
+     */
+    public CacheToken getCacheToken() {
+      return cacheToken;
+    }
+
+    /**
+     * internal logic; external users of batch validation should ignore this property
+     * 
+     * @param cacheToken
+     */
+    public void setCacheToken(CacheToken cacheToken) {
+      this.cacheToken = cacheToken;
+    }
+    
+    
+  }
+
   public class PackageVersion {
     private String id;
     private String version;
@@ -620,6 +669,8 @@ public interface IWorkerContext {
    */
   public ValidationResult validateCode(ValidationOptions options, Coding code, ValueSet vs);
 
+  public void validateCodeBatch(ValidationOptions options, List<? extends CodingValidationRequest> codes, ValueSet vs);
+  
   /**
    * returns the recommended tla for the type  (from the structure definitions)
    * 

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

@@ -138,6 +138,7 @@ public class CodeSystemRenderer extends TerminologyRenderer {
     boolean display = false;
     boolean hierarchy = false;
     boolean version = false;
+    boolean ignoreStatus = false;
     List<PropertyComponent> properties = new ArrayList<>();
     for (PropertyComponent cp : cs.getProperty()) {
       if (showPropertyInTable(cp)) {
@@ -147,12 +148,15 @@ public class CodeSystemRenderer extends TerminologyRenderer {
         }
         if (exists) {
           properties.add(cp);
+          if ("status".equals(cp.getCode())) {
+            ignoreStatus = true;
+          }
         }
       }
     }
     for (ConceptDefinitionComponent c : cs.getConcept()) {
       commentS = commentS || conceptsHaveComments(c);
-      deprecated = deprecated || conceptsHaveDeprecated(cs, c);
+      deprecated = deprecated || conceptsHaveDeprecated(cs, c, ignoreStatus);
       display = display || conceptsHaveDisplay(c);
       version = version || conceptsHaveVersion(c);
       hierarchy = hierarchy || c.hasConcept();
@@ -255,11 +259,11 @@ public class CodeSystemRenderer extends TerminologyRenderer {
     return false;
   }
 
-  private boolean conceptsHaveDeprecated(CodeSystem cs, ConceptDefinitionComponent c) {
+  private boolean conceptsHaveDeprecated(CodeSystem cs, ConceptDefinitionComponent c, boolean ignoreStatus) {
-    if (CodeSystemUtilities.isDeprecated(cs, c))
+    if (CodeSystemUtilities.isDeprecated(cs, c, ignoreStatus))
       return true;
     for (ConceptDefinitionComponent g : c.getConcept())
-      if (conceptsHaveDeprecated(cs, g))
+      if (conceptsHaveDeprecated(cs, g, ignoreStatus))
         return true;
     return false;
   }
@@ -325,7 +329,7 @@ public class CodeSystemRenderer extends TerminologyRenderer {
     }
     if (deprecated) {
       td = tr.td();
-      Boolean b = CodeSystemUtilities.isDeprecated(cs, c);
+      Boolean b = CodeSystemUtilities.isDeprecated(cs, c, false);
       if (b !=  null && b) {
         smartAddText(td, getContext().getWorker().translator().translate("xhtml-gen-cs", "Deprecated", getContext().getLang()));
         hasExtensions = true;

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

@@ -16,6 +16,7 @@ import org.hl7.fhir.r5.model.StringType;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext;
 import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
+import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 
 public class OperationOutcomeRenderer extends ResourceRenderer {
@@ -89,4 +90,11 @@ public class OperationOutcomeRenderer extends ResourceRenderer {
     return display((OperationOutcome) r);
   }
 
+  public static String toString(OperationOutcome oo) {
+    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
+    for (OperationOutcomeIssueComponent issue : oo.getIssue()) {
+      b.append(issue.getSeverity().toCode()+": "+issue.getDetails().getText());
+    }
+    return b.toString();
+  }
 }

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

@@ -270,7 +270,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
     return null;
   }
 
-  private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
+  private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode parent, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
     if (ew == null)
       return;
 
@@ -361,7 +361,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
           } else {
             x.an(rw.getId());
             ResourceRenderer rr = RendererFactory.factory(rw, context.copy().setAddGeneratedNarrativeHeader(false));
-            rr.render(x.blockquote(), rw);
+            rr.render(parent.blockquote(), rw);
           }
         }
       } else {
@@ -598,7 +598,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
 
   private void generateByProfile(ResourceWrapper res, StructureDefinition profile, BaseWrapper e, List<ElementDefinition> allElements, ElementDefinition defn, List<ElementDefinition> children,  XhtmlNode x, String path, boolean showCodeDetails, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
     if (children.isEmpty()) {
-      renderLeaf(res, e, defn, x, false, showCodeDetails, readDisplayHints(defn), path, indent);
+      renderLeaf(res, e, defn, x, x, false, showCodeDetails, readDisplayHints(defn), path, indent);
     } else {
       for (PropertyWrapper p : splitExtensions(profile, e.children())) {
         if (p.hasValues()) {
@@ -626,7 +626,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
                     if (renderAsList(child) && p.getValues().size() > 1) {
                       XhtmlNode list = x.ul();
                       for (BaseWrapper v : p.getValues())
-                        renderLeaf(res, v, child, list.li(), false, showCodeDetails, displayHints, path, indent);
+                        renderLeaf(res, v, child, x, list.li(), false, showCodeDetails, displayHints, path, indent);
                     } else {
                       boolean first = true;
                       for (BaseWrapper v : p.getValues()) {
@@ -634,7 +634,7 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
                           first = false;
                         else
                           para.tx(", ");
-                        renderLeaf(res, v, child, para, false, showCodeDetails, displayHints, path, indent);
+                        renderLeaf(res, v, child, x, para, false, showCodeDetails, displayHints, path, indent);
                       }
                     }
                   }
@@ -730,10 +730,12 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
   private void addColumnValues(ResourceWrapper res, XhtmlNode tr, List<ElementDefinition> grandChildren, BaseWrapper v, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
     for (ElementDefinition e : grandChildren) {
       PropertyWrapper p = v.getChildByName(e.getPath().substring(e.getPath().lastIndexOf(".")+1));
+      XhtmlNode td = tr.td();
       if (p == null || p.getValues().size() == 0 || p.getValues().get(0) == null)
-        tr.td().tx(" ");
+        td.tx(" ");
-      else
+      else {
-        renderLeaf(res, p.getValues().get(0), e, tr.td(), false, showCodeDetails, displayHints, path, indent);
+        renderLeaf(res, p.getValues().get(0), e, td, td, false, showCodeDetails, displayHints, path, indent);
+      }
     }
   }
 

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

@@ -208,11 +208,13 @@ public class CodeSystemUtilities {
     defineCodeSystemProperty(cs, "child", "The concept identified in this property is a child of the concept on which it is a property. The property type will be 'code'. The meaning of parent/child relationships is defined by the hierarchyMeaning attribute", PropertyType.CODE);
   }
 
-  public static boolean isDeprecated(CodeSystem cs, ConceptDefinitionComponent def)  {
+  public static boolean isDeprecated(CodeSystem cs, ConceptDefinitionComponent def, boolean ignoreStatus)  {
     try {
       for (ConceptPropertyComponent p : def.getProperty()) {
+        if (!ignoreStatus) {
           if (p.getCode().equals("status") && p.hasValue() && p.hasValueCodeType() && p.getValueCodeType().getCode().equals("deprecated"))
             return true;
+        }
         // this, though status should also be set
         if (p.getCode().equals("deprecationDate") && p.hasValue() && p.getValue() instanceof DateTimeType) 
           return ((DateTimeType) p.getValue()).before(new DateTimeType(Calendar.getInstance()));

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

@@ -34,6 +34,7 @@ package org.hl7.fhir.r5.terminologies;
 import java.util.Map;
 
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CapabilityStatement;
 import org.hl7.fhir.r5.model.Parameters;
 import org.hl7.fhir.r5.model.TerminologyCapabilities;
@@ -52,4 +53,5 @@ public interface TerminologyClient {
   public TerminologyClient setRetryCount(int retryCount) throws FHIRException;
   public CapabilityStatement getCapabilitiesStatementQuick() throws FHIRException;
   public Parameters lookupCode(Map<String, String> params) throws FHIRException;
+  public Bundle validateBatch(Bundle batch);
 }

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

@@ -402,19 +402,22 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
 
   private boolean inComponent(ConceptSetComponent vsi, String system, String code, boolean only) throws FHIRException {
     for (UriType uri : vsi.getValueSet()) {
-      if (inImport(uri.getValue(), system, code))
+      if (inImport(uri.getValue(), system, code)) {
         return true;
       }
+    }
 
-    if (!vsi.hasSystem())
+    if (!vsi.hasSystem()) {
       return false;
-    
+    }
     if (only && system == null) {
       // whether we know the system or not, we'll accept the stated codes at face value
-      for (ConceptReferenceComponent cc : vsi.getConcept())
+      for (ConceptReferenceComponent cc : vsi.getConcept()) {
-        if (cc.getCode().equals(code)) 
+        if (cc.getCode().equals(code)) {
           return true;
         }
+      }
+    }
     
     if (!system.equals(vsi.getSystem()))
       return false;
@@ -443,14 +446,17 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
       List<ConceptDefinitionComponent> list = cs.getConcept();
       boolean ok = validateCodeInConceptList(code, cs, list);
       if (ok && vsi.hasConcept()) {
-        for (ConceptReferenceComponent cc : vsi.getConcept())
+        for (ConceptReferenceComponent cc : vsi.getConcept()) {
-          if (cc.getCode().equals(code)) 
+          if (cc.getCode().equals(code)) { 
             return true;
+          }
+        }
         return false;
-      } else
+      } else {
         return ok;
       }
     }
+  }
 
   private boolean codeInFilter(CodeSystem cs, String system, ConceptSetFilterComponent f, String code) throws FHIRException {
     if ("concept".equals(f.getProperty()))

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

@@ -293,7 +293,7 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
       if (exclusion.getCode().equals(def.getCode()))
         return; // excluded.
     }
-    if (!CodeSystemUtilities.isDeprecated(cs, def)) {
+    if (!CodeSystemUtilities.isDeprecated(cs, def, false)) {
       ValueSetExpansionContainsComponent np = null;
       boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
       boolean inc = CodeSystemUtilities.isInactive(cs, def);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/FHIRToolingClient.java

@@ -513,7 +513,6 @@ public class FHIRToolingClient {
 	}
 	
 	@SuppressWarnings("unchecked")
-	
 	public <T extends Resource> OperationOutcome validate(Class<T> resourceClass, T resource, String id) {
 		ResourceRequest<T> result = null;
 		try {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java

@@ -333,6 +333,7 @@ public class I18nConstants {
   public static final String RESOURCE_RES_ID_PROHIBITED = "Resource_RES_ID_Prohibited";
   public static final String RESOURCE_TYPE_MISMATCH_FOR___ = "Resource_type_mismatch_for___";
   public static final String SAME_ID_ON_MULTIPLE_ELEMENTS__IN_ = "Same_id_on_multiple_elements__in_";
+  public static final String SD_MUST_HAVE_DERIVATION = "SD_MUST_HAVE_DERIVATION";
   public static final String SEARCHPARAMETER_BASE_WRONG = "SEARCHPARAMETER_BASE_WRONG";
   public static final String SEARCHPARAMETER_EXP_WRONG = "SEARCHPARAMETER_EXP_WRONG";
   public static final String SEARCHPARAMETER_NOTFOUND = "SEARCHPARAMETER_NOTFOUND";

org.hl7.fhir.utilities/src/main/resources/Messages.properties

@@ -570,3 +570,4 @@ XHTML_XHTML_DOCTYPE_ILLEGAL = Malformed XHTML: Found a DocType declaration, and
 PACKAGE_VERSION_MISMATCH = FHIR Version mismatch in package {0}: version is {2} but must be {1} (path: {3})
 VALUESET_REFERENCE_UNKNOWN = The value set import {0} could not be found so cannot be checked
 VALUESET_REFERENCE_INVALID_TYPE = The value set import {0} points to a resource of type {1} which is not valid
+SD_MUST_HAVE_DERIVATION = StructureDefinition {0} must have a derivation, since it has a baseDefinition

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java

@@ -24,6 +24,7 @@ import org.hl7.fhir.r5.model.ElementDefinition;
 import org.hl7.fhir.r5.model.ExpressionNode;
 import org.hl7.fhir.r5.model.ExpressionNode.Kind;
 import org.hl7.fhir.r5.model.ExpressionNode.Operation;
+import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
 import org.hl7.fhir.r5.model.SearchParameter;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.utils.FHIRPathEngine;
@@ -66,6 +67,8 @@ public class StructureDefinitionValidator extends BaseValidator {
       sd.setSnapshot(null);
       StructureDefinition base = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
       if (warning(errors, IssueType.NOTFOUND, stack.getLiteralPath(), base != null, I18nConstants.UNABLE_TO_FIND_BASE__FOR_, sd.getBaseDefinition(), "StructureDefinition, so can't check the differential")) {
+        if (rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), sd.hasDerivation(), I18nConstants.SD_MUST_HAVE_DERIVATION, sd.getUrl())) {
+          if (sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
             List<ValidationMessage> msgs = new ArrayList<>();
             ProfileUtilities pu = new ProfileUtilities(context, msgs, null);
             pu.generateSnapshot(base, sd, sd.getUrl(), "http://hl7.org/fhir", sd.getName());
@@ -81,12 +84,14 @@ public class StructureDefinitionValidator extends BaseValidator {
                 errors.add(msg);
               }
             }
-      }
             if (!snapshot.isEmpty()) {
               int was = snapshot.size();
               int is = sd.getSnapshot().getElement().size();
               rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), was == is, I18nConstants.SNAPSHOT_EXISTING_PROBLEM, was, is);
             }
+          }
+        }
+      }
     } catch (FHIRException | IOException e) {
       rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), false, I18nConstants.ERROR_GENERATING_SNAPSHOT, e.getMessage());
     }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/ValueSetValidator.java

@@ -1,9 +1,11 @@
 package org.hl7.fhir.validation.instance.type;
 
+import java.util.ArrayList;
 import java.util.List;
 
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.context.IWorkerContext.CodingValidationRequest;
 import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
 import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.model.CodeSystem;
@@ -19,10 +21,26 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
 import org.hl7.fhir.utilities.validation.ValidationOptions;
 import org.hl7.fhir.validation.BaseValidator;
 import org.hl7.fhir.validation.TimeTracker;
+import org.hl7.fhir.validation.instance.type.ValueSetValidator.VSCodingValidationRequest;
 import org.hl7.fhir.validation.instance.utils.NodeStack;
 
 public class ValueSetValidator extends BaseValidator {
 
+  public class VSCodingValidationRequest extends CodingValidationRequest {
+
+    private NodeStack stack;
+
+    public VSCodingValidationRequest(NodeStack stack, Coding code) {
+      super(code);
+      this.stack = stack;
+    }
+
+    public NodeStack getStack() {
+      return stack;
+    }
+    
+  }
+
   public ValueSetValidator(IWorkerContext context, TimeTracker timeTracker) {
     super(context);
     source = Source.InstanceValidator;
@@ -58,7 +76,6 @@ public class ValueSetValidator extends BaseValidator {
   private void validateValueSetInclude(List<ValidationMessage> errors, Element include, NodeStack stack) {
     String system = include.getChildValue("system");
     String version = include.getChildValue("version");
-    boolean systemOk = true;
     List<Element> valuesets = include.getChildrenByName("valueSet");
     int i = 0;
     for (Element ve : valuesets) {
@@ -79,13 +96,31 @@ public class ValueSetValidator extends BaseValidator {
     List<Element> concepts = include.getChildrenByName("concept");
     List<Element> filters = include.getChildrenByName("filter");
     if (!Utilities.noString(system)) {
+      boolean systemOk = true;
       int cc = 0;
+      List<VSCodingValidationRequest> batch = new ArrayList<>();
+      boolean first = true;
       for (Element concept : concepts) {
-        if (systemOk && !validateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version)) {
+        // we treat the first differently because we want to know if tbe system is worth validating. if it is, then we batch the rest
-          systemOk = false;
+        if (first) {
+          systemOk = validateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version);
+          first = false;
+        } else if (systemOk) {
+          batch.add(prepareValidateValueSetIncludeConcept(errors, concept, stack.push(concept, cc, null, null), system, version));
         }
         cc++;
       }    
+      if (batch.size() > 0) {
+        context.validateCodeBatch(ValidationOptions.defaults(), batch, null);
+        for (VSCodingValidationRequest cv : batch) {
+          if (version == null) {
+            warning(errors, IssueType.BUSINESSRULE, cv.getStack().getLiteralPath(), cv.getResult().isOk(), I18nConstants.VALUESET_INCLUDE_INVALID_CONCEPT_CODE, system, cv.getCoding().getCode());
+          } else {
+            warning(errors, IssueType.BUSINESSRULE, cv.getStack().getLiteralPath(), cv.getResult().isOk(), I18nConstants.VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER, system, version, cv.getCoding().getCode());
+          }
+        }
+      }
+      
       int cf = 0;
       for (Element filter : filters) {
         if (systemOk && !validateValueSetIncludeFilter(errors, include, stack.push(filter, cf, null, null), system, version)) {
@@ -121,6 +156,15 @@ public class ValueSetValidator extends BaseValidator {
     return true;
   }
 
+  private VSCodingValidationRequest prepareValidateValueSetIncludeConcept(List<ValidationMessage> errors, Element concept, NodeStack stack, String system, String version) {
+    String code = concept.getChildValue("code");
+    Coding c = new Coding(system, code, null);
+    if (version != null) {
+       c.setVersion(version);
+    }
+    return new VSCodingValidationRequest(stack, c);
+  }
+
   private boolean validateValueSetIncludeFilter(List<ValidationMessage> errors, Element include, NodeStack push, String system, String version) {
     return true;
   }

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java

@@ -99,6 +99,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
   private String name;
 
    private static final String DEF_TX = "http://tx.fhir.org";
+//  private static final String DEF_TX = "http://local.fhir.org:960";
   private static Map<String, ValidationEngine> ve = new HashMap<>();
   private static ValidationEngine vCurr;