more revisions to tests

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

@@ -363,9 +363,13 @@ public class CodeSystemUtilities {
   }
   
   public static boolean isInactive(CodeSystem cs, ConceptDefinitionComponent def) throws FHIRException {
+    StandardsStatus ss = ToolingExtensions.getStandardsStatus(def);
+    if (ss == StandardsStatus.DEPRECATED || ss == StandardsStatus.WITHDRAWN) {
+      return true;
+    }
     for (ConceptPropertyComponent p : def.getProperty()) {
       if ("status".equals(p.getCode()) && p.hasValueStringType()) {
-        return "inactive".equals(p.getValueStringType().primitiveValue()) || "retired".equals(p.getValueStringType().primitiveValue());
+        return "inactive".equals(p.getValueStringType().primitiveValue()) || "retired".equals(p.getValueStringType().primitiveValue()) || "deprecated".equals(p.getValueStringType().primitiveValue());
       }
       if ("inactive".equals(p.getCode()) && p.hasValueBooleanType()) {
         return p.getValueBooleanType().getValue();
@@ -886,6 +890,10 @@ public class CodeSystemUtilities {
 
   public static DataType getProperty(CodeSystem cs, String code, String property) {
     ConceptDefinitionComponent def = getCode(cs, code);
+    return getProperty(cs, def, property);
+  }
+  
+  public static DataType getProperty(CodeSystem cs, ConceptDefinitionComponent def, String property) {
     ConceptPropertyComponent cp = getProperty(def, property);
     return cp == null ? null : cp.getValue();
   }
@@ -905,5 +913,18 @@ public class CodeSystemUtilities {
     }
     return false;
   }
+
+  public static String getStatus(CodeSystem cs, ConceptDefinitionComponent cc) {
+    StandardsStatus ss = ToolingExtensions.getStandardsStatus(cc);
+    if (ss == StandardsStatus.DEPRECATED || ss == StandardsStatus.WITHDRAWN) {
+      return ss.toCode();
+    }
+    DataType v = getProperty(cs, cc, "status");
+    if (v == null || !v.isPrimitive()) {
+      return null;
+    } else {
+      return v.primitiveValue();
+    }
+  }
 }
 

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

@@ -13,12 +13,12 @@ import java.util.ArrayList;
 
 public class TerminologyOperationContext {
 
-  public class TerminologyServiceProtectionException extends FHIRException {
+  public static class TerminologyServiceProtectionException extends FHIRException {
 
     private TerminologyServiceErrorClass error;
     private IssueType type;
 
-    protected TerminologyServiceProtectionException(String message, TerminologyServiceErrorClass error, IssueType type) {
+    public TerminologyServiceProtectionException(String message, TerminologyServiceErrorClass error, IssueType type) {
       super(message);
       this.error = error;
       this.type = type;

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

@@ -143,7 +143,7 @@ public class ValueSetProcessBase {
   }
 
   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()));
+    List<OperationOutcomeIssueComponent> iss = makeIssue(IssueSeverity.INFORMATION, IssueType.BUSINESSRULE, path, context.formatMessage(msg, resource.getVersionedUrl()));
 
     // this is a testing hack - see TerminologyServiceTests
     iss.get(0).setUserData("status-msg-name", "warning-"+id);

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

@@ -81,6 +81,7 @@ import org.hl7.fhir.r5.terminologies.providers.CodeSystemProvider;
 import org.hl7.fhir.r5.terminologies.providers.SpecialCodeSystem;
 import org.hl7.fhir.r5.terminologies.providers.URICodeSystem;
 import org.hl7.fhir.r5.terminologies.utilities.TerminologyOperationContext;
+import org.hl7.fhir.r5.terminologies.utilities.TerminologyOperationContext.TerminologyServiceProtectionException;
 import org.hl7.fhir.r5.terminologies.utilities.TerminologyServiceErrorClass;
 import org.hl7.fhir.r5.terminologies.utilities.ValueSetProcessBase;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
@@ -195,6 +196,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
     ValidationProcessInfo info = new ValidationProcessInfo();
 
     CodeableConcept vcc = new CodeableConcept();
+    
     if (options.getValueSetMode() != ValueSetMode.CHECK_MEMERSHIP_ONLY) {
       int i = 0;
       for (Coding c : code.getCoding()) {
@@ -262,6 +264,9 @@ public class ValueSetValidator extends ValueSetProcessBase {
         info.getIssues().addAll(makeIssue(IssueSeverity.ERROR, IssueType.CODEINVALID, path, msg));
       }
     }
+    if (vcc.hasCoding() && code.hasText()) {
+      vcc.setText(code.getText());
+    }
     if (!checkRequiredSupplements(info)) {
       return new ValidationResult(IssueSeverity.ERROR, info.getIssues().get(info.getIssues().size()-1).getDetails().getText(), info.getIssues());
     } else if (info.hasErrors()) {
@@ -295,7 +300,8 @@ public class ValueSetValidator extends ValueSetProcessBase {
 
   private boolean checkRequiredSupplements(ValidationProcessInfo info) {
     if (!requiredSupplements.isEmpty()) {
-      info.getIssues().addAll(makeIssue(IssueSeverity.ERROR, IssueType.NOTFOUND, null, context.formatMessagePlural(requiredSupplements.size(), I18nConstants.VALUESET_SUPPLEMENT_MISSING, CommaSeparatedStringBuilder.build(requiredSupplements))));
+      String msg= context.formatMessagePlural(requiredSupplements.size(), I18nConstants.VALUESET_SUPPLEMENT_MISSING, CommaSeparatedStringBuilder.build(requiredSupplements));
+      throw new TerminologyServiceProtectionException(msg, TerminologyServiceErrorClass.BUSINESS_RULE, IssueType.NOTFOUND);
     }
     return requiredSupplements.isEmpty();
   }
@@ -529,6 +535,8 @@ public class ValueSetValidator extends ValueSetProcessBase {
             res.setMessage("Code found in include, however: " + res.getMessage());
             res.getIssues().addAll(makeIssue(IssueSeverity.WARNING, IssueType.EXCEPTION, path, res.getMessage()));
           }
+        } else if (res == null) {
+          res = new ValidationResult(system, wv, null, null);
         }
       } else if ((res != null && !res.isOk())) {
         String msg = context.formatMessagePlural(1, I18nConstants.NONE_OF_THE_PROVIDED_CODES_ARE_IN_THE_VALUE_SET_, valueset.getVersionedUrl(), code.toString());
@@ -676,18 +684,19 @@ public class ValueSetValidator extends ValueSetProcessBase {
     if (vcc != null) {
       vcc.addCoding(vc);
     }
-    if (CodeSystemUtilities.isInactive(cs, cc)) {
+
-      info.addIssue(makeIssue(IssueSeverity.WARNING, IssueType.EXPIRED, path, context.formatMessage(I18nConstants.INACTIVE_CODE_WARNING, cc.getCode())));
+    boolean inactive = (CodeSystemUtilities.isInactive(cs, cc));
-    }
+    String status = inactive ? (CodeSystemUtilities.getStatus(cs, cc)) : null;
+
     boolean ws = false;     
     if (code.getDisplay() == null) {
-      return new ValidationResult(code.getSystem(), cs.getVersion(), cc, vc.getDisplay());
+      return new ValidationResult(code.getSystem(), cs.getVersion(), cc, vc.getDisplay()).setStatus(inactive, status);
     }
     CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(", ", " or ");
     if (cc.hasDisplay() && isOkLanguage(cs.getLanguage())) {
       b.append("'"+cc.getDisplay()+"'");
       if (code.getDisplay().equalsIgnoreCase(cc.getDisplay())) {
-        return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs));
+        return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs)).setStatus(inactive, status);
       } else if (Utilities.normalize(code.getDisplay()).equals(Utilities.normalize(cc.getDisplay()))) {
         ws = true;
       }
@@ -698,7 +707,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
       if (isOkLanguage(ds.getLanguage())) {
         b.append("'"+ds.getValue()+"'");
         if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
-          return new ValidationResult(code.getSystem(),cs.getVersion(),  cc, getPreferredDisplay(cc, cs));
+          return new ValidationResult(code.getSystem(),cs.getVersion(),  cc, getPreferredDisplay(cc, cs)).setStatus(inactive, status);
         }
         if (Utilities.normalize(code.getDisplay()).equalsIgnoreCase(Utilities.normalize(ds.getValue()))) {
           ws = true;
@@ -712,7 +721,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
         if (vs.getCc().hasDisplay() && isOkLanguage(vs.getValueset().getLanguage())) {
           b.append("'"+vs.getCc().getDisplay()+"'");
           if (code.getDisplay().equalsIgnoreCase(vs.getCc().getDisplay())) {
-            return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs));
+            return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs)).setStatus(inactive, status);
           }
         }
         for (ConceptReferenceDesignationComponent ds : vs.getCc().getDesignation()) {
@@ -720,7 +729,7 @@ public class ValueSetValidator extends ValueSetProcessBase {
           if (isOkLanguage(ds.getLanguage())) {
             b.append("'"+ds.getValue()+"'");
             if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
-              return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs));
+              return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs)).setStatus(inactive, status);
             }
           }
         }
@@ -728,10 +737,10 @@ public class ValueSetValidator extends ValueSetProcessBase {
     }
     if (b.count() == 0) {
       String msg = context.formatMessagePlural(options.getLanguages().size(), I18nConstants.NO_VALID_DISPLAY_FOUND, code.getSystem(), code.getCode(), code.getDisplay(), options.langSummary());
-      return new ValidationResult(IssueSeverity.WARNING, msg, code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs), makeIssue(IssueSeverity.WARNING, IssueType.INVALID, path+".display", msg));      
+      return new ValidationResult(IssueSeverity.WARNING, msg, code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs), makeIssue(IssueSeverity.WARNING, IssueType.INVALID, path+".display", msg)).setStatus(inactive, status);      
     } else {
       String msg = context.formatMessagePlural(b.count(), ws ? I18nConstants.DISPLAY_NAME_WS_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF : I18nConstants.DISPLAY_NAME_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF, code.getSystem(), code.getCode(), b.toString(), code.getDisplay(), options.langSummary());
-      return new ValidationResult(dispWarningStatus(), msg, code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs), makeIssue(dispWarning(), IssueType.INVALID, path+".display", msg));
+      return new ValidationResult(dispWarningStatus(), msg, code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs), makeIssue(dispWarning(), IssueType.INVALID, path+".display", msg)).setStatus(inactive, status);
     }
   }
 

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

@@ -255,7 +255,7 @@ public class TxTester {
       TxTesterSorters.sortValueSet(vs);
       vsj = new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(vs);
     } catch (EFhirClientException e) {
-      OperationOutcome oo = e.getServerErrors().get(0); 
+      OperationOutcome oo = e.getServerError(); 
       TxTesterScrubbers.scrubOO(oo, tight);
       vsj = new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(oo);
     }
@@ -279,7 +279,7 @@ public class TxTester {
       TxTesterSorters.sortParameters(po);
       pj = new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(po);
     } catch (EFhirClientException e) {
-      OperationOutcome oo = e.getServerErrors().get(0); 
+      OperationOutcome oo = e.getServerError(); 
       oo.setText(null);
       pj = new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(oo);
     }

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

@@ -31,6 +31,10 @@ public class TxTesterSorters {
   }
 
 
+  public static void sortOperationOutcome(OperationOutcome oo) {
+    Collections.sort(oo.getIssue(), new TxTesterSorters.OperationIssueSorter());
+  }
+  
   public static void sortValueSet(ValueSet vs) {
     Collections.sort(vs.getExtension(), new TxTesterSorters.ExtensionSorter());
     if (vs.hasExpansion()) {

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/terminology/tests/TerminologyServiceTests.java

@@ -95,7 +95,7 @@ public class TerminologyServiceTests {
 
     List<Object[]> objects = new ArrayList<Object[]>(examples.size());
     for (String id : names) {
-        objects.add(new Object[]{id, examples.get(id)});
+      objects.add(new Object[]{id, examples.get(id)});
     }
     return objects;
   }
@@ -208,6 +208,7 @@ public class TerminologyServiceTests {
       }
       e.getDetails().setText(vse.getError());
       oo.addIssue(e);
+      TxTesterSorters.sortOperationOutcome(oo);
       TxTesterScrubbers.scrubOO(oo, false);
 
       String ooj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(oo);
@@ -242,7 +243,7 @@ public class TerminologyServiceTests {
       options = options.withLanguage(p.getParameterString("displayLanguage"));
     }
     if (p.hasParameter("valueSetMode") && "CHECK_MEMBERSHIP_ONLY".equals(p.getParameterString("valueSetMode"))) {
-       options = options.withCheckValueSetOnly();
+      options = options.withCheckValueSetOnly();
     }
     if (p.hasParameter("mode") && "lenient-display-validation".equals(p.getParameterString("mode"))) {
       options = options.setDisplayWarningMode(true);
@@ -265,51 +266,73 @@ public class TerminologyServiceTests {
     } else {
       throw new Error("validate not done yet for this steup");
     }
-    org.hl7.fhir.r5.model.Parameters res = new org.hl7.fhir.r5.model.Parameters();
+    if (vm.getSeverity() == org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity.FATAL) {
-    if (vm.getSystem() != null) {
-      res.addParameter("system", new UriType(vm.getSystem()));
-    }
-    if (vm.getCode() != null) {
-      res.addParameter("code", new CodeType(vm.getCode()));
-    }
-    if (vm.getSeverity() == org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity.ERROR) {
-      res.addParameter("result", false);
-    } else {
-      res.addParameter("result", true);
-    }
-    if (vm.getMessage() != null) {
-      res.addParameter("message", vm.getMessage());
-    }
-    if (vm.getVersion() != null) {
-      res.addParameter("version", vm.getVersion());
-    }
-    if (vm.getDisplay() != null) {
-      res.addParameter("display", vm.getDisplay());
-    }
-    if (vm.getCodeableConcept() != null) {
-      res.addParameter("codeableConcept", vm.getCodeableConcept());
-    }
-    if (vm.getUnknownSystems() != null) {
-      for (String s : vm.getUnknownSystems()) {
-        res.addParameter("x-caused-by-unknown-system", new CanonicalType(s));
-      }
-    }
-    if (vm.getIssues().size() > 0) {
       OperationOutcome oo = new OperationOutcome();
       oo.getIssue().addAll(vm.getIssues());
-      res.addParameter().setName("issues").setResource(oo);
+      TxTesterSorters.sortOperationOutcome(oo);
-    }
+      TxTesterScrubbers.scrubOO(oo, false);
-    TxTesterSorters.sortParameters(res);
-    TxTesterScrubbers.scrubParams(res);
       
-    String pj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(res);
+      String pj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(oo);
-    String diff = CompareUtilities.checkJsonSrcIsSame(resp, pj, ext);
+      String diff = CompareUtilities.checkJsonSrcIsSame(resp, pj, ext);
-    if (diff != null) {
+      if (diff != null) {
-      Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
+        Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
-      TextFile.stringToFile(pj, fp); 
+        TextFile.stringToFile(pj, fp); 
-      System.out.println("Test "+name+"failed: "+diff);
+        System.out.println("Test "+name+"failed: "+diff);
+      }
+      Assertions.assertTrue(diff == null, diff);
+    } else {
+      org.hl7.fhir.r5.model.Parameters res = new org.hl7.fhir.r5.model.Parameters();
+      if (vm.getSystem() != null) {
+        res.addParameter("system", new UriType(vm.getSystem()));
+      }
+      if (vm.getCode() != null) {
+        res.addParameter("code", new CodeType(vm.getCode()));
+      }
+      if (vm.getSeverity() == org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity.ERROR) {
+        res.addParameter("result", false);
+      } else {
+        res.addParameter("result", true);
+      }
+      if (vm.getMessage() != null) {
+        res.addParameter("message", vm.getMessage());
+      }
+      if (vm.getVersion() != null) {
+        res.addParameter("version", vm.getVersion());
+      }
+      if (vm.getDisplay() != null) {
+        res.addParameter("display", vm.getDisplay());
+      }
+      if (vm.getCodeableConcept() != null) {
+        res.addParameter("codeableConcept", vm.getCodeableConcept());
+      }
+      if (vm.isInactive()) {
+        res.addParameter("inactive", true);
+      }
+      if (vm.getStatus() != null) {
+        res.addParameter("status", vm.getStatus());
+      }
+      if (vm.getUnknownSystems() != null) {
+        for (String s : vm.getUnknownSystems()) {
+          res.addParameter("x-caused-by-unknown-system", new CanonicalType(s));
+        }
+      }
+      if (vm.getIssues().size() > 0) {
+        OperationOutcome oo = new OperationOutcome();
+        oo.getIssue().addAll(vm.getIssues());
+        res.addParameter().setName("issues").setResource(oo);
+      }
+      TxTesterSorters.sortParameters(res);
+      TxTesterScrubbers.scrubParams(res);
+
+      String pj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(res);
+      String diff = CompareUtilities.checkJsonSrcIsSame(resp, pj, ext);
+      if (diff != null) {
+        Utilities.createDirectory(Utilities.getDirectoryForFile(fp));
+        TextFile.stringToFile(pj, fp); 
+        System.out.println("Test "+name+"failed: "+diff);
+      }
+      Assertions.assertTrue(diff == null, diff);
     }
-    Assertions.assertTrue(diff == null, diff);
   }
 
   public Resource loadResource(String filename) throws IOException, FHIRFormatError, FileNotFoundException, FHIRException, DefinitionException {