Merge pull request #215 from hapifhir/gg-work

R2B fixes

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_14_50.java

@@ -1482,6 +1482,8 @@ public class VersionConvertor_14_50 {
           tgt.setBase(convertElementDefinitionBaseComponent(src.getBase()));
         if (src.hasContentReference())
           tgt.setContentReferenceElement(convertUri(src.getContentReferenceElement()));
+        // work around for problem in R2B definitions:
+        if (!src.hasContentReference()) {
           for (org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent t : src.getType()) convertTypeRefComponent(t, tgt.getType());
           if (src.hasDefaultValue())
             tgt.setDefaultValue(convertType(src.getDefaultValue()));
@@ -1516,6 +1518,7 @@ public class VersionConvertor_14_50 {
           if (src.hasBinding())
             tgt.setBinding(convertElementDefinitionBindingComponent(src.getBinding()));
           for (org.hl7.fhir.dstu2016may.model.ElementDefinition.ElementDefinitionMappingComponent t : src.getMapping()) tgt.addMapping(convertElementDefinitionMappingComponent(t));
+        }
         return tgt;
     }
 

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

@@ -134,7 +134,7 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
         cs = findSpecialCodeSystem(system);
       }
       if (cs == null) {
-        warningMessage = "Unable to resolve system "+system+" - system is not specified or implicit";
+        warningMessage = "Unable to resolve system "+system;
         if (!inExpansion)
           throw new FHIRException(warningMessage);
       }
@@ -144,8 +144,12 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
           throw new FHIRException(warningMessage);
       }
 
-      if (cs!=null)
+      if (cs!=null) {
         res = validateCode(code, cs);
+      } else {
+        // it's in the expansion, but we could find it in a code system
+        res = findCodeInExpansion(code);
+      }
     } else {
       inExpansion = checkExpansion(code);
     }
@@ -175,13 +179,38 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
     return null;
   }
 
-  boolean checkExpansion(Coding code) {
+  private ValidationResult findCodeInExpansion(Coding code) {
+    if (valueset==null || !valueset.hasExpansion())
+      return null;
+    return findCodeInExpansion(code, valueset.getExpansion().getContains());
+  }
+  
+  private ValidationResult findCodeInExpansion(Coding code, List<ValueSetExpansionContainsComponent> contains) {
+    for (ValueSetExpansionContainsComponent containsComponent: contains) {
+      if (containsComponent.getSystem().equals(code.getSystem()) && containsComponent.getCode().equals(code.getCode())) {
+        ConceptDefinitionComponent ccd = new ConceptDefinitionComponent();
+        ccd.setCode(containsComponent.getCode());
+        ccd.setDisplay(containsComponent.getDisplay());
+        ValidationResult res = new ValidationResult(ccd);
+        return res;
+      }
+      if (containsComponent.hasContains()) {
+        ValidationResult res = findCodeInExpansion(code, containsComponent.getContains());
+        if (res != null) {
+          return res;
+        }
+      }
+    }
+    return null;
+  }
+  
+  private boolean checkExpansion(Coding code) {
     if (valueset==null || !valueset.hasExpansion())
       return false;
     return checkExpansion(code, valueset.getExpansion().getContains());
   }
 
-  boolean checkExpansion(Coding code, List<ValueSetExpansionContainsComponent> contains) {
+  private boolean checkExpansion(Coding code, List<ValueSetExpansionContainsComponent> contains) {
     for (ValueSetExpansionContainsComponent containsComponent: contains) {
       if (containsComponent.getSystem().equals(code.getSystem()) && containsComponent.getCode().equals(code.getCode()))
         return true;

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

@@ -30,6 +30,8 @@ public class XVerExtensionManager {
     BadVersion, Unknown, Invalid, Valid
   }
 
+  public static final String XVER_EXT_MARKER = "XVER_EXT_MARKER";
+
   private Map<String, JsonObject> lists = new HashMap<>();
   private IWorkerContext context;
 
@@ -81,6 +83,7 @@ public class XVerExtensionManager {
     JsonObject path = root.getAsJsonObject(e);
     
     StructureDefinition sd = new StructureDefinition();
+    sd.setUserData(XVER_EXT_MARKER, "true");
     sd.setUrl(url);
     sd.setVersion(context.getVersion());
     sd.setFhirVersion(FHIRVersion.fromCode(context.getVersion()));

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

@@ -26,6 +26,7 @@ public class I18nConstants {
   public final static String CODESYSTEM_CS_VS_MISMATCH = "CodeSystem_CS_VS_MisMatch";
   public final static String CODESYSTEM_CS_VS_WRONGSYSTEM = "CodeSystem_CS_VS_WrongSystem";
   public final static String EXTENSION_EXT_CONTEXT_WRONG = "Extension_EXT_Context_Wrong";
+  public final static String EXTENSION_EXT_CONTEXT_WRONG_XVER = "EXTENSION_EXT_CONTEXT_WRONG_XVER";
   public final static String EXTENSION_EXT_COUNT_MISMATCH = "Extension_EXT_Count_Mismatch";
   public final static String EXTENSION_EXT_COUNT_NOTFOUND = "Extension_EXT_Count_NotFound";
   public final static String EXTENSION_EXT_FIXED_BANNED = "Extension_EXT_Fixed_Banned";

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

@@ -498,3 +498,4 @@ TYPE_SPECIFIC_CHECKS_DT_DECIMAL_CHARS = Found {0} decimal places which exceeds t
 Validation_VAL_Profile_WrongType = Specified profile type was "{0}", but found type "{1}"
 Validation_VAL_Profile_WrongType2 = Type mismatch processing profile {0} at path {1}: The element type is {4}, but the profile {3} is for a different type {2}
 VALIDATION_VAL_ILLEGAL_TYPE_CONSTRAINT = Illegal constraint in profile {0} at path {1} - cannot constrain to type {2} from base types {3}
+EXTENSION_EXT_CONTEXT_WRONG_XVER = The extension {0} from FHIR version {3} is not allowed to be used at this point (allowed = {1}; this element is [{2}; this is a warning since contexts may be renamed between FHIR versions)

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/tests/PackageCacheTests.java

@@ -10,6 +10,7 @@ import org.junit.jupiter.api.Test;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.List;
 
 public class PackageCacheTests {
 
@@ -17,7 +18,11 @@ public class PackageCacheTests {
   public void testPath() throws IOException {
     PackageCacheManager cache = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
     cache.clear();
-    Assertions.assertTrue(cache.listPackages().isEmpty());
+    List<String> list = cache.listPackages();
+    if (!list.isEmpty()) {
+      System.out.println("remaining packages: "+list.toString());
+    }
+    Assertions.assertTrue(list.isEmpty());
     NpmPackage npm = cache.loadPackage("hl7.fhir.pubpack", "0.0.3");
     npm.loadAllFiles();
     Assertions.assertNotNull(npm);
@@ -30,6 +35,7 @@ public class PackageCacheTests {
     npm.save(dir);
     NpmPackage npm2 = cache.loadPackage("hl7.fhir.pubpack", "file:" + dir.getAbsolutePath());
     Assertions.assertNotNull(npm2);
-    Assertions.assertFalse(cache.listPackages().isEmpty());
+    list = cache.listPackages();
+    Assertions.assertFalse(list.isEmpty());
   }
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java

@@ -1567,17 +1567,26 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       }
     }
     if (!ok) {
+      if (definition.hasUserData(XVerExtensionManager.XVER_EXT_MARKER)) {
+        warning(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.EXTENSION_EXT_CONTEXT_WRONG_XVER, extUrl, contexts.toString(), plist.toString());
+      } else {
         rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.EXTENSION_EXT_CONTEXT_WRONG, extUrl, contexts.toString(), plist.toString());        
+      }
       return false;
     } else {
       if (definition.hasContextInvariant()) {
         for (StringType s : definition.getContextInvariant()) {
           if (!fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), container, fpe.parse(s.getValue()))) {
+            if (definition.hasUserData(XVerExtensionManager.XVER_EXT_MARKER)) {
+              warning(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.PROFILE_EXT_NOT_HERE, extUrl, s.getValue());              
+              return true;
+            } else {
               rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.getLiteralPath(), false, I18nConstants.PROFILE_EXT_NOT_HERE, extUrl, s.getValue());
               return false;
             }
           }
         }
+      }
       return true;
     }
   }