Add ValueSet expansion support, fix profile bugs

HapiWorkerContext needed ValueSet expansion support for validation, now that resources are found and loaded.
ParserBase had a bug when comparing names (was not looking at IdPart)
Profiles had errors in FHIRPaths using invalid $context name

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/hapi/validation/HapiWorkerContext.java

@@ -31,13 +31,18 @@ import org.hl7.fhir.dstu2016may.model.ValueSet.ConceptReferenceComponent;
 import org.hl7.fhir.dstu2016may.model.ValueSet.ConceptSetComponent;
 import org.hl7.fhir.dstu2016may.model.ValueSet.ValueSetExpansionComponent;
 import org.hl7.fhir.dstu2016may.model.ValueSet.ValueSetExpansionContainsComponent;
+import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpander;
 import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
+import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpanderFactory;
+import org.hl7.fhir.dstu2016may.terminologies.ValueSetExpanderSimple;
 import org.hl7.fhir.dstu2016may.utils.IWorkerContext;
 import org.hl7.fhir.dstu2016may.validation.IResourceValidator;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
-public final class HapiWorkerContext implements IWorkerContext  {
+public final class HapiWorkerContext implements IWorkerContext, ValueSetExpanderFactory  {
 	private final FhirContext myCtx;
 	private Map<String, Resource> myFetchedResourceCache = new HashMap<String, Resource>();
 	private IValidationSupport myValidationSupport;
@@ -201,8 +206,8 @@ public final class HapiWorkerContext implements IWorkerContext  {
 				}
 			}
 		}
-		
+
-		
+
 		boolean caseSensitive = true;
 		if (isNotBlank(theSystem)) {
 			CodeSystem system = fetchCodeSystem(theSystem);
@@ -259,10 +264,27 @@ public final class HapiWorkerContext implements IWorkerContext  {
 		return new ValidationResult(IssueSeverity.ERROR, "Unknown code[" + theCode + "] in system[" + theSystem + "]");
 	}
 
+	@Override
+	public ValueSetExpander getExpander() {
+		ValueSetExpanderSimple retVal = new ValueSetExpanderSimple(this, this);
+		return retVal;
+	}
 
 	@Override
 	public ValueSetExpansionOutcome expandVS(ValueSet theSource, boolean theCacheOk) {
-		throw new UnsupportedOperationException();
+		ValueSetExpansionOutcome vso;
+		try {
+			vso = getExpander().expand(theSource);
+		} catch (InvalidRequestException e) {
+			throw e;
+		} catch (Exception e) {
+			throw new InternalErrorException(e);
+		}
+		if (vso.getError() != null) {
+			throw new InvalidRequestException(vso.getError());
+		} else {
+			return vso;
+		}
 	}
 
 	@Override

hapi-fhir-structures-dstu2.1/src/main/java/org/hl7/fhir/dstu2016may/metamodel/ParserBase.java

@@ -25,13 +25,13 @@ import org.hl7.fhir.utilities.Utilities;
 public abstract class ParserBase {
 
   interface IErrorNotifier {
-    
+
   }
   public enum ValidationPolicy { NONE, QUICK, EVERYTHING }
 
 	public static boolean isPrimitive(String code) {
-		return Utilities.existsInList(code, 
+		return Utilities.existsInList(code,
-				"xhtml", "boolean", "integer", "string", "decimal", "uri", "base64Binary", "instant", "date", "dateTime", 
+				"xhtml", "boolean", "integer", "string", "decimal", "uri", "base64Binary", "instant", "date", "dateTime",
 				"time", "code", "oid", "id", "markdown", "unsignedInt", "positiveInt", "xhtml", "base64Binary");
 	}
 
@@ -49,12 +49,12 @@ public abstract class ParserBase {
 	  this.policy = policy;
 	  this.errors = errors;
 	}
-	
+
 	public abstract Element parse(InputStream stream) throws Exception;
 
 	public abstract void compose(Element e, OutputStream destination, OutputStyle style, String base)  throws Exception;
 
-	
+
 	public void logError(int line, int col, String path, IssueType type, String message, IssueSeverity level) throws FHIRFormatError {
 	  if (policy == ValidationPolicy.EVERYTHING) {
 	    ValidationMessage msg = new ValidationMessage(Source.InstanceValidator, type, line, col, path, message, level);
@@ -62,8 +62,8 @@ public abstract class ParserBase {
 	  } else if (level == IssueSeverity.FATAL || (level == IssueSeverity.ERROR && policy == ValidationPolicy.QUICK))
 	    throw new FHIRFormatError(message+String.format(" at line %d col %d", line, col));
 	}
-	
+
-	
+
 	protected StructureDefinition getDefinition(int line, int col, String ns, String name) throws FHIRFormatError {
     if (ns == null) {
       logError(line, col, name, IssueType.STRUCTURE, "This cannot be parsed as a FHIR object (no namespace)", IssueSeverity.FATAL);
@@ -74,7 +74,7 @@ public abstract class ParserBase {
       return null;
   	}
 	  for (StructureDefinition sd : context.allStructures()) {
-	    if (name.equals(sd.getId())) {
+	    if (name.equals(sd.getIdElement().getIdPart())) {
 	      if((ns == null || ns.equals(FormatUtilities.FHIR_NS)) && !ToolingExtensions.hasExtension(sd, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace"))
 	        return sd;
 	      String sns = ToolingExtensions.readStringExtension(sd, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace");
@@ -92,7 +92,7 @@ public abstract class ParserBase {
       return null;
   	}
 	  for (StructureDefinition sd : context.allStructures()) {
-	    if (name.equals(sd.getId())) {
+	    if (name.equals(sd.getIdElement().getIdPart())) {
 	      return sd;
 	    }
 	  }
@@ -100,7 +100,7 @@ public abstract class ParserBase {
 	  return null;
   }
 
-  
+
 	protected List<Property> getChildProperties(Property property, String elementName, String statedType) throws DefinitionException {
 		ElementDefinition ed = property.getDefinition();
 		StructureDefinition sd = property.getStructure();
@@ -128,12 +128,12 @@ public abstract class ParserBase {
 				    if (t == null && ToolingExtensions.hasExtension(ed, "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaultype"))
 				      t = ToolingExtensions.readStringExtension(ed, "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaultype");
 				    boolean ok = false;
-		        for (TypeRefComponent tr : ed.getType()) 
+		        for (TypeRefComponent tr : ed.getType())
-		          if (tr.getCode().equals(t)) 
+		          if (tr.getCode().equals(t))
 		            ok = true;
 		         if (!ok)
 		           throw new DefinitionException("Type '"+t+"' is not an acceptable type for '"+elementName+"' on property "+property.getDefinition().getPath());
-				    
+
 				  } else {
 				    t = elementName.substring(tail(ed.getPath()).length() - 3);
 				    if (isPrimitive(lowFirst(t)))

hapi-fhir-validation-resources-dstu2.1/src/main/resources/org/hl7/fhir/dstu2016may/profile/profiles-resources.xml

@@ -20460,7 +20460,7 @@
        <key value="dom-3"/>
        <severity value="error"/>
        <human value="If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource"/>
-       <expression value="contained.select(('#'+id in $context.descendents().reference).not()).empty()"/>
+       <expression value="contained.select(('#'+id in %resource.descendents().reference).not()).empty()"/>
        <xpath value="not(exists(for $id in f:contained/*/@id return $id[not(ancestor::f:contained/parent::*/descendant::f:reference/@value=concat('#', $id))]))"/>
       </constraint>
       <constraint>
@@ -20649,7 +20649,7 @@
        <key value="dom-3"/>
        <severity value="error"/>
        <human value="If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource"/>
-       <expression value="contained.select(('#'+id in $context.descendents().reference).not()).empty()"/>
+       <expression value="contained.select(('#'+id in %resource.descendents().reference).not()).empty()"/>
        <xpath value="not(exists(for $id in f:contained/*/@id return $id[not(ancestor::f:contained/parent::*/descendant::f:reference/@value=concat('#', $id))]))"/>
       </constraint>
       <constraint>
@@ -121071,7 +121071,7 @@
        <key value="obs-7"/>
        <severity value="error"/>
        <human value="Component code SHALL not be same as observation code"/>
-       <expression value="component.where(code = $context.code).empty()"/>
+       <expression value="component.where(code = %resource.code).empty()"/>
        <xpath value="not(exists(f:component/f:code)) or count(for $coding in f:code/f:coding return parent::*/f:component/f:code/f:coding[f:code/@value=$coding/f:code/@value and f:system/@value=$coding/f:system/@value])=0"/>
       </constraint>
       <mapping>
@@ -122307,7 +122307,7 @@
        <key value="obs-7"/>
        <severity value="error"/>
        <human value="Component code SHALL not be same as observation code"/>
-       <expression value="component.where(code = $context.code).empty()"/>
+       <expression value="component.where(code = %resource.code).empty()"/>
        <xpath value="not(exists(f:component/f:code)) or count(for $coding in f:code/f:coding return parent::*/f:component/f:code/f:coding[f:code/@value=$coding/f:code/@value and f:system/@value=$coding/f:system/@value])=0"/>
       </constraint>
       <mapping>
@@ -154515,7 +154515,7 @@
        <key value="sdf-8"/>
        <severity value="error"/>
        <human value="In any snapshot or differential, all the elements except the first have to have a path that starts with the path of the first + &quot;.&quot;"/>
-       <expression value="snapshot.element.tail().all(path.startsWith($context.snapshot.element.first().path+'.')) and differential.element.tail().all(path.startsWith($context.differential.element.first().path+'.'))"/>
+       <expression value="snapshot.element.tail().all(path.startsWith(%resource.snapshot.element.first().path+'.')) and differential.element.tail().all(path.startsWith(%resource.differential.element.first().path+'.'))"/>
        <xpath value="string-join(for $elementName in f:*[self::f:snapshot or self::f:differential]/f:element[position()>1]/f:path/@value return if (starts-with($elementName, concat($elementName/ancestor::f:element/parent::f:*/f:element[1]/f:path/@value, '.'))) then '' else $elementName,'')=''"/>
       </constraint>
       <constraint>
@@ -155580,7 +155580,7 @@
        <key value="sdf-8"/>
        <severity value="error"/>
        <human value="In any snapshot or differential, all the elements except the first have to have a path that starts with the path of the first + &quot;.&quot;"/>
-       <expression value="snapshot.element.tail().all(path.startsWith($context.snapshot.element.first().path+'.')) and differential.element.tail().all(path.startsWith($context.differential.element.first().path+'.'))"/>
+       <expression value="snapshot.element.tail().all(path.startsWith(%resource.snapshot.element.first().path+'.')) and differential.element.tail().all(path.startsWith(%resource.differential.element.first().path+'.'))"/>
        <xpath value="string-join(for $elementName in f:*[self::f:snapshot or self::f:differential]/f:element[position()>1]/f:path/@value return if (starts-with($elementName, concat($elementName/ancestor::f:element/parent::f:*/f:element[1]/f:path/@value, '.'))) then '' else $elementName,'')=''"/>
       </constraint>
       <constraint>

hapi-fhir-validation-resources-dstu2.1/src/main/resources/org/hl7/fhir/dstu2016may/profile/profiles-types.xml

@@ -4681,7 +4681,7 @@
        <key value="ref-1"/>
        <severity value="error"/>
        <human value="SHALL have a local reference if the resource is provided inline"/>
-       <expression value="reference.startsWith('#').not() or ($context.reference.substring(1).trace('url') in $resource.contained.id.trace('ids'))"/>
+       <expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %resource.contained.id.trace('ids'))"/>
        <xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])"/>
       </constraint>
       <mapping>
@@ -4779,7 +4779,7 @@
        <key value="ref-1"/>
        <severity value="error"/>
        <human value="SHALL have a local reference if the resource is provided inline"/>
-       <expression value="reference.startsWith('#').not() or ($context.reference.substring(1).trace('url') in $resource.contained.id.trace('ids'))"/>
+       <expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %resource.contained.id.trace('ids'))"/>
        <xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])"/>
       </constraint>
       <mapping>