Merge pull request #1379 from hapifhir/2023-08-gg-terminology-status

warnings for status on terminology resources

RELEASE_NOTES.md

@@ -2,8 +2,11 @@
 
 * Fix invalid integer detection
 * Improved invariant checking
+* Create warnings for status on terminology resources
 
 ## Other code changes
 
 * Update obligation handling code for split definitions
 * Update ICF importer to handle grouping levels
+* fix up copy directory for case differences
+

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

@@ -1490,6 +1490,8 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
     String system = null;
     String code = null;
     String version = null;
+    List<OperationOutcomeIssueComponent> issues = new ArrayList<>();
+
     TerminologyServiceErrorClass err = TerminologyServiceErrorClass.UNKNOWN;
     for (ParametersParameterComponent p : pOut.getParameter()) {
       if (p.hasValue()) {
@@ -1506,7 +1508,19 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
         } else if (p.getName().equals("code")) {
           code = ((PrimitiveType<?>) p.getValue()).asStringValue();
         } else if (p.getName().equals("x-caused-by-unknown-system")) {
-          err = TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED;         
+          err = TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED;
+        } else if (p.getName().equals("warning-withdrawn")) {
+          OperationOutcomeIssueComponent iss = new OperationOutcomeIssueComponent(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.INFORMATION, org.hl7.fhir.r5.model.OperationOutcome.IssueType.EXPIRED);
+          iss.getDetails().setText(formatMessage(I18nConstants.MSG_WITHDRAWN, ((PrimitiveType<?>) p.getValue()).asStringValue()));              
+          issues.add(iss);
+        } else if (p.getName().equals("warning-deprecated")) {
+          OperationOutcomeIssueComponent iss = new OperationOutcomeIssueComponent(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.INFORMATION, org.hl7.fhir.r5.model.OperationOutcome.IssueType.EXPIRED);
+          iss.getDetails().setText(formatMessage(I18nConstants.MSG_DEPRECATED, ((PrimitiveType<?>) p.getValue()).asStringValue()));              
+          issues.add(iss);
+        } else if (p.getName().equals("warning-retired")) {
+          OperationOutcomeIssueComponent iss = new OperationOutcomeIssueComponent(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.INFORMATION, org.hl7.fhir.r5.model.OperationOutcome.IssueType.EXPIRED);
+          iss.getDetails().setText(formatMessage(I18nConstants.MSG_RETIRED, ((PrimitiveType<?>) p.getValue()).asStringValue()));              
+          issues.add(iss);
         } else if (p.getName().equals("cause")) {
           try {
             IssueType it = IssueType.fromCode(((StringType) p.getValue()).getValue());
@@ -1524,15 +1538,18 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
         }
       }
     }
+    ValidationResult res = null;
     if (!ok) {
-      return new ValidationResult(IssueSeverity.ERROR, message+" (from "+tcc.getClient().getId()+")", err, null).setTxLink(txLog.getLastId());
+      res = new ValidationResult(IssueSeverity.ERROR, message+" (from "+tcc.getClient().getId()+")", err, null).setTxLink(txLog.getLastId());
     } else if (message != null && !message.equals("No Message returned")) { 
-      return new ValidationResult(IssueSeverity.WARNING, message+" (from "+tcc.getClient().getId()+")", system, version, new ConceptDefinitionComponent().setDisplay(display).setCode(code), display, null).setTxLink(txLog.getLastId());
+      res = new ValidationResult(IssueSeverity.WARNING, message+" (from "+tcc.getClient().getId()+")", system, version, new ConceptDefinitionComponent().setDisplay(display).setCode(code), display, null).setTxLink(txLog.getLastId());
     } else if (display != null) {
-      return new ValidationResult(system, version, new ConceptDefinitionComponent().setDisplay(display).setCode(code), display).setTxLink(txLog.getLastId());
+      res = new ValidationResult(system, version, new ConceptDefinitionComponent().setDisplay(display).setCode(code), display).setTxLink(txLog.getLastId());
     } else {
-      return new ValidationResult(system, version, new ConceptDefinitionComponent().setCode(code), null).setTxLink(txLog.getLastId());
+      res = new ValidationResult(system, version, new ConceptDefinitionComponent().setCode(code), null).setTxLink(txLog.getLastId());
     }
+    res.setIssues(issues );
+    return res;
   }
 
   // --------------------------------------------------------------------------------------------------------------------------------------------------------

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

@@ -124,7 +124,7 @@ public interface IWorkerContext {
     private List<OperationOutcomeIssueComponent> issues = new ArrayList<>();
     private CodeableConcept codeableConcept;
     private Set<String> unknownSystems;
-
+    
     @Override
     public String toString() {
       return "ValidationResult [definition=" + definition + ", system=" + system + ", severity=" + severity + ", message=" + message + ", errorClass="
@@ -315,6 +315,14 @@ public interface IWorkerContext {
       }
     }
 
+    public void setIssues(List<OperationOutcomeIssueComponent> issues) {
+      if (this.issues != null) {
+        issues.addAll(this.issues);
+      }
+      this.issues = issues;
+      
+    }
+
   }
 
   public class CodingValidationRequest {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Parameters.java

@@ -1753,6 +1753,14 @@ public String toString() {
         return true;
     }
     return false;
+  } 
+
+  public boolean hasParameterValue(String name, String value) {
+    for (ParametersParameterComponent p : getParameter()) {
+      if (p.getName().equals(name) && p.hasValue() && value.equals(p.getValue().primitiveValue()))
+        return true;
+    }
+    return false;
   }
 
   public boolean hasParameter(String name) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ValueSet.java

@@ -2839,12 +2839,24 @@ public class ValueSet extends MetadataResource {
           , total, offset, parameter, property, contains);
       }
 
-  public String fhirType() {
+      public boolean hasParameterValue(String name, String value) {
-    return "ValueSet.expansion";
+        for (ValueSetExpansionParameterComponent p : getParameter()) {
+          if (name.equals(p.getName()) && p.hasValue() && value.equals(p.getValue().primitiveValue())) {
+            return true;
+          }
+        }
+        return false;
+      }
 
-  }
+      public void addParameter(String name, DataType value) {
+        getParameter().add(new ValueSetExpansionParameterComponent(name).setValue(value));
+      }
+      
+      public String fhirType() {
+        return "ValueSet.expansion";
+      }
 
-  }
+    }
 
     @Block()
     public static class ValueSetExpansionParameterComponent extends BackboneElement implements IBaseBackboneElement {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/expansion/ValueSetExpander.java

@@ -124,7 +124,6 @@ public class ValueSetExpander extends ValueSetProcessBase {
 
   private static final boolean REPORT_VERSION_ANYWAY = true;
   
-  private IWorkerContext context;
   private ValueSet focus;
   private List<String> allErrors = new ArrayList<>();
   private List<String> requiredSupplements = new ArrayList<>();
@@ -151,9 +150,9 @@ public class ValueSetExpander extends ValueSetProcessBase {
   
   private ValueSetExpansionContainsComponent addCode(WorkingContext wc, String system, String code, String display, String dispLang, ValueSetExpansionContainsComponent parent, List<ConceptDefinitionDesignationComponent> designations, Parameters expParams, 
       boolean isAbstract, boolean inactive, String definition, List<ValueSet> filters, boolean noInactive, boolean deprecated, List<ValueSetExpansionPropertyComponent> vsProp, 
-      List<ConceptPropertyComponent> csProps, List<org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent> expProps, List<Extension> csExtList, List<Extension> vsExtList) throws ETooCostly {
+      List<ConceptPropertyComponent> csProps, List<org.hl7.fhir.r5.model.ValueSet.ConceptPropertyComponent> expProps, List<Extension> csExtList, List<Extension> vsExtList, ValueSetExpansionComponent exp) throws ETooCostly {
  
-    if (filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code))
+    if (filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code, exp))
       return null;
     if (noInactive && inactive) {
       return null;
@@ -285,10 +284,12 @@ public class ValueSetExpander extends ValueSetProcessBase {
     return n;
   }
 
-  private boolean filterContainsCode(List<ValueSet> filters, String system, String code) {
+  private boolean filterContainsCode(List<ValueSet> filters, String system, String code, ValueSetExpansionComponent exp) {
-    for (ValueSet vse : filters)
+    for (ValueSet vse : filters) {
+      checkCanonical(exp, vse);
       if (expansionContainsCode(vse.getExpansion().getContains(), system, code))
         return true;
+    }
     return false;
   }
 
@@ -312,18 +313,18 @@ public class ValueSetExpander extends ValueSetProcessBase {
     return null;
   }
 
-  private void addCodeAndDescendents(WorkingContext wc, ValueSetExpansionContainsComponent focus, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc)  throws FHIRException, ETooCostly {
+  private void addCodeAndDescendents(WorkingContext wc, ValueSetExpansionContainsComponent focus, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp)  throws FHIRException, ETooCostly {
     focus.checkNoModifiers("Expansion.contains", "expanding");
     ValueSetExpansionContainsComponent np = null;
     for (String code : getCodesForConcept(focus, expParams)) {
       ValueSetExpansionContainsComponent t = addCode(wc, focus.getSystem(), code, focus.getDisplay(), vsSrc.getLanguage(), parent, 
-           convert(focus.getDesignation()), expParams, focus.getAbstract(), focus.getInactive(), focus.getExtensionString(ToolingExtensions.EXT_DEFINITION), filters, noInactive, false, vsProps, null, focus.getProperty(), null, focus.getExtension());
+           convert(focus.getDesignation()), expParams, focus.getAbstract(), focus.getInactive(), focus.getExtensionString(ToolingExtensions.EXT_DEFINITION), filters, noInactive, false, vsProps, null, focus.getProperty(), null, focus.getExtension(), exp);
       if (np == null) {
         np = t;
       }
     }
     for (ValueSetExpansionContainsComponent c : focus.getContains())
-      addCodeAndDescendents(wc, c, np, expParams, filters, noInactive, vsProps, vsSrc);
+      addCodeAndDescendents(wc, c, np, expParams, filters, noInactive, vsProps, vsSrc, exp);
   }
   
   private List<String> getCodesForConcept(ValueSetExpansionContainsComponent focus, Parameters expParams) {
@@ -349,8 +350,8 @@ public class ValueSetExpander extends ValueSetProcessBase {
     return list;
   }
 
-  private void addCodeAndDescendents(WorkingContext wc,CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, 
+  private void addCodeAndDescendents(WorkingContext wc, CodeSystem cs, String system, ConceptDefinitionComponent def, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters, 
-        ConceptDefinitionComponent exclusion, ConceptFilter filterFunc, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, List<WorkingContext> otherFilters)  throws FHIRException, ETooCostly {
+        ConceptDefinitionComponent exclusion, ConceptFilter filterFunc, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, List<WorkingContext> otherFilters, ValueSetExpansionComponent exp)  throws FHIRException, ETooCostly {
     def.checkNoModifiers("Code in Code System", "expanding");
     if (exclusion != null) {
       if (exclusion.getCode().equals(def.getCode()))
@@ -362,19 +363,19 @@ public class ValueSetExpander extends ValueSetProcessBase {
     boolean dep = CodeSystemUtilities.isDeprecated(cs, def, false);
     if ((includeAbstract || !abs)  && filterFunc.includeConcept(cs, def) && passesOtherFilters(otherFilters, cs, def.getCode())) {
       for (String code : getCodesForConcept(def, expParams)) {
-        ValueSetExpansionContainsComponent t = addCode(wc, system, code, def.getDisplay(), cs.getLanguage(), parent, def.getDesignation(), expParams, abs, inc, def.getDefinition(), filters, noInactive, dep, vsProps, def.getProperty(), null, def.getExtension(), null);
+        ValueSetExpansionContainsComponent t = addCode(wc, system, code, def.getDisplay(), cs.getLanguage(), parent, def.getDesignation(), expParams, abs, inc, def.getDefinition(), filters, noInactive, dep, vsProps, def.getProperty(), null, def.getExtension(), null, exp);
         if (np == null) {
           np = t;
         }
       }
     }
     for (ConceptDefinitionComponent c : def.getConcept()) {
-      addCodeAndDescendents(wc, cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive, vsProps, otherFilters);
+      addCodeAndDescendents(wc, cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive, vsProps, otherFilters, exp);
     }
     if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
       List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
       for (ConceptDefinitionComponent c : children)
-        addCodeAndDescendents(wc, cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive, vsProps, otherFilters);
+        addCodeAndDescendents(wc, cs, system, c, np, expParams, filters, exclusion, filterFunc, noInactive, vsProps, otherFilters, exp);
     }
   }
 
@@ -401,7 +402,7 @@ public class ValueSetExpander extends ValueSetProcessBase {
 
   
 
-  private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params, Parameters expParams, List<ValueSet> filters, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc) throws ETooCostly, FHIRException {
+  private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params, Parameters expParams, List<ValueSet> filters, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp) throws ETooCostly, FHIRException {
     if (expand != null) {
       if (expand.getContains().size() > maxExpansionSize)
         throw failCostly(context.formatMessage(I18nConstants.VALUESET_TOO_COSTLY, vsSrc.getUrl(), ">" + Integer.toString(expand.getContains().size())));
@@ -410,7 +411,7 @@ public class ValueSetExpander extends ValueSetProcessBase {
           params.add(p);
       }
 
-      copyImportContains(expand.getContains(), null, expParams, filters, noInactive, vsProps, vsSrc);
+      copyImportContains(expand.getContains(), null, expParams, filters, noInactive, vsProps, vsSrc, exp);
     }
   }
 
@@ -450,8 +451,6 @@ public class ValueSetExpander extends ValueSetProcessBase {
       throw fail("not done yet - multiple filters");
   }
 
-
-
   private void excludeCodes(WorkingContext wc, ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params) {
     for (ValueSetExpansionContainsComponent c : expand.getContains()) {
       excludeCode(wc, c.getSystem(), c.getCode());
@@ -460,8 +459,9 @@ public class ValueSetExpander extends ValueSetProcessBase {
 
   private boolean existsInParams(List<ValueSetExpansionParameterComponent> params, String name, DataType value) {
     for (ValueSetExpansionParameterComponent p : params) {
-      if (p.getName().equals(name) && PrimitiveType.compareDeep(p.getValue(), value, false))
+      if (p.getName().equals(name) && PrimitiveType.compareDeep(p.getValue(), value, false)) {
         return true;
+      }
     }
     return false;
   }
@@ -503,6 +503,7 @@ public class ValueSetExpander extends ValueSetProcessBase {
     focus.setExpansion(new ValueSet.ValueSetExpansionComponent());
     focus.getExpansion().setTimestampElement(DateTimeType.now());
     focus.getExpansion().setIdentifier(Factory.createUUID()); 
+    checkCanonical(focus.getExpansion(), focus);
     for (ParametersParameterComponent p : expParams.getParameter()) {
       if (Utilities.existsInList(p.getName(), "includeDesignations", "excludeNested", "activeOnly", "offset", "count")) {
         focus.getExpansion().addParameter().setName(p.getName()).setValue(p.getValue());
@@ -642,6 +643,7 @@ public class ValueSetExpander extends ValueSetProcessBase {
         throw fail("Unable to find imported value set " + value);
       }
     }
+    checkCanonical(exp, vs);
     if (noInactive) {
       expParams = expParams.copy();
       expParams.addParameter("activeOnly", true);
@@ -714,12 +716,12 @@ public class ValueSetExpander extends ValueSetProcessBase {
     }
   }
 
-  private void copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filter, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc) throws FHIRException, ETooCostly {
+  private void copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filter, boolean noInactive, List<ValueSetExpansionPropertyComponent> vsProps, ValueSet vsSrc, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly {
     for (ValueSetExpansionContainsComponent c : list) {
       c.checkNoModifiers("Imported Expansion in Code System", "expanding");
       ValueSetExpansionContainsComponent np = addCode(dwc, c.getSystem(), c.getCode(), c.getDisplay(), vsSrc.getLanguage(), parent, null, expParams, c.getAbstract(), c.getInactive(), c.getExtensionString(ToolingExtensions.EXT_DEFINITION), 
-          filter, noInactive, false, vsProps, null, c.getProperty(), null, c.getExtension());
+          filter, noInactive, false, vsProps, null, c.getProperty(), null, c.getExtension(), exp);
-      copyImportContains(c.getContains(), np, expParams, filter, noInactive, vsProps, vsSrc);
+      copyImportContains(c.getContains(), np, expParams, filter, noInactive, vsProps, vsSrc, exp);
     }
   }
 
@@ -734,9 +736,10 @@ public class ValueSetExpander extends ValueSetProcessBase {
       if (imports.isEmpty()) // though this is not supposed to be the case
         return;
       ValueSet base = imports.get(0);
+      checkCanonical(exp, base);
       imports.remove(0);
       base.checkNoModifiers("Imported ValueSet", "expanding");
-      copyImportContains(base.getExpansion().getContains(), null, expParams, imports, noInactive, base.getExpansion().getProperty(), base);
+      copyImportContains(base.getExpansion().getContains(), null, expParams, imports, noInactive, base.getExpansion().getProperty(), base, exp);
     } else {
       CodeSystem cs = context.fetchSupplementedCodeSystem(inc.getSystem());
       if (ValueSetUtilities.isServerSide(inc.getSystem()) || (cs == null || (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT))) {
@@ -783,7 +786,7 @@ public class ValueSetExpander extends ValueSetProcessBase {
       }
     }
     for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) {
-      addCodeAndDescendents(dwc, cc, null, expParams, imports, noInactive, vsProps, vs);
+      addCodeAndDescendents(dwc, cc, null, expParams, imports, noInactive, vsProps, vs, exp);
     }
   }
 
@@ -795,6 +798,7 @@ public class ValueSetExpander extends ValueSetProcessBase {
       else
         throw failTSE("Unable to find code system " + inc.getSystem().toString());
     }
+    checkCanonical(exp, cs);
     cs.checkNoModifiers("Code System", "expanding");
     if (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT)
       throw failTSE("Code system " + inc.getSystem().toString() + " is incomplete");
@@ -813,7 +817,7 @@ public class ValueSetExpander extends ValueSetProcessBase {
     if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
       // special case - add all the code system
       for (ConceptDefinitionComponent def : cs.getConcept()) {
-        addCodeAndDescendents(dwc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), null);
+        addCodeAndDescendents(dwc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), null, exp);
       }
       if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
         addFragmentWarning(exp, cs);
@@ -846,7 +850,7 @@ public class ValueSetExpander extends ValueSetProcessBase {
           isAbstract = CodeSystemUtilities.isNotSelectable(cs, def);
         }
         addCode(dwc, inc.getSystem(), c.getCode(), !Utilities.noString(c.getDisplay()) ? c.getDisplay() : def == null ? null : def.getDisplay(), c.hasDisplay() ? vsSrc.getLanguage() : cs.getLanguage(), null, mergeDesignations(def, convertDesignations(c.getDesignation())), 
-            expParams, isAbstract, inactive, def == null ? null : def.getDefinition(), imports, noInactive, false, exp.getProperty(), def != null ? def.getProperty() : null, null, def == null ? null : def.getExtension(), c.getExtension());
+            expParams, isAbstract, inactive, def == null ? null : def.getDefinition(), imports, noInactive, false, exp.getProperty(), def != null ? def.getProperty() : null, null, def == null ? null : def.getExtension(), c.getExtension(), exp);
       }
     }
     if (inc.getFilter().size() > 0) {
@@ -876,14 +880,14 @@ public class ValueSetExpander extends ValueSetProcessBase {
       ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
       if (def == null)
         throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
-      addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters);
+      addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
     } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISNOTA) {
       // special: all codes in the target code system that are not under the value
       ConceptDefinitionComponent defEx = getConceptForCode(cs.getConcept(), fc.getValue());
       if (defEx == null)
         throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
       for (ConceptDefinitionComponent def : cs.getConcept()) {
-        addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters);
+        addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
       }
     } else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
       // special: all codes in the target code system under the value
@@ -891,11 +895,11 @@ public class ValueSetExpander extends ValueSetProcessBase {
       if (def == null)
         throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
       for (ConceptDefinitionComponent c : def.getConcept())
-        addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters);
+        addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
       if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
         List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
         for (ConceptDefinitionComponent c : children)
-          addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters);
+          addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
       }
 
     } else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
@@ -907,18 +911,18 @@ public class ValueSetExpander extends ValueSetProcessBase {
           if (def.getDisplay().contains(fc.getValue()) && passesOtherFilters(filters, cs, def.getCode())) {
             for (String code : getCodesForConcept(def, expParams)) {
               ValueSetExpansionContainsComponent t = addCode(wc, inc.getSystem(), code, def.getDisplay(), cs.getLanguage(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def),
-                  def.getDefinition(), imports, noInactive, false, exp.getProperty(), def.getProperty(), null, def.getExtension(), null);
+                  def.getDefinition(), imports, noInactive, false, exp.getProperty(), def.getProperty(), null, def.getExtension(), null, exp);
             }
           }
         }
       }
     } else if (isDefinedProperty(cs, fc.getProperty())) {
       for (ConceptDefinitionComponent def : cs.getConcept()) {
-        addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(allErrors, fc, getPropertyDefinition(cs, fc.getProperty())), noInactive, exp.getProperty(), filters);
+        addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(allErrors, fc, getPropertyDefinition(cs, fc.getProperty())), noInactive, exp.getProperty(), filters, exp);
       }
     } else if ("code".equals(fc.getProperty()) && fc.getOp() == FilterOperator.REGEX) {
       for (ConceptDefinitionComponent def : cs.getConcept()) {
-        addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new RegexFilter(allErrors, fc.getValue()), noInactive, exp.getProperty(), filters);
+        addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new RegexFilter(allErrors, fc.getValue()), noInactive, exp.getProperty(), filters, exp);
       }
     } else {
       throw fail("Filter by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/utilities/ValueSetProcessBase.java

@@ -1,20 +1,31 @@
 package org.hl7.fhir.r5.terminologies.utilities;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
 
+import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.model.BooleanType;
+import org.hl7.fhir.r5.model.CanonicalResource;
+import org.hl7.fhir.r5.model.DataType;
+import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.r5.model.OperationOutcome.IssueType;
+import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
 import org.hl7.fhir.r5.model.Extension;
 import org.hl7.fhir.r5.model.Parameters;
-import org.hl7.fhir.r5.model.ValueSet;
-import org.hl7.fhir.r5.model.BooleanType;
-import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent;
-import org.hl7.fhir.r5.model.DataType;
 import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
-import org.hl7.fhir.r5.model.PrimitiveType;
+import org.hl7.fhir.r5.model.UriType;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
+import org.hl7.fhir.utilities.StandardsStatus;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.i18n.I18nConstants;
+import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 
 public class ValueSetProcessBase {
 
+  protected IWorkerContext context;
+  
   public static class AlternateCodesProcessingRules {
     private boolean all;
     private List<String> uses = new ArrayList<>();
@@ -77,6 +88,88 @@ public class ValueSetProcessBase {
     }
   }
 
+
+  protected List<OperationOutcomeIssueComponent> makeIssue(IssueSeverity level, IssueType type, String location, String message) {
+    OperationOutcomeIssueComponent result = new OperationOutcomeIssueComponent();
+    switch (level) {
+    case ERROR:
+      result.setSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.ERROR);
+      break;
+    case FATAL:
+      result.setSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.FATAL);
+      break;
+    case INFORMATION:
+      result.setSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.INFORMATION);
+      break;
+    case WARNING:
+      result.setSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.WARNING);
+      break;
+    }
+    result.setCode(type);
+    result.addLocation(location);
+    result.getDetails().setText(message);
+    ArrayList<OperationOutcomeIssueComponent> list = new ArrayList<>();
+    list.add(result);
+    return list;
+  }
+  
+  public void checkCanonical(List<OperationOutcomeIssueComponent> issues, String path, CanonicalResource resource) {
+    if (resource != null) {
+      StandardsStatus standardsStatus = ToolingExtensions.getStandardsStatus(resource);
+      if (standardsStatus == StandardsStatus.DEPRECATED) {
+        addToIssues(issues, makeStatusIssue(path, "deprecated", I18nConstants.MSG_DEPRECATED, resource));
+      } else if (standardsStatus == StandardsStatus.WITHDRAWN) {
+        addToIssues(issues, makeStatusIssue(path, "withdrawn", I18nConstants.MSG_WITHDRAWN, resource));
+      } else if (resource.getStatus() == PublicationStatus.RETIRED) {
+        addToIssues(issues, makeStatusIssue(path, "retired", I18nConstants.MSG_RETIRED, resource));
+      }
+    }
+  }
+
+  private List<OperationOutcomeIssueComponent> makeStatusIssue(String path, String id, String msg, CanonicalResource resource) {
+    List<OperationOutcomeIssueComponent> iss = makeIssue(IssueSeverity.INFORMATION, IssueType.EXPIRED, path, context.formatMessage(msg, resource.getVersionedUrl()));
+
+    // this is a testing hack - see TerminologyServiceTests
+    iss.get(0).setUserData("status-msg-name", "warning-"+id);
+    iss.get(0).setUserData("status-msg-value", new UriType(resource.getVersionedUrl()));
+    
+    return iss;
+  }
+  
+  private void addToIssues(List<OperationOutcomeIssueComponent> issues, List<OperationOutcomeIssueComponent> toAdd) {
+    for (OperationOutcomeIssueComponent t : toAdd) {
+      boolean found = false;
+      for (OperationOutcomeIssueComponent i : issues) {
+        if (i.getSeverity() == t.getSeverity() && i.getCode() == t.getCode() && i.getDetails().getText().equals(t.getDetails().getText())) { // ignore location
+          found = true;
+        }
+      }
+      if (!found) {
+        issues.add(t);
+      }
+    }    
+  }
+
+  public void checkCanonical(ValueSetExpansionComponent params, CanonicalResource resource) {
+    if (resource != null) {
+      StandardsStatus standardsStatus = ToolingExtensions.getStandardsStatus(resource);
+      if (standardsStatus == StandardsStatus.DEPRECATED) {
+        if (!params.hasParameterValue("warning-deprecated", resource.getVersionedUrl())) {
+          params.addParameter("warning-deprecated", new UriType(resource.getVersionedUrl()));
+        } 
+      } else if (standardsStatus == StandardsStatus.WITHDRAWN) {
+        if (!params.hasParameterValue("warning-withdrawn", resource.getVersionedUrl())) {
+          params.addParameter("warning-withdrawn", new UriType(resource.getVersionedUrl()));
+        } 
+      } else if (resource.getStatus() == PublicationStatus.RETIRED) {
+        if (!params.hasParameterValue("warning-retired", resource.getVersionedUrl())) {
+          params.addParameter("warning-retired", new UriType(resource.getVersionedUrl()));
+        } 
+      }
+    }
+  }
+            
+                         
   protected AlternateCodesProcessingRules altCodeParams = new AlternateCodesProcessingRules(false);
   protected AlternateCodesProcessingRules allAltCodes = new AlternateCodesProcessingRules(true);
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/validation/ValueSetValidator.java

@@ -97,7 +97,6 @@ import com.google.j2objc.annotations.ReflectionSupport.Level;
 public class ValueSetValidator extends ValueSetProcessBase {
 
   private ValueSet valueset;
-  private IWorkerContext context;
   private Map<String, ValueSetValidator> inner = new HashMap<>();
   private ValidationOptions options;
   private ValidationContextCarrier localContext;
@@ -229,7 +228,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
       
       for (Coding c : code.getCoding()) {
         b.append(c.getSystem()+(c.hasVersion() ? "|"+c.getVersion() : "")+"#"+c.getCode());
-        Boolean ok = codeInValueSet(c.getSystem(), c.getVersion(), c.getCode(), info);
+        Boolean ok = codeInValueSet(path, c.getSystem(), c.getVersion(), c.getCode(), info);
         if (ok == null && result != null && result == false) {
           result = null;
         } else if (ok != null && ok) {
@@ -338,30 +337,6 @@ public class ValueSetValidator extends ValueSetProcessBase {
     return versionTest == null && VersionUtilities.versionsMatch(versionTest, versionActual);
   }
 
-  private List<OperationOutcomeIssueComponent> makeIssue(IssueSeverity level, IssueType type, String location, String message) {
-    OperationOutcomeIssueComponent result = new OperationOutcomeIssueComponent();
-    switch (level) {
-    case ERROR:
-      result.setSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.ERROR);
-      break;
-    case FATAL:
-      result.setSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.FATAL);
-      break;
-    case INFORMATION:
-      result.setSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.INFORMATION);
-      break;
-    case WARNING:
-      result.setSeverity(org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity.WARNING);
-      break;
-    }
-    result.setCode(type);
-    result.addLocation(location);
-    result.getDetails().setText(message);
-    ArrayList<OperationOutcomeIssueComponent> list = new ArrayList<>();
-    list.add(result);
-    return list;
-  }
-  
   public ValidationResult validateCode(Coding code) throws FHIRException {
     return validateCode("Coding", code); 
   }
@@ -375,6 +350,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
     boolean inInclude = false;
     List<OperationOutcomeIssueComponent> issues = new ArrayList<>();
     VersionInfo vi = new VersionInfo(this);
+    checkCanonical(issues, path, valueset);
 
     String system = code.hasSystem() ? code.getSystem() : getValueSetSystemOrNull();
     if (options.getValueSetMode() != ValueSetMode.CHECK_MEMERSHIP_ONLY) {
@@ -434,6 +410,8 @@ public class ValueSetValidator extends ValueSetProcessBase {
             }
           }
         }
+      } else {
+        checkCanonical(issues, path, cs);
       }
       if (cs != null && cs.hasSupplements()) {
         String msg = context.formatMessage(I18nConstants.CODESYSTEM_CS_NO_SUPPLEMENT, cs.getUrl());
@@ -462,6 +440,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
           throw new FHIRException("Unable to evaluate based on empty code system");
         }
         res = validateCode(path, code, cs, null);
+        res.setIssues(issues);
       } else if (cs == null && valueset.hasExpansion() && inExpansion) {
         // we just take the value set as face value then
         res = new ValidationResult(system, wv, new ConceptDefinitionComponent().setCode(code.getCode()).setDisplay(code.getDisplay()), code.getDisplay());
@@ -486,7 +465,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
     // then, if we have a value set, we check it's in the value set
     if (valueset != null && options.getValueSetMode() != ValueSetMode.NO_MEMBERSHIP_CHECK) {
       if ((res==null || res.isOk())) { 
-        Boolean ok = codeInValueSet(system, wv, code.getCode(), info);
+        Boolean ok = codeInValueSet(path, system, wv, code.getCode(), info);
         if (ok == null || !ok) {
           if (res == null) {
             res = new ValidationResult((IssueSeverity) null, null, info.getIssues());
@@ -982,14 +961,11 @@ public class ValueSetValidator extends ValueSetProcessBase {
     return true;
   }
   
-  public Boolean codeInValueSet(String system, String version, String code, ValidationProcessInfo info) throws FHIRException {
-    return codeInValueSet("code", system, version, code, info);
-  }
-  
   public Boolean codeInValueSet(String path, String system, String version, String code, ValidationProcessInfo info) throws FHIRException {
     if (valueset == null) {
       return false;
     }
+    checkCanonical(info.getIssues(), path, valueset);
     Boolean result = false;
     VersionInfo vi = new VersionInfo(this);
       
@@ -1029,15 +1005,15 @@ public class ValueSetValidator extends ValueSetProcessBase {
       if (isValueSetUnionImports()) {
         ok = false;
         for (UriType uri : vsi.getValueSet()) {
-          if (inImport(uri.getValue(), system, version, code)) {
+          if (inImport(path, uri.getValue(), system, version, code, info)) {
             return true;
           }
         }
       } else {
-        ok = inImport(vsi.getValueSet().get(0).getValue(), system, version, code);
+        ok = inImport(path, vsi.getValueSet().get(0).getValue(), system, version, code, info);
         for (int i = 1; i < vsi.getValueSet().size(); i++) {
           UriType uri = vsi.getValueSet().get(i);
-          ok = ok && inImport(uri.getValue(), system, version, code); 
+          ok = ok && inImport(path, uri.getValue(), system, version, code, info); 
         }
       }
     }
@@ -1097,6 +1073,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
         return null;
       }
     } else {
+      checkCanonical(info.getIssues(), path, cs);
       if (vsi.hasFilter()) {
         ok = true;
         for (ConceptSetFilterComponent f : vsi.getFilter()) {
@@ -1231,12 +1208,12 @@ public class ValueSetValidator extends ValueSetProcessBase {
     return vsc;
   }
 
-  private boolean inImport(String uri, String system, String version, String code) throws FHIRException {
+  private boolean inImport(String path, String uri, String system, String version, String code, ValidationProcessInfo info) throws FHIRException {
     ValueSetValidator vs = getVs(uri);
     if (vs == null) {
       return false;
     } else {
-      Boolean ok = vs.codeInValueSet(system, version, code, null);
+      Boolean ok = vs.codeInValueSet(path, system, version, code, info);
       return ok != null && ok;
     }
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/CompareUtilities.java

@@ -45,7 +45,7 @@ public class CompareUtilities extends BaseTestingUtilities {
     String result = compareXml(expected, actual);
     if (result != null && SHOW_DIFF) {
       String diff = getDiffTool();
-      if (new File(diff).exists() || Utilities.isToken(diff)) {
+      if (diff != null && new File(diff).exists() || Utilities.isToken(diff)) {
         Runtime.getRuntime().exec(new String[]{diff, expected, actual});
       }
     }

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

@@ -65,8 +65,9 @@ public class CSFile extends File {
     //attempt to open a file triggers a directory listing
     if (exists()) 
     {
-    	if(!this.getCanonicalFile().getName().equals(this.getName()))
+    	if(!this.getCanonicalFile().getName().equals(this.getName())) {
     		throw new Error("Case mismatch of file "+ pathname+": found "+this.getCanonicalFile().getName());
+    	}
     }
   }
 

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

@@ -35,7 +35,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 
 public enum StandardsStatus {
 
-  EXTERNAL, INFORMATIVE, DRAFT, TRIAL_USE, DEPRECATED, NORMATIVE;
+  EXTERNAL, INFORMATIVE, DRAFT, TRIAL_USE, DEPRECATED, NORMATIVE, WITHDRAWN;
 
   public String toDisplay() {
     switch (this) {
@@ -51,6 +51,8 @@ public enum StandardsStatus {
       return "External";
     case DEPRECATED: 
       return "Deprecated";
+    case WITHDRAWN: 
+      return "Withdrawn";
     }
     return "?";
   }
@@ -66,9 +68,11 @@ public enum StandardsStatus {
     case INFORMATIVE:
       return "informative";
     case DEPRECATED: 
-    return "deprecated";
+      return "deprecated";
     case EXTERNAL:
       return "external";
+    case WITHDRAWN: 
+      return "Withdrawn";
     }
     return "?";
   }
@@ -93,6 +97,8 @@ public enum StandardsStatus {
       return EXTERNAL;
     if (value.equalsIgnoreCase("DEPRECATED"))
       return DEPRECATED;
+    if (value.equalsIgnoreCase("WITHDRAWN"))
+      return WITHDRAWN;
     throw new FHIRException("Incorrect Standards Status '"+value+"'");
   }
 
@@ -110,6 +116,8 @@ public enum StandardsStatus {
       return "XD";
     case EXTERNAL:
       return "X";
+    case WITHDRAWN:
+      return "W";
     }
     return "?";
   }
@@ -125,6 +133,7 @@ public enum StandardsStatus {
     case INFORMATIVE:
       return "#ffffe6";
     case DEPRECATED: 
+    case WITHDRAWN: 
       return "#ffcccc";
     case EXTERNAL:
       return "#e6ffff";
@@ -143,6 +152,7 @@ public enum StandardsStatus {
     case INFORMATIVE:
       return "#ffffec";
     case DEPRECATED: 
+    case WITHDRAWN:
       return "#ffcccc";
     case EXTERNAL:
       return "#ecffff";
@@ -159,6 +169,8 @@ public enum StandardsStatus {
       return (tgtSS == NORMATIVE || tgtSS == EXTERNAL );
     if (this == DEPRECATED)
       return (tgtSS == DEPRECATED );
+    if (this == WITHDRAWN)
+      return (tgtSS == WITHDRAWN );
     return false;
   }
 

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

@@ -307,7 +307,18 @@ public class Utilities {
     CSFile src = new CSFile(sourceFolder);
     if (!src.exists())
       throw new FHIRException("Folder " + sourceFolder + " not found");
-    createDirectory(destFolder);
+    File dst = new File(destFolder);
+    if(!dst.getCanonicalFile().getName().equals(dst.getName())) {
+      File tmp = new File(destFolder+System.currentTimeMillis());
+      if (!dst.renameTo(tmp)) {
+        throw new IOException("fixing case from "+dst.getCanonicalFile().getName()+" to "+tmp.getName()+" failed");
+      }
+      if (!tmp.renameTo(dst)) {
+        throw new IOException("fixing case from "+tmp.getCanonicalFile().getName()+" to "+dst.getName()+" failed");
+      }
+    } else if (!dst.exists()) {    
+      createDirectory(destFolder);
+    }
 
     String[] files = src.list();
     for (String f : files) {
@@ -318,7 +329,7 @@ public class Utilities {
       } else {
         if (notifier != null)
           notifier.copyFile(sourceFolder + File.separator + f, destFolder + File.separator + f);
-        copyFile(new CSFile(sourceFolder + File.separator + f), new CSFile(destFolder + File.separator + f));
+        copyFile(new CSFile(sourceFolder + File.separator + f), new /*CS*/File(destFolder + File.separator + f)); // case doesn't have to match on the target
       }
     }
   }
@@ -358,6 +369,10 @@ public class Utilities {
         createDirectory(destFile.getParent());
       }
       destFile.createNewFile();
+    } else if (!destFile.getCanonicalFile().getName().equals(destFile.getName())) {
+      // case mismatch
+      destFile.delete();
+      destFile.createNewFile();
     }
 
     FileInputStream source = null;

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

@@ -950,6 +950,9 @@ public class I18nConstants {
   public static final String FHIRPATH_OFTYPE_IMPOSSIBLE = "FHIRPATH_OFTYPE_IMPOSSIBLE";
   public static final String ED_SEARCH_EXPRESSION_ERROR = "ED_SEARCH_EXPRESSION_ERROR";
   public static final String SD_EXTENSION_URL_MISMATCH = "SD_EXTENSION_URL_MISMATCH";
+  public static final String MSG_DEPRECATED = "MSG_DEPRECATED";
+  public static final String MSG_WITHDRAWN = "MSG_WITHDRAWN";
+  public static final String MSG_RETIRED = "MSG_RETIRED";
 
 
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java

@@ -1266,6 +1266,11 @@ public class NpmPackage {
     return Utilities.existsInList(npm.asString("type"), "fhir.core", "Core");
   }
 
+  public boolean isCoreExamples() {
+    return name().startsWith("hl7.fhir.r") && name().endsWith(".examples");
+  }
+  
+  
   public boolean isTx() {
     return npm.asString("name").startsWith("hl7.terminology");
   }
@@ -1369,5 +1374,5 @@ public class NpmPackage {
   public void setSize(int size) {
     this.size = size;
   }
-  
+
 }

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

@@ -1005,4 +1005,7 @@ FHIRPATH_COLLECTION_STATUS_OPERATION_LEFT = The left side is inherently a collec
 FHIRPATH_COLLECTION_STATUS_OPERATION_RIGHT = The right side is inherently a collection, and so this expression ''{0}'' may fail or return false if there is more than one item in the content being evaluated
 FHIRPATH_OFTYPE_IMPOSSIBLE = The type specified in ofType is {1} which is not a possible candidate for the existing types ({0}) in the expression {2}. Check the paths and types to be sure this is what is intended
 ED_SEARCH_EXPRESSION_ERROR = Error in search expression ''{0}'': {1}
-SD_EXTENSION_URL_MISMATCH = The fixed value for the extension URL is {1} which doesn''t match the canonical URL {0}
+SD_EXTENSION_URL_MISMATCH = The fixed value for the extension URL is {1} which doesn''t match the canonical URL {0}
+MSG_DEPRECATED = Reference to deprecated item {0}
+MSG_WITHDRAWN = Reference to withdrawn item {0}
+MSG_RETIRED = Reference to retired item {0}

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/UtilitiesTest.java

@@ -422,5 +422,46 @@ class UtilitiesTest {
     Assertions.assertFalse("\u0009\n\u000B\u000C\r\u0020\u0085\u00A0\u1680\u2000\u2001\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200A\u2028\u2029\u202F\u205F\u3000".matches(".+"));
     Assertions.assertFalse("\u0009\n\u000B\u000C\r\u0020\u0085\u00A0\u1680\u2000\u2001\u2002\u2003\u2004\u2005\u2006\u2007\u2008\u2009\u200A\u2028\u2029\u202F\u205F\u3000".matches("^.+$"));
   }
-  
+
+  @Test
+  @DisplayName("directory copy case tests")
+  void testFDirectoryCopy() throws IOException {
+    String src = Utilities.path("[tmp]", "test", "copy-source");
+    String dst = Utilities.path("[tmp]", "test", "copy-dest");
+    makeDir (src);
+    makeFile(Utilities.path(src, "Test.txt"), "source1");
+    makeDir (Utilities.path(src, "SUB"));
+    makeFile(Utilities.path(src, "SUB", "TEST.txt"), "source2");
+
+    makeDir (dst);
+    makeFile(Utilities.path(dst, "test.txt"), "dest1");
+    makeDir (Utilities.path(dst, "sub"));
+    makeFile(Utilities.path(dst, "sub", "test.txt"), "dest2");
+    
+    Utilities.copyDirectory(src, dst, null);
+    
+    checkDir (dst);
+    checkFile(Utilities.path(dst, "Test.txt"), "source1");
+    checkDir (Utilities.path(dst, "SUB"));
+    checkFile(Utilities.path(dst, "SUB", "TEST.txt"), "source2");
+  }
+
+  private void checkFile(String path, String content) throws IOException {
+    Assertions.assertTrue(new CSFile(path).exists());
+    Assertions.assertEquals(content, TextFile.fileToString(path));
+  }
+
+  private void checkDir(String path) throws IOException {
+    Assertions.assertTrue(new CSFile(path).exists());
+  }
+
+  private void makeFile(String path, String content) throws IOException {
+    TextFile.stringToFile(content, path);
+  }
+
+  private void makeDir(String path) throws IOException {
+    Utilities.createDirectory(path);
+    Utilities.clearDirectory(path);
+  }
 }
+

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/IgLoader.java

@@ -520,12 +520,14 @@ public class IgLoader implements IValidationEngineLoader {
       }
     }
 
-    if (loadInContext) {
+    if (!pi.isCoreExamples()) {
-//      getContext().getLoadedPackages().add(pi.name() + "#" + pi.version());
+      if (loadInContext) {
-      getContext().loadFromPackage(pi, ValidatorUtils.loaderForVersion(pi.fhirVersion()));
+        //      getContext().getLoadedPackages().add(pi.name() + "#" + pi.version());
-    }
+        getContext().loadFromPackage(pi, ValidatorUtils.loaderForVersion(pi.fhirVersion()));
-    for (String s : pi.listResources("CodeSystem", "ConceptMap", "ImplementationGuide", "CapabilityStatement", "SearchParameter", "Conformance", "StructureMap", "ValueSet", "StructureDefinition")) {
+      }
-      res.put(s, TextFile.streamToBytes(pi.load("package", s)));
+      for (String s : pi.listResources("CodeSystem", "ConceptMap", "ImplementationGuide", "CapabilityStatement", "SearchParameter", "Conformance", "StructureMap", "ValueSet", "StructureDefinition")) {
+        res.put(s, TextFile.streamToBytes(pi.load("package", s)));
+      }
     }
     String ini = "[FHIR]\r\nversion=" + pi.fhirVersion() + "\r\n";
     res.put("version.info", ini.getBytes());

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxTesterSorters.java

@@ -3,7 +3,11 @@ package org.hl7.fhir.validation.special;
 import java.util.Collections;
 import java.util.Comparator;
 
+import org.hl7.fhir.ParametersParameter;
+import org.hl7.fhir.r5.model.Base;
 import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.OperationOutcome;
+import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
 import org.hl7.fhir.r5.model.Parameters;
 import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
 import org.hl7.fhir.r5.model.ValueSet;
@@ -16,8 +20,14 @@ import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionPropertyComponent;
 public class TxTesterSorters {
 
 
+
   public static void sortParameters(Parameters po) {
     Collections.sort(po.getParameter(), new TxTesterSorters.ParameterSorter());
+    for (ParametersParameterComponent p : po.getParameter()) {
+      if (p.getResource() != null && p.getResource() instanceof OperationOutcome) {
+        Collections.sort(((OperationOutcome) p.getResource()).getIssue(), new TxTesterSorters.OperationIssueSorter());
+      }
+    }
   }
   
 
@@ -43,7 +53,24 @@ public class TxTesterSorters {
   }
 
   
-  
+
+  public static class OperationIssueSorter implements Comparator<OperationOutcomeIssueComponent> {
+
+    @Override
+    public int compare(OperationOutcomeIssueComponent o1, OperationOutcomeIssueComponent o2) {
+      if (o1.hasSeverity() && o2.hasSeverity() && o1.getSeverity() != o2.getSeverity()) {
+        return o1.getSeverity().compareTo(o2.getSeverity());
+      }
+      if (o1.hasCode() && o2.hasCode() && o1.getCode() != o2.getCode()) {
+        return o1.getCode().compareTo(o2.getCode());
+      }
+      if (o1.getDetails().hasText() && o2.getDetails().hasText() && !o1.getDetails().getText().equals(o2.getDetails().getText())) {
+        return o1.getDetails().getText().compareTo(o2.getDetails().getText());
+      }
+      return 0;
+    }
+  }
+
   public static class DesignationSorter implements Comparator<ConceptReferenceDesignationComponent> {
 
     @Override