performance improvement for element model parsing - thanks Brian Postlethwaite

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

@@ -47,6 +47,7 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
   private List<StructureDefinition> allStructuresList = new ArrayList<StructureDefinition>();
   private List<String> canonicalResourceNames;
   private List<String> concreteResourceNames;
+  private Set<String> concreteResourceNameSet;
   
   public ContextUtilities(IWorkerContext context) {
     super();
@@ -317,6 +318,9 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
 
   @Override
   public boolean isResource(String t) {
+    if (getConcreteResourceSet().contains(t)) {
+      return true;
+    }
     StructureDefinition sd;
     try {
       sd = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/"+t);
@@ -370,16 +374,22 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
     return null;
   }
 
-  public List<String>  getConcreteResources() {
+  public Set<String> getConcreteResourceSet() {
-    if (concreteResourceNames == null) {
+    if (concreteResourceNameSet == null) {
-      concreteResourceNames =  new ArrayList<>();
+      concreteResourceNameSet =  new HashSet<>();
       Set<String> names = new HashSet<>();
       for (StructureDefinition sd : allStructures()) {
         if (sd.getKind() == StructureDefinitionKind.RESOURCE && !sd.getAbstract()) {
           names.add(sd.getType());
         }
       }
-      concreteResourceNames.addAll(Utilities.sorted(names));
+    }
+    return concreteResourceNameSet;
+  }
+
+  public List<String> getConcreteResources() {
+    if (concreteResourceNames == null) {
+      concreteResourceNames.addAll(Utilities.sorted(concreteResourceNameSet));
     }
     return concreteResourceNames;
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java

@@ -514,7 +514,7 @@ public class Element extends Base implements NamedItem {
   }
 
   private boolean isDataType(Base v) {
-    return v instanceof DataType && new ContextUtilities(property.getContext()).getTypeNames().contains(v.fhirType());
+    return v instanceof DataType && property.getContextUtils().getTypeNames().contains(v.fhirType());
   }
 
   @Override

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/FmlParser.java

@@ -134,7 +134,7 @@ public class FmlParser extends ParserBase {
     lexer.token("conceptmap");
     Element map = structureMap.makeElement("contained");
     StructureDefinition sd = context.fetchTypeDefinition("ConceptMap");
-    map.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd), SpecialElement.fromProperty(map.getElementProperty() != null ? map.getElementProperty() : map.getProperty()), map.getProperty());
+    map.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities()), SpecialElement.fromProperty(map.getElementProperty() != null ? map.getElementProperty() : map.getProperty()), map.getProperty());
     map.setType("ConceptMap");
     Element eid = map.makeElement("id").markLocation(lexer.getCurrentLocation());
     String id = lexer.readConstant("map id");
@@ -225,6 +225,8 @@ public class FmlParser extends ParserBase {
     String token = lexer.take();
     if (token.equals("-"))
       return ConceptMapRelationship.RELATEDTO;
+    if (token.equals("=")) // temporary
+      return ConceptMapRelationship.RELATEDTO;
     if (token.equals("=="))
       return ConceptMapRelationship.EQUIVALENT;
     if (token.equals("!="))

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java

@@ -86,22 +86,15 @@ public class JsonParser extends ParserBase {
   private JsonCreator json;
   private boolean allowComments;
 
-  private ProfileUtilities profileUtilities;
   private Element baseElement;
-  private ContextUtilities contextUtilities;
 
   public JsonParser(IWorkerContext context, ProfileUtilities utilities) {
-    super(context);
+    super(context, utilities);
 
-    this.profileUtilities = utilities;
-    contextUtilities = new ContextUtilities(context);
   }
 
   public JsonParser(IWorkerContext context) {
     super(context);
-
-    this.profileUtilities = new ProfileUtilities(this.context, null, null, new FHIRPathEngine(context));
-    contextUtilities = new ContextUtilities(context);
   }
 
   public Element parse(String source, String type) throws Exception {
@@ -128,7 +121,7 @@ public class JsonParser extends ParserBase {
       nEd.addType().setCode(type);
       nEd.setMax(obj.getProperties().get(0).getValue().isJsonArray() ? "*" : "1"); 
     }
-    Element result = new Element(type, new Property(context, sd.getSnapshot().getElement().get(0), sd, this.profileUtilities)).setFormat(FhirFormat.JSON);
+    Element result = new Element(type, new Property(context, sd.getSnapshot().getElement().get(0), sd, this.getProfileUtilities(), this.getContextUtilities())).setFormat(FhirFormat.JSON);
     result.setPath(type);
     checkObject(focusFragment.getErrors(), obj, result, path);
     result.setType(type);
@@ -199,7 +192,7 @@ public class JsonParser extends ParserBase {
       name = sd.getType();
       path = sd.getTypeTail();
     }
-    baseElement = new Element(name, new Property(context, sd.getSnapshot().getElement().get(0), sd, this.profileUtilities)).setFormat(FhirFormat.JSON);
+    baseElement = new Element(name, new Property(context, sd.getSnapshot().getElement().get(0), sd, this.getProfileUtilities(), this.getContextUtilities())).setFormat(FhirFormat.JSON);
     checkObject(errors, object, baseElement, path);
     baseElement.markLocation(line(object), col(object));
     baseElement.setType(name);
@@ -259,9 +252,9 @@ public class JsonParser extends ParserBase {
     if (policy != ValidationPolicy.NONE) {
       for (JsonProperty e : children) {
         if (e.getTag() == 0) {
-          StructureDefinition sd = element.getProperty().isLogical() ? contextUtilities.fetchByJsonName(e.getName()) : null;
+          StructureDefinition sd = element.getProperty().isLogical() ? getContextUtilities().fetchByJsonName(e.getName()) : null;
           if (sd != null) {
-            Property property = new Property(context, sd.getSnapshot().getElementFirstRep(), sd, element.getProperty().getUtils());
+            Property property = new Property(context, sd.getSnapshot().getElementFirstRep(), sd, element.getProperty().getUtils(), element.getProperty().getContextUtils());
             parseChildItem(errors, path, children, element, property);
           } else if ("fhir_comments".equals(e.getName()) && (VersionUtilities.isR2BVer(context.getVersion()) || VersionUtilities.isR2Ver(context.getVersion()))) {
             if (!e.getValue().isJsonArray()) {
@@ -341,7 +334,7 @@ public class JsonParser extends ParserBase {
           if (type == null) {
             logError(errors, ValidationMessage.NO_RULE_DATE, line(je), col(je), path, IssueType.STRUCTURE, this.context.formatMessage(I18nConstants.UNRECOGNISED_PROPERTY_TYPE, describeType(je), property.getName(), property.typeSummary()), IssueSeverity.ERROR);
           } else if (property.hasType(type)) {
-            Property np = new Property(property.getContext(), property.getDefinition(), property.getStructure(), property.getUtils(), type);
+            Property np = new Property(property.getContext(), property.getDefinition(), property.getStructure(), property.getUtils(), property.getContextUtils(), type);
             parseChildPrimitive(errors, jp, getJsonPropertyByName("_"+property.getJsonName(), children), context, np, path, property.getName(), false);
           } else {
             logError(errors, ValidationMessage.NO_RULE_DATE, line(je), col(je), path, IssueType.STRUCTURE, this.context.formatMessage(I18nConstants.UNRECOGNISED_PROPERTY_TYPE_WRONG, describeType(je), property.getName(), type, property.typeSummary()), IssueSeverity.ERROR);
@@ -474,7 +467,7 @@ public class JsonParser extends ParserBase {
               if (type == null) {
                 logError(errors, ValidationMessage.NO_RULE_DATE, line(pv.getValue()), col(pv.getValue()), path, IssueType.STRUCTURE, this.context.formatMessage(I18nConstants.UNRECOGNISED_PROPERTY_TYPE, describeType(pv.getValue()), propV.getName(), propV.typeSummary()), IssueSeverity.ERROR);
               } else if (propV.hasType(type)) {
-                pvl = new Property(propV.getContext(), propV.getDefinition(), propV.getStructure(), propV.getUtils(), type);
+                pvl = new Property(propV.getContext(), propV.getDefinition(), propV.getStructure(), propV.getUtils(), propV.getContextUtils(), type);
                 ok = true;
               } else {
                 logError(errors, ValidationMessage.NO_RULE_DATE, line(pv.getValue()), col(pv.getValue()), path, IssueType.STRUCTURE, this.context.formatMessage(I18nConstants.UNRECOGNISED_PROPERTY_TYPE_WRONG, describeType(pv.getValue()), propV.getName(), type, propV.typeSummary()), IssueSeverity.ERROR);
@@ -713,7 +706,7 @@ public class JsonParser extends ParserBase {
       if (sd == null) {
         logError(errors, ValidationMessage.NO_RULE_DATE, line(res), col(res), npath, IssueType.INVALID, context.formatMessage(I18nConstants.CONTAINED_RESOURCE_DOES_NOT_APPEAR_TO_BE_A_FHIR_RESOURCE_UNKNOWN_NAME_, name), IssueSeverity.FATAL);			    
       } else {
-        parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd, this.profileUtilities), SpecialElement.fromProperty(parent.getProperty()), elementProperty);
+        parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd, this.getProfileUtilities(), this.getContextUtilities()), SpecialElement.fromProperty(parent.getProperty()), elementProperty);
         parent.setType(name);
         parseChildren(errors, npath, res, parent, true, null);
       }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ParserBase.java

@@ -39,8 +39,10 @@ import java.util.List;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
 import org.hl7.fhir.r5.context.ContextUtilities;
 import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.fhirpath.FHIRPathEngine;
 import org.hl7.fhir.r5.formats.FormatUtilities;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.model.StructureDefinition;
@@ -89,14 +91,26 @@ public abstract class ParserBase {
   protected IdRenderingPolicy idPolicy = IdRenderingPolicy.All;
   protected StructureDefinition logical;
   protected IDigitalSignatureServices signatureServices;
-  
+  private ProfileUtilities profileUtilities;
-	public ParserBase(IWorkerContext context) {
+  private ContextUtilities contextUtilities;
+
+	public ParserBase(IWorkerContext context, ProfileUtilities utilities) {
 		super();
 		this.context = context;
+    this.profileUtilities = utilities;
+    contextUtilities = new ContextUtilities(context);
 		policy = ValidationPolicy.NONE;
 	}
 
-	public void setupValidation(ValidationPolicy policy) {
+	public ParserBase(IWorkerContext context) {
+	  super();
+    this.context = context;
+    this.profileUtilities = new ProfileUtilities(context, null, null, new FHIRPathEngine(context));
+    contextUtilities = new ContextUtilities(context);
+    policy = ValidationPolicy.NONE;
+  }
+
+  public void setupValidation(ValidationPolicy policy) {
 	  this.policy = policy;
 	}
 
@@ -215,19 +229,19 @@ public abstract class ParserBase {
     // first pass: only look at base definitions
 	  for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) {
 	    if (sd.getUrl().equals("http://hl7.org/fhir/StructureDefinition/"+name)) {
-	      new ContextUtilities(context).generateSnapshot(sd); 
+	      contextUtilities.generateSnapshot(sd); 
 	      return sd;
 	    }
 	  }
     for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) {
       if (name.equals(sd.getTypeName()) && sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
-        new ContextUtilities(context).generateSnapshot(sd); 
+        contextUtilities.generateSnapshot(sd); 
         return sd;
       }
     }
     for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) {
       if (name.equals(sd.getUrl()) && sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
-        new ContextUtilities(context).generateSnapshot(sd); 
+        contextUtilities.generateSnapshot(sd); 
         return sd;
       }
     }
@@ -304,4 +318,22 @@ public abstract class ParserBase {
       return element.getNamedChildValue("reference");
     }
   }
+
+  public IWorkerContext getContext() {
+    return context;
+  }
+
+  public ValidationPolicy getPolicy() {
+    return policy;
+  }
+
+  public ProfileUtilities getProfileUtilities() {
+    return profileUtilities;
+  }
+
+  public ContextUtilities getContextUtilities() {
+    return contextUtilities;
+  }
+  
+  
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Property.java

@@ -38,6 +38,7 @@ import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
 import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.SourcedChildDefinitions;
+import org.hl7.fhir.r5.context.ContextUtilities;
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.fhirpath.TypeDetails;
 import org.hl7.fhir.r5.formats.FormatUtilities;
@@ -60,21 +61,24 @@ public class Property {
 	private ElementDefinition definition;
 	private StructureDefinition structure;
   private ProfileUtilities profileUtilities;
+  private ContextUtilities utils;
   private TypeRefComponent type;
 
-  public Property(IWorkerContext context, ElementDefinition definition, StructureDefinition structure, ProfileUtilities profileUtilities) {
+  public Property(IWorkerContext context, ElementDefinition definition, StructureDefinition structure, ProfileUtilities profileUtilities, ContextUtilities utils) {
 		this.context = context;
 		this.definition = definition;
 		this.structure = structure;
+		this.utils = utils;
     this.profileUtilities = profileUtilities;
 	}
 
 
-  public Property(IWorkerContext context, ElementDefinition definition, StructureDefinition structure, ProfileUtilities profileUtilities, String type) {
+  public Property(IWorkerContext context, ElementDefinition definition, StructureDefinition structure, ProfileUtilities profileUtilities, ContextUtilities utils, String type) {
     this.context = context;
     this.definition = definition;
     this.structure = structure;
     this.profileUtilities = profileUtilities;
+    this.utils = utils;
     for (TypeRefComponent tr : definition.getType()) {
       if (tr.getWorkingCode().equals(type)) {
         this.type = tr;
@@ -83,7 +87,7 @@ public class Property {
   }
   
 	public Property(IWorkerContext context, ElementDefinition definition, StructureDefinition structure) {
-    this(context, definition, structure, new ProfileUtilities(context, null, null));
+    this(context, definition, structure, new ProfileUtilities(context, null, null), new ContextUtilities(context));
 	}
 
 	public String getName() {
@@ -265,10 +269,10 @@ public class Property {
 	public boolean isResource() {
 	  if (type != null) {
 	    String tc = type.getCode();
-      return (("Resource".equals(tc) || "DomainResource".equals(tc)) ||  Utilities.existsInList(tc, context.getResourceNames()));
+      return (("Resource".equals(tc) || "DomainResource".equals(tc)) || utils.isResource(tc));
 	  } else if (definition.getType().size() > 0) {
       String tc = definition.getType().get(0).getCode();
-      return definition.getType().size() == 1 && (("Resource".equals(tc) || "DomainResource".equals(tc)) ||  Utilities.existsInList(tc, context.getResourceNames()));
+      return definition.getType().size() == 1 && (("Resource".equals(tc) || "DomainResource".equals(tc)) ||  utils.isResource(tc));
     }
 	  else {
 	    return !definition.getPath().contains(".") && (structure.getKind() == StructureDefinitionKind.RESOURCE);
@@ -425,7 +429,7 @@ public class Property {
     }
     List<Property> properties = new ArrayList<Property>();
     for (ElementDefinition child : children.getList()) {
-      properties.add(new Property(context, child, sd, this.profileUtilities));
+      properties.add(new Property(context, child, sd, this.profileUtilities, this.utils));
     }
     profileUtilities.getCachedPropertyList().put(cacheKey, properties);
     return properties;
@@ -485,7 +489,7 @@ public class Property {
     }
     List<Property> properties = new ArrayList<Property>();
     for (ElementDefinition child : children.getList()) {
-      properties.add(new Property(context, child, sd, this.profileUtilities));
+      properties.add(new Property(context, child, sd, this.profileUtilities, this.utils));
     }
     return properties;
   }
@@ -613,6 +617,9 @@ public class Property {
   public ProfileUtilities getUtils() {
     return profileUtilities;
   }
+  public ContextUtilities getContextUtils() {
+    return utils;
+  }
 
   public boolean isJsonPrimitiveChoice() {
     return ToolingExtensions.readBoolExtension(definition, ToolingExtensions.EXT_JSON_PRIMITIVE_CHOICE);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ResourceParser.java

@@ -50,7 +50,7 @@ public class ResourceParser extends ParserBase {
     if (sd == null) {
       throw new FHIRException("No definition exists for "+resource.fhirType());
     }
-    Property p = new Property(context, sd.getSnapshot().getElement().get(0), sd, new ProfileUtilities(context, null, null));
+    Property p = new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities());
     String path = resource.fhirType();
     
     Element e = new Element(resource.fhirType(), p);
@@ -106,7 +106,7 @@ public class ResourceParser extends ParserBase {
             StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(v.fhirType(), null));
             if (sd == null)
               throw new FHIRFormatError(context.formatMessage(I18nConstants.CONTAINED_RESOURCE_DOES_NOT_APPEAR_TO_BE_A_FHIR_RESOURCE_UNKNOWN_NAME_, v.fhirType()));
-            n.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd), SpecialElement.fromProperty(n.getProperty()), p);
+            n.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities()), SpecialElement.fromProperty(n.getProperty()), p);
             n.setType(v.fhirType());
             parseChildren(npath, v, n);
           } else {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/TurtleParser.java

@@ -151,7 +151,7 @@ public class TurtleParser extends ParserBase {
     if (sd == null)
       return null;
 
-    Element result = new Element(name, new Property(context, sd.getSnapshot().getElement().get(0), sd)).setFormat(FhirFormat.TURTLE);
+    Element result = new Element(name, new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities())).setFormat(FhirFormat.TURTLE);
     result.markLocation(cmp.getLine(), cmp.getCol());
     result.setType(name);
     parseChildren(errors, src, path, cmp, result, false);
@@ -279,7 +279,7 @@ public class TurtleParser extends ParserBase {
     
     Element n = new Element(tail(name), property).markLocation(object.getLine(), object.getCol()).setFormat(FhirFormat.TURTLE);
     element.getChildren().add(n);
-    n.updateProperty(new Property(this.context, sd.getSnapshot().getElement().get(0), sd), SpecialElement.fromProperty(n.getProperty()), property);
+    n.updateProperty(new Property(this.context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities()), SpecialElement.fromProperty(n.getProperty()), property);
     n.setType(rt);
     parseChildren(errors, src, npath, obj, n, false);
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/VerticalBarParser.java

@@ -456,7 +456,7 @@ public class VerticalBarParser extends ParserBase {
   @Override
   public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRFormatError, DefinitionException, FHIRException {
     StructureDefinition sd = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/v2/StructureDefinition/Message");
-    Element message = new Element("Message", new Property(context, sd.getSnapshot().getElementFirstRep(), sd));
+    Element message = new Element("Message", new Property(context, sd.getSnapshot().getElementFirstRep(), sd, getProfileUtilities(), getContextUtilities()));
     byte[] content = TextFile.streamToBytes(inStream);
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
     VerticalBarParserReader reader = new VerticalBarParserReader(new BufferedInputStream(stream), charset);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java

@@ -231,7 +231,7 @@ public class XmlParser extends ParserBase {
     if (sd == null)
       return null;
 
-    Element result = new Element(element.getLocalName(), new Property(context, sd.getSnapshot().getElement().get(0), sd)).setFormat(FhirFormat.XML);
+    Element result = new Element(element.getLocalName(), new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities())).setFormat(FhirFormat.XML);
     result.setPath(element.getLocalName());
     checkElement(errors, element, result, path, result.getProperty(), false);
     result.markLocation(line(element, false), col(element, false));
@@ -321,7 +321,7 @@ public class XmlParser extends ParserBase {
   
   public Element parse(List<ValidationMessage> errors, org.w3c.dom.Element base, String type) throws Exception {
     StructureDefinition sd = getDefinition(errors, 0, 0, FormatUtilities.FHIR_NS, type);
-    Element result = new Element(base.getLocalName(), new Property(context, sd.getSnapshot().getElement().get(0), sd)).setFormat(FhirFormat.XML).setNativeObject(base);
+    Element result = new Element(base.getLocalName(), new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities())).setFormat(FhirFormat.XML).setNativeObject(base);
     result.setPath(base.getLocalName());
     String path = "/"+pathPrefix(base.getNamespaceURI())+base.getLocalName();
     checkElement(errors, base, result, path, result.getProperty(), false);
@@ -662,7 +662,7 @@ public class XmlParser extends ParserBase {
     StructureDefinition sd = context.fetchResource(StructureDefinition.class, ProfileUtilities.sdNs(name, null));
     if (sd == null)
       throw new FHIRFormatError(context.formatMessage(I18nConstants.CONTAINED_RESOURCE_DOES_NOT_APPEAR_TO_BE_A_FHIR_RESOURCE_UNKNOWN_NAME_, res.getLocalName()));
-    parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd), SpecialElement.fromProperty(parent.getProperty()), elementProperty);
+    parent.updateProperty(new Property(context, sd.getSnapshot().getElement().get(0), sd, getProfileUtilities(), getContextUtilities()), SpecialElement.fromProperty(parent.getProperty()), elementProperty);
     parent.setType(name);
     parseChildren(errors, res.getLocalName(), res, parent);
   }