package org.hl7.fhir.r4.utils;

// remember group resolution
// trace - account for which wasn't transformed in the source

import java.io.IOException;
import java.util.ArrayList;
import java.util.EnumSet;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.UUID;

import org.hl7.fhir.r4.conformance.ProfileUtilities;
import org.hl7.fhir.r4.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r4.context.IWorkerContext;
import org.hl7.fhir.r4.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r4.elementmodel.Element;
import org.hl7.fhir.r4.elementmodel.Property;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupUnmappedMode;
import org.hl7.fhir.r4.model.ConceptMap.SourceElementComponent;
import org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent;
import org.hl7.fhir.r4.model.Constants;
import org.hl7.fhir.r4.model.ContactDetail;
import org.hl7.fhir.r4.model.ContactPoint;
import org.hl7.fhir.r4.model.DecimalType;
import org.hl7.fhir.r4.model.ElementDefinition;
import org.hl7.fhir.r4.model.ElementDefinition.ElementDefinitionMappingComponent;
import org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r4.model.Enumeration;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r4.model.ExpressionNode;
import org.hl7.fhir.r4.model.ExpressionNode.CollectionStatus;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
import org.hl7.fhir.r4.model.PrimitiveType;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.ResourceFactory;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionMappingComponent;
import org.hl7.fhir.r4.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r4.model.StructureMap;
import org.hl7.fhir.r4.model.StructureMap.StructureMapContextType;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupInputComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleDependentComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleSourceComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleTargetComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupRuleTargetParameterComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapGroupTypeMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapInputMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapSourceListMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapTargetListMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapModelMode;
import org.hl7.fhir.r4.model.StructureMap.StructureMapStructureComponent;
import org.hl7.fhir.r4.model.StructureMap.StructureMapTransform;
import org.hl7.fhir.r4.model.Type;
import org.hl7.fhir.r4.model.TypeDetails;
import org.hl7.fhir.r4.model.TypeDetails.ProfiledType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.r4.utils.FHIRLexer.FHIRLexerException;
import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.xhtml.NodeType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;

/**
 * Services in this class:
 * 
 * string render(map) - take a structure and convert it to text
 * map parse(text) - take a text representation and parse it 
 * getTargetType(map) - return the definition for the type to create to hand in 
 * transform(appInfo, source, map, target) - transform from source to target following the map
 * analyse(appInfo, map) - generate profiles and other analysis artifacts for the targets of the transform
 * map generateMapFromMappings(StructureDefinition) - build a mapping from a structure definition with loigcal mappings
 *  
 * @author Grahame Grieve
 *
 */
public class StructureMapUtilities {

        public class ResolvedGroup {
    public StructureMapGroupComponent target;
    public StructureMap targetMap;
  }
  public static final String MAP_WHERE_CHECK = "map.where.check";
  public static final String MAP_WHERE_LOG = "map.where.log";
        public static final String MAP_WHERE_EXPRESSION = "map.where.expression";
        public static final String MAP_SEARCH_EXPRESSION = "map.search.expression";
        public static final String MAP_EXPRESSION = "map.transform.expression";
  private static final boolean RENDER_MULTIPLE_TARGETS_ONELINE = true;
  private static final String AUTO_VAR_NAME = "vvv";

        public interface ITransformerServices {
                //    public boolean validateByValueSet(Coding code, String valuesetId);
          public void log(String message); // log internal progress
          public Base createType(Object appInfo, String name) throws FHIRException;
    public Base createResource(Object appInfo, Base res, boolean atRootofTransform); // an already created resource is provided; this is to identify/store it
                public Coding translate(Object appInfo, Coding source, String conceptMapUrl) throws FHIRException;
                //    public Coding translate(Coding code)
                //    ValueSet validation operation
                //    Translation operation
                //    Lookup another tree of data
                //    Create an instance tree
                //    Return the correct string format to refer to a tree (input or output)
    public Base resolveReference(Object appContext, String url) throws FHIRException;
    public List<Base> performSearch(Object appContext, String url) throws FHIRException;
        }

        private class FFHIRPathHostServices implements IEvaluationContext{

    public Base resolveConstant(Object appContext, String name) throws PathEngineException {
      Variables vars = (Variables) appContext;
      Base res = vars.get(VariableMode.INPUT, name);
      if (res == null)
        res = vars.get(VariableMode.OUTPUT, name);
      return res;
    }

    @Override
    public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException {
      if (!(appContext instanceof VariablesForProfiling)) 
        throw new Error("Internal Logic Error (wrong type '"+appContext.getClass().getName()+"' in resolveConstantType)");
      VariablesForProfiling vars = (VariablesForProfiling) appContext;
      VariableForProfiling v = vars.get(null, name);
      if (v == null)
        throw new PathEngineException("Unknown variable '"+name+"' from variables "+vars.summary());
      return v.property.types;
    }

    @Override
    public boolean log(String argument, List<Base> focus) {
      throw new Error("Not Implemented Yet");
    }

    @Override
    public FunctionDetails resolveFunction(String functionName) {
      return null; // throw new Error("Not Implemented Yet");
    }

    @Override
    public TypeDetails checkFunction(Object appContext, String functionName, List<TypeDetails> parameters) throws PathEngineException {
      throw new Error("Not Implemented Yet");
    }

    @Override
    public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> parameters) {
      throw new Error("Not Implemented Yet");
    }

    @Override
    public Base resolveReference(Object appContext, String url) throws FHIRException {
      if (services == null)
        return null;
      return services.resolveReference(appContext, url);
    }

    @Override
    public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
      IResourceValidator val = worker.newValidator();
      List<ValidationMessage> valerrors = new ArrayList<ValidationMessage>();
      if (item instanceof Resource) {
        val.validate(appContext, valerrors, (Resource) item, url);
        boolean ok = true;
        for (ValidationMessage v : valerrors)
          ok = ok && v.getLevel().isError();
        return ok;
      }
      throw new NotImplementedException("Not done yet (FFHIRPathHostServices.conformsToProfile), when item is element");
    }
          
        }
        private IWorkerContext worker;
        private FHIRPathEngine fpe;
        private ITransformerServices services;
  private ProfileKnowledgeProvider pkp;
  private Map<String, Integer> ids = new HashMap<String, Integer>(); 

        public StructureMapUtilities(IWorkerContext worker, ITransformerServices services, ProfileKnowledgeProvider pkp) {
                super();
                this.worker = worker;
                this.services = services;
                this.pkp = pkp;
                fpe = new FHIRPathEngine(worker);
                fpe.setHostServices(new FFHIRPathHostServices());
        }

        public StructureMapUtilities(IWorkerContext worker, ITransformerServices services) {
                super();
                this.worker = worker;
                this.services = services;
                fpe = new FHIRPathEngine(worker);
    fpe.setHostServices(new FFHIRPathHostServices());
        }

  public StructureMapUtilities(IWorkerContext worker) {
    super();
    this.worker = worker;
    fpe = new FHIRPathEngine(worker);
    fpe.setHostServices(new FFHIRPathHostServices());
  }

        public static String render(StructureMap map) {
                StringBuilder b = new StringBuilder();
                b.append("map \"");
                b.append(map.getUrl());
                b.append("\" = \"");
                b.append(Utilities.escapeJava(map.getName()));
                b.append("\"\r\n\r\n");

                renderConceptMaps(b, map);
                renderUses(b, map);
                renderImports(b, map);
                for (StructureMapGroupComponent g : map.getGroup())
                        renderGroup(b, g);
                return b.toString();
        }

        private static void renderConceptMaps(StringBuilder b, StructureMap map) {
    for (Resource r : map.getContained()) {
      if (r instanceof ConceptMap) {
        produceConceptMap(b, (ConceptMap) r);
      }
    }
  }

  private static void produceConceptMap(StringBuilder b, ConceptMap cm) {
    b.append("conceptmap \"");
    b.append(cm.getId());
    b.append("\" {\r\n");
    Map<String, String> prefixesSrc = new HashMap<String, String>();
    Map<String, String> prefixesTgt = new HashMap<String, String>();
    char prefix = 's';
    for (ConceptMapGroupComponent cg : cm.getGroup()) {
      if (!prefixesSrc.containsKey(cg.getSource())) {
        prefixesSrc.put(cg.getSource(), String.valueOf(prefix));
        b.append("  prefix ");
        b.append(prefix);
        b.append(" = \"");
        b.append(cg.getSource());
        b.append("\"\r\n");
        prefix++;
      }
      if (!prefixesTgt.containsKey(cg.getTarget())) {
        prefixesTgt.put(cg.getTarget(), String.valueOf(prefix));
        b.append("  prefix ");
        b.append(prefix);
        b.append(" = \"");
        b.append(cg.getTarget());
        b.append("\"\r\n");
        prefix++;
      }
    }
    b.append("\r\n");
    for (ConceptMapGroupComponent cg : cm.getGroup()) {
      if (cg.hasUnmapped()) {
        b.append("  unmapped for ");
        b.append(prefix);
        b.append(" = ");
        b.append(cg.getUnmapped().getMode());
        b.append("\r\n"); 
      }   
    }
    
    for (ConceptMapGroupComponent cg : cm.getGroup()) {
      for (SourceElementComponent ce : cg.getElement()) {
        b.append("  ");
        b.append(prefixesSrc.get(cg.getSource()));
        b.append(":");
        b.append(ce.getCode());
        b.append(" ");
        b.append(getChar(ce.getTargetFirstRep().getEquivalence()));
        b.append(" ");
        b.append(prefixesTgt.get(cg.getTarget()));
        b.append(":");
        b.append(ce.getTargetFirstRep().getCode());
        b.append("\r\n");
      }
    }
    b.append("}\r\n\r\n");
  }

  private static Object getChar(ConceptMapEquivalence equivalence) {
    switch (equivalence) {
    case RELATEDTO: return "-";
    case EQUAL: return "=";
    case EQUIVALENT: return "==";
    case DISJOINT: return "!=";
    case UNMATCHED: return "--";
    case WIDER: return "<=";
    case SUBSUMES: return "<-";
    case NARROWER: return ">=";
    case SPECIALIZES: return ">-";
    case INEXACT: return "~";
    default: return "??";
    }
  }

  private static void renderUses(StringBuilder b, StructureMap map) {
                for (StructureMapStructureComponent s : map.getStructure()) {
                        b.append("uses \"");
                        b.append(s.getUrl());
      b.append("\" ");
      if (s.hasAlias()) {
        b.append("alias ");
        b.append(s.getAlias());
        b.append(" ");
      }
      b.append("as ");
                        b.append(s.getMode().toCode());
                        b.append("\r\n");
                        renderDoco(b, s.getDocumentation());
                }
                if (map.hasStructure())
                        b.append("\r\n");
        }

        private static void renderImports(StringBuilder b, StructureMap map) {
                for (UriType s : map.getImport()) {
                        b.append("imports \"");
                        b.append(s.getValue());
                        b.append("\"\r\n");
                }
                if (map.hasImport())
                        b.append("\r\n");
        }

  public static String groupToString(StructureMapGroupComponent g) {
    StringBuilder b = new StringBuilder();
    renderGroup(b, g);
    return b.toString();
  }
  
  private static void renderGroup(StringBuilder b, StructureMapGroupComponent g) {
                b.append("group ");
    switch (g.getTypeMode()) {
    case TYPES: 
                 b.append("for types");
                 break;
    case TYPEANDTYPES: 
                 b.append("for type+types ");
                 break;
    default: // NONE, NULL
    }
                b.append(g.getName());
                if (g.hasExtends()) {
                        b.append(" extends ");
                        b.append(g.getExtends());
                }
                if (g.hasDocumentation()) 
                        renderDoco(b, g.getDocumentation());
                b.append("\r\n");
                for (StructureMapGroupInputComponent gi : g.getInput()) {
                        b.append("  input ");
                        b.append(gi.getName());
                        if (gi.hasType()) {
                                b.append(" : ");
                                b.append(gi.getType());
                        }
                        b.append(" as ");
                        b.append(gi.getMode().toCode());
                        b.append("\r\n");
                }
                if (g.hasInput())
                        b.append("\r\n");
                for (StructureMapGroupRuleComponent r : g.getRule()) {
                        renderRule(b, r, 2);
                }
                b.append("\r\nendgroup\r\n");
        }

  public static String ruleToString(StructureMapGroupRuleComponent r) {
    StringBuilder b = new StringBuilder();
    renderRule(b, r, 0);
    return b.toString();
  }
  
        private static void renderRule(StringBuilder b, StructureMapGroupRuleComponent r, int indent) {
                for (int i = 0; i < indent; i++)
                        b.append(' ');
                b.append(r.getName());
                b.append(" : for ");
                boolean canBeAbbreviated = checkisSimple(r);
                
                boolean first = true;
                for (StructureMapGroupRuleSourceComponent rs : r.getSource()) {
                        if (first)
                                first = false;
                        else
                                b.append(", ");
                        renderSource(b, rs, canBeAbbreviated);
                }
                if (r.getTarget().size() > 1) {
                        b.append(" make ");
                        first = true;
                        for (StructureMapGroupRuleTargetComponent rt : r.getTarget()) {
                                if (first)
                                        first = false;
                                else
                                        b.append(", ");
                                if (RENDER_MULTIPLE_TARGETS_ONELINE)
                b.append(' ');
                                else {
                                b.append("\r\n");
                                for (int i = 0; i < indent+4; i++)
                                        b.append(' ');
                                }
                                renderTarget(b, rt, false);
                        }
                } else if (r.hasTarget()) { 
                        b.append(" make ");
                        renderTarget(b, r.getTarget().get(0), canBeAbbreviated);
                }
                if (!canBeAbbreviated) {
                  if (r.hasRule()) {
                    b.append(" then {\r\n");
                    renderDoco(b, r.getDocumentation());
                    for (StructureMapGroupRuleComponent ir : r.getRule()) {
                      renderRule(b, ir, indent+2);
                    }
                    for (int i = 0; i < indent; i++)
                      b.append(' ');
                    b.append("}\r\n");
                  } else {
                    if (r.hasDependent()) {
                      b.append(" then ");
                      first = true;
                      for (StructureMapGroupRuleDependentComponent rd : r.getDependent()) {
                        if (first)
                          first = false;
                        else
                          b.append(", ");
                        b.append(rd.getName());
                        b.append("(");
                        boolean ifirst = true;
                        for (StringType rdp : rd.getVariable()) {
                          if (ifirst)
                            ifirst = false;
                          else
                            b.append(", ");
                          b.append(rdp.asStringValue());
                        }
                        b.append(")");
                      }
                    }
                  }
                }
    renderDoco(b, r.getDocumentation());
    b.append("\r\n");
        }

  private static boolean checkisSimple(StructureMapGroupRuleComponent r) {
    return 
          (r.getSource().size() == 1 && r.getSourceFirstRep().hasElement() && r.getSourceFirstRep().hasVariable()) && 
          (r.getTarget().size() == 1 && r.getTargetFirstRep().hasVariable() && (r.getTargetFirstRep().getTransform() == null || r.getTargetFirstRep().getTransform() == StructureMapTransform.CREATE) && r.getTargetFirstRep().getParameter().size() == 0) &&
          (r.getDependent().size() == 0);
  }

  public static String sourceToString(StructureMapGroupRuleSourceComponent r) {
    StringBuilder b = new StringBuilder();
    renderSource(b, r, false);
    return b.toString();
  }
  
        private static void renderSource(StringBuilder b, StructureMapGroupRuleSourceComponent rs, boolean abbreviate) {
                b.append(rs.getContext());
                if (rs.getContext().equals("@search")) {
      b.append('(');
      b.append(rs.getElement());
      b.append(')');
                } else if (rs.hasElement()) {
                        b.append('.');
                        b.append(rs.getElement());
                }
                if (rs.hasType()) {
      b.append(" : ");
      b.append(rs.getType());
      if (rs.hasMin()) {
        b.append(" ");
        b.append(rs.getMin());
        b.append("..");
        b.append(rs.getMax());
      }
                }
                
                if (rs.hasListMode()) {
                        b.append(" ");
                                b.append(rs.getListMode().toCode());
                }
                if (rs.hasDefaultValue()) {
                  b.append(" default ");
                  assert rs.getDefaultValue() instanceof StringType;
                  b.append("\""+Utilities.escapeJson(((StringType) rs.getDefaultValue()).asStringValue())+"\"");
                }
                if (!abbreviate && rs.hasVariable()) {
                        b.append(" as ");
                        b.append(rs.getVariable());
                }
                if (rs.hasCondition())  {
                        b.append(" where ");
                        b.append(rs.getCondition());
                }
                if (rs.hasCheck())  {
                        b.append(" check ");
                        b.append(rs.getCheck());
                }
    if (rs.hasLogMessage()) {
      b.append(" log ");
      b.append(rs.getLogMessage());
    }
        }

  public static String targetToString(StructureMapGroupRuleTargetComponent rt) {
    StringBuilder b = new StringBuilder();
    renderTarget(b, rt, false);
    return b.toString();
  }
        
        private static void renderTarget(StringBuilder b, StructureMapGroupRuleTargetComponent rt, boolean abbreviate) {
          if (rt.hasContext()) {
            if (rt.getContextType() == StructureMapContextType.TYPE)
              b.append("@");
                b.append(rt.getContext());
                if (rt.hasElement())  {
                        b.append('.');
                        b.append(rt.getElement());
                }
          }
                if (!abbreviate && rt.hasTransform()) {
            if (rt.hasContext()) 
                        b.append(" = ");
                        if (rt.getTransform() == StructureMapTransform.COPY && rt.getParameter().size() == 1) {
                                renderTransformParam(b, rt.getParameter().get(0));
      } else if (rt.getTransform() == StructureMapTransform.EVALUATE && rt.getParameter().size() == 1) {
        b.append("(");
        b.append("\""+((StringType) rt.getParameter().get(0).getValue()).asStringValue()+"\"");
        b.append(")");
                        } else if (rt.getTransform() == StructureMapTransform.EVALUATE && rt.getParameter().size() == 2) {
                                b.append(rt.getTransform().toCode());
                                b.append("(");
                                b.append(((IdType) rt.getParameter().get(0).getValue()).asStringValue());
                                b.append("\""+((StringType) rt.getParameter().get(1).getValue()).asStringValue()+"\"");
                                b.append(")");
                        } else {
                                b.append(rt.getTransform().toCode());
                                b.append("(");
                                boolean first = true;
                                for (StructureMapGroupRuleTargetParameterComponent rtp : rt.getParameter()) {
                                        if (first)
                                                first = false;
                                        else
                                                b.append(", ");
                                        renderTransformParam(b, rtp);
                                }
                                b.append(")");
                        }
                }
                if (!abbreviate && rt.hasVariable()) {
                        b.append(" as ");
                        b.append(rt.getVariable());
                }
                for (Enumeration<StructureMapTargetListMode> lm : rt.getListMode()) {
                        b.append(" ");
                        b.append(lm.getValue().toCode());
                        if (lm.getValue() == StructureMapTargetListMode.SHARE) {
                                b.append(" ");
                                b.append(rt.getListRuleId());
                        }
                }
        }

  public static String paramToString(StructureMapGroupRuleTargetParameterComponent rtp) {
    StringBuilder b = new StringBuilder();
    renderTransformParam(b, rtp);
    return b.toString();
  }
        
        private static void renderTransformParam(StringBuilder b, StructureMapGroupRuleTargetParameterComponent rtp) {
          try {
                if (rtp.hasValueBooleanType())
                        b.append(rtp.getValueBooleanType().asStringValue());
                else if (rtp.hasValueDecimalType())
                        b.append(rtp.getValueDecimalType().asStringValue());
                else if (rtp.hasValueIdType())
                        b.append(rtp.getValueIdType().asStringValue());
                else if (rtp.hasValueDecimalType())
                        b.append(rtp.getValueDecimalType().asStringValue());
                else if (rtp.hasValueIntegerType())
                        b.append(rtp.getValueIntegerType().asStringValue());
                else 
              b.append("\""+Utilities.escapeJava(rtp.getValueStringType().asStringValue())+"\"");
          } catch (FHIRException e) {
            e.printStackTrace();
            b.append("error!");
          }
        }

        private static void renderDoco(StringBuilder b, String doco) {
                if (Utilities.noString(doco))
                        return;
                b.append(" // ");
                b.append(doco.replace("\r\n", " ").replace("\r", " ").replace("\n", " "));
        }

        public StructureMap parse(String text) throws FHIRException {
                FHIRLexer lexer = new FHIRLexer(text);
                if (lexer.done())
                        throw lexer.error("Map Input cannot be empty");
                lexer.skipComments();
                lexer.token("map");
                StructureMap result = new StructureMap();
                result.setUrl(lexer.readConstant("url"));
                lexer.token("=");
                result.setName(lexer.readConstant("name"));
                lexer.skipComments();

                while (lexer.hasToken("conceptmap"))
                        parseConceptMap(result, lexer);

                while (lexer.hasToken("uses"))
                        parseUses(result, lexer);
                while (lexer.hasToken("imports"))
                        parseImports(result, lexer);

                parseGroup(result, lexer);

                while (!lexer.done()) {
                        parseGroup(result, lexer);    
                }

                return result;
        }

        private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
                lexer.token("conceptmap");
                ConceptMap map = new ConceptMap();
                String id = lexer.readConstant("map id");
                if (!id.startsWith("#"))
                        lexer.error("Concept Map identifier must start with #");
                map.setId(id);
                map.setStatus(PublicationStatus.DRAFT); // todo: how to add this to the text format
                result.getContained().add(map);
                lexer.token("{");
                lexer.skipComments();
                //        lexer.token("source");
                //        map.setSource(new UriType(lexer.readConstant("source")));
                //        lexer.token("target");
                //        map.setSource(new UriType(lexer.readConstant("target")));
                Map<String, String> prefixes = new HashMap<String, String>();
                while (lexer.hasToken("prefix")) {
                        lexer.token("prefix");
                        String n = lexer.take();
                        lexer.token("=");
                        String v = lexer.readConstant("prefix url");
                        prefixes.put(n, v);
                }
                while (lexer.hasToken("unmapped")) {
                  lexer.token("unmapped");
      lexer.token("for");
      String n = readPrefix(prefixes, lexer);
      ConceptMapGroupComponent g = getGroup(map, n, null);
                  lexer.token("=");
      String v = lexer.take();
      if (v.equals("provided")) {
        g.getUnmapped().setMode(ConceptMapGroupUnmappedMode.PROVIDED);
      } else
        lexer.error("Only unmapped mode PROVIDED is supported at this time");
                }
                while (!lexer.hasToken("}")) {
                  String srcs = readPrefix(prefixes, lexer);
                        lexer.token(":");
      String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
                  ConceptMapEquivalence eq = readEquivalence(lexer);
                  String tgts = (eq != ConceptMapEquivalence.UNMATCHED) ? readPrefix(prefixes, lexer) : "";
                  ConceptMapGroupComponent g = getGroup(map, srcs, tgts);
                        SourceElementComponent e = g.addElement();
                        e.setCode(sc);
      if (e.getCode().startsWith("\""))
        e.setCode(lexer.processConstant(e.getCode()));
                        TargetElementComponent tgt = e.addTarget();
                        if (eq != ConceptMapEquivalence.EQUIVALENT)
                          tgt.setEquivalence(eq);
                        if (tgt.getEquivalence() != ConceptMapEquivalence.UNMATCHED) {
                                lexer.token(":");
                                tgt.setCode(lexer.take());
                                if (tgt.getCode().startsWith("\""))
                                  tgt.setCode(lexer.processConstant(tgt.getCode()));
                        }
                        if (lexer.hasComment())
                                tgt.setComment(lexer.take().substring(2).trim());
                }
                lexer.token("}");
        }


        private ConceptMapGroupComponent getGroup(ConceptMap map, String srcs, String tgts) {
          for (ConceptMapGroupComponent grp : map.getGroup()) {
            if (grp.getSource().equals(srcs)) 
              if ((tgts == null && !grp.hasTarget()) || (tgts != null && tgts.equals(grp.getTarget())))
              return grp;
          }
          ConceptMapGroupComponent grp = map.addGroup(); 
    grp.setSource(srcs);
    grp.setTarget(tgts);
    return grp;
  }


        private String readPrefix(Map<String, String> prefixes, FHIRLexer lexer) throws FHIRLexerException {
                String prefix = lexer.take();
                if (!prefixes.containsKey(prefix))
                        throw lexer.error("Unknown prefix '"+prefix+"'");
                return prefixes.get(prefix);
        }


        private ConceptMapEquivalence readEquivalence(FHIRLexer lexer) throws FHIRLexerException {
                String token = lexer.take();
    if (token.equals("-"))
      return ConceptMapEquivalence.RELATEDTO;
    if (token.equals("="))
      return ConceptMapEquivalence.EQUAL;
                if (token.equals("=="))
                        return ConceptMapEquivalence.EQUIVALENT;
                if (token.equals("!="))
                        return ConceptMapEquivalence.DISJOINT;
                if (token.equals("--"))
                        return ConceptMapEquivalence.UNMATCHED;
                if (token.equals("<="))
                        return ConceptMapEquivalence.WIDER;
                if (token.equals("<-"))
                        return ConceptMapEquivalence.SUBSUMES;
                if (token.equals(">="))
                        return ConceptMapEquivalence.NARROWER;
                if (token.equals(">-"))
                        return ConceptMapEquivalence.SPECIALIZES;
                if (token.equals("~"))
                        return ConceptMapEquivalence.INEXACT;
                throw lexer.error("Unknown equivalence token '"+token+"'");
        }


        private void parseUses(StructureMap result, FHIRLexer lexer) throws FHIRException {
                lexer.token("uses");
                StructureMapStructureComponent st = result.addStructure();
                st.setUrl(lexer.readConstant("url"));
                if (lexer.hasToken("alias")) {
            lexer.token("alias");
                  st.setAlias(lexer.take());
                }
                lexer.token("as");
                st.setMode(StructureMapModelMode.fromCode(lexer.take()));
                lexer.skipToken(";");
                if (lexer.hasComment()) {
                        st.setDocumentation(lexer.take().substring(2).trim());
                }
                lexer.skipComments();
        }

        private void parseImports(StructureMap result, FHIRLexer lexer) throws FHIRException {
                lexer.token("imports");
                result.addImport(lexer.readConstant("url"));
                lexer.skipToken(";");
                if (lexer.hasComment()) {
                        lexer.next();
                }
                lexer.skipComments();
        }

        private void parseGroup(StructureMap result, FHIRLexer lexer) throws FHIRException {
                lexer.token("group");
                StructureMapGroupComponent group = result.addGroup();
                if (lexer.hasToken("for")) {
                  lexer.token("for");
                  if ("type".equals(lexer.getCurrent())) {
        lexer.token("type");
        lexer.token("+");
        lexer.token("types");
        group.setTypeMode(StructureMapGroupTypeMode.TYPEANDTYPES);
                  } else {
                    lexer.token("types");
        group.setTypeMode(StructureMapGroupTypeMode.TYPES);
                  }
                } else
                  group.setTypeMode(StructureMapGroupTypeMode.NONE);
                group.setName(lexer.take());
                if (lexer.hasToken("extends")) {
                        lexer.next();
                        group.setExtends(lexer.take());
                }
                lexer.skipComments();
                while (lexer.hasToken("input")) 
                        parseInput(group, lexer);
                while (!lexer.hasToken("endgroup")) {
                        if (lexer.done())
                                throw lexer.error("premature termination expecting 'endgroup'");
                        parseRule(result, group.getRule(), lexer);
                }
                lexer.next();
                lexer.skipComments();
        }

        private void parseInput(StructureMapGroupComponent group, FHIRLexer lexer) throws FHIRException {
                lexer.token("input");
                StructureMapGroupInputComponent input = group.addInput();
                input.setName(lexer.take());
                if (lexer.hasToken(":")) {
                        lexer.token(":");
                        input.setType(lexer.take());
                }
                lexer.token("as");
                input.setMode(StructureMapInputMode.fromCode(lexer.take()));
                if (lexer.hasComment()) {
                        input.setDocumentation(lexer.take().substring(2).trim());
                }
                lexer.skipToken(";");
                lexer.skipComments();
        }

        private void parseRule(StructureMap map, List<StructureMapGroupRuleComponent> list, FHIRLexer lexer) throws FHIRException {
                StructureMapGroupRuleComponent rule = new StructureMapGroupRuleComponent(); 
                list.add(rule);
                rule.setName(lexer.takeDottedToken());
                lexer.token(":");
                lexer.token("for");
                boolean done = false;
                while (!done) {
                        parseSource(rule, lexer);
                        done = !lexer.hasToken(",");
                        if (!done)
                                lexer.next();
                }
                if (lexer.hasToken("make")) {
                        lexer.token("make");
                        done = false;
                        while (!done) {
                                parseTarget(rule, lexer);
                                done = !lexer.hasToken(",");
                                if (!done)
                                        lexer.next();
                        }
                }
                if (lexer.hasToken("then")) {
                        lexer.token("then");
                        if (lexer.hasToken("{")) {
                                lexer.token("{");
                                if (lexer.hasComment()) {
                                        rule.setDocumentation(lexer.take().substring(2).trim());
                                }
                                lexer.skipComments();
                                while (!lexer.hasToken("}")) {
                                        if (lexer.done())
                                                throw lexer.error("premature termination expecting '}' in nested group");
                                        parseRule(map, rule.getRule(), lexer);
                                }      
                                lexer.token("}");
                        } else {
                                done = false;
                                while (!done) {
                                        parseRuleReference(rule, lexer);
                                        done = !lexer.hasToken(",");
                                        if (!done)
                                                lexer.next();
                                }
                        }
                } else if (lexer.hasComment()) {
                        rule.setDocumentation(lexer.take().substring(2).trim());
                }
                if (isSimpleSyntax(rule)) {
                  rule.getSourceFirstRep().setVariable(AUTO_VAR_NAME);
                  rule.getTargetFirstRep().setVariable(AUTO_VAR_NAME);
                  rule.getTargetFirstRep().setTransform(StructureMapTransform.CREATE); // with no parameter - e.g. imply what is to be created
                  // no dependencies - imply what is to be done based on types
                }
                lexer.skipComments();
        }

        private boolean isSimpleSyntax(StructureMapGroupRuleComponent rule) {
    return 
        (rule.getSource().size() == 1 && rule.getSourceFirstRep().hasContext() && rule.getSourceFirstRep().hasElement() && !rule.getSourceFirstRep().hasVariable()) &&
        (rule.getTarget().size() == 1 && rule.getTargetFirstRep().hasContext() && rule.getTargetFirstRep().hasElement() && !rule.getTargetFirstRep().hasVariable() && !rule.getTargetFirstRep().hasParameter()) &&
        (rule.getDependent().size() == 0 && rule.getRule().size() == 0);
  }

  private void parseRuleReference(StructureMapGroupRuleComponent rule, FHIRLexer lexer) throws FHIRLexerException {
                StructureMapGroupRuleDependentComponent ref = rule.addDependent();
                ref.setName(lexer.take());
                lexer.token("(");
                boolean done = false;
                while (!done) {
                        ref.addVariable(lexer.take());
                        done = !lexer.hasToken(",");
                        if (!done)
                                lexer.next();
                }
                lexer.token(")");
        }

        private void parseSource(StructureMapGroupRuleComponent rule, FHIRLexer lexer) throws FHIRException {
                StructureMapGroupRuleSourceComponent source = rule.addSource();
                source.setContext(lexer.take());
                if (source.getContext().equals("search") && lexer.hasToken("(")) {
            source.setContext("@search");
      lexer.take();
      ExpressionNode node = fpe.parse(lexer);
      source.setUserData(MAP_SEARCH_EXPRESSION, node);
      source.setElement(node.toString());
      lexer.token(")");
                } else if (lexer.hasToken(".")) {
                        lexer.token(".");
                        source.setElement(lexer.take());
                }
                if (lexer.hasToken(":")) {
                  // type and cardinality
                  lexer.token(":");
                  source.setType(lexer.takeDottedToken());
                  if (!lexer.hasToken("as", "first", "last", "not_first", "not_last", "only_one", "default")) {
                    source.setMin(lexer.takeInt());
                    lexer.token("..");
                    source.setMax(lexer.take());
                  }
                }
                if (lexer.hasToken("default")) {
                  lexer.token("default");
                  source.setDefaultValue(new StringType(lexer.readConstant("default value")));
                }
                if (Utilities.existsInList(lexer.getCurrent(), "first", "last", "not_first", "not_last", "only_one"))
                        source.setListMode(StructureMapSourceListMode.fromCode(lexer.take()));

                if (lexer.hasToken("as")) {
                        lexer.take();
                        source.setVariable(lexer.take());
                }
                if (lexer.hasToken("where")) {
                        lexer.take();
                        ExpressionNode node = fpe.parse(lexer);
                        source.setUserData(MAP_WHERE_EXPRESSION, node);
                        source.setCondition(node.toString());
                }
                if (lexer.hasToken("check")) {
                        lexer.take();
                        ExpressionNode node = fpe.parse(lexer);
                        source.setUserData(MAP_WHERE_CHECK, node);
                        source.setCheck(node.toString());
                }
    if (lexer.hasToken("log")) {
      lexer.take();
      ExpressionNode node = fpe.parse(lexer);
      source.setUserData(MAP_WHERE_CHECK, node);
      source.setLogMessage(node.toString());
    }
        }

        private void parseTarget(StructureMapGroupRuleComponent rule, FHIRLexer lexer) throws FHIRException {
                StructureMapGroupRuleTargetComponent target = rule.addTarget();
                String start = lexer.take();
                if (lexer.hasToken(".")) {
            target.setContext(start);
            target.setContextType(StructureMapContextType.VARIABLE);
            start = null;
                        lexer.token(".");
                        target.setElement(lexer.take());
                }
                String name;
                boolean isConstant = false;
                if (lexer.hasToken("=")) {
                  if (start != null)
              target.setContext(start);
                        lexer.token("=");
                        isConstant = lexer.isConstant(true);
                        name = lexer.take();
                } else 
                  name = start;
                
                if ("(".equals(name)) {
                  // inline fluentpath expression
      target.setTransform(StructureMapTransform.EVALUATE);
      ExpressionNode node = fpe.parse(lexer);
      target.setUserData(MAP_EXPRESSION, node);
      target.addParameter().setValue(new StringType(node.toString()));
      lexer.token(")");
                } else if (lexer.hasToken("(")) {
                                target.setTransform(StructureMapTransform.fromCode(name));
                                lexer.token("(");
                                if (target.getTransform() == StructureMapTransform.EVALUATE) {
                                        parseParameter(target, lexer);
                                        lexer.token(",");
                                        ExpressionNode node = fpe.parse(lexer);
                                        target.setUserData(MAP_EXPRESSION, node);
                                        target.addParameter().setValue(new StringType(node.toString()));
                                } else { 
                                        while (!lexer.hasToken(")")) {
                                                parseParameter(target, lexer);
                                                if (!lexer.hasToken(")"))
                                                        lexer.token(",");
                                        }       
                                }
                                lexer.token(")");
                } else if (name != null) {
                                target.setTransform(StructureMapTransform.COPY);
                                if (!isConstant) {
                                        String id = name;
                                        while (lexer.hasToken(".")) {
                                                id = id + lexer.take() + lexer.take();
                                        }
                                        target.addParameter().setValue(new IdType(id));
                                }
                                else 
                                        target.addParameter().setValue(readConstant(name, lexer));
                        }
                if (lexer.hasToken("as")) {
                        lexer.take();
                        target.setVariable(lexer.take());
                }
                while (Utilities.existsInList(lexer.getCurrent(), "first", "last", "share", "collate")) {
                        if (lexer.getCurrent().equals("share")) {
                                target.addListMode(StructureMapTargetListMode.SHARE);
                                lexer.next();
                                target.setListRuleId(lexer.take());
                        } else if (lexer.getCurrent().equals("first")) 
                                target.addListMode(StructureMapTargetListMode.FIRST);
                        else
                                target.addListMode(StructureMapTargetListMode.LAST);
                        lexer.next();
                }
        }


        private void parseParameter(StructureMapGroupRuleTargetComponent target, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
                if (!lexer.isConstant(true)) {
                        target.addParameter().setValue(new IdType(lexer.take()));
                } else if (lexer.isStringConstant())
                        target.addParameter().setValue(new StringType(lexer.readConstant("??")));
                else {
                        target.addParameter().setValue(readConstant(lexer.take(), lexer));
                }
        }

        private Type readConstant(String s, FHIRLexer lexer) throws FHIRLexerException {
                if (Utilities.isInteger(s))
                        return new IntegerType(s);
                else if (Utilities.isDecimal(s))
                        return new DecimalType(s);
                else if (Utilities.existsInList(s, "true", "false"))
                        return new BooleanType(s.equals("true"));
                else 
                        return new StringType(lexer.processConstant(s));        
        }

        public StructureDefinition getTargetType(StructureMap map) throws FHIRException {
          boolean found = false;
          StructureDefinition res = null;
          for (StructureMapStructureComponent uses : map.getStructure()) {
            if (uses.getMode() == StructureMapModelMode.TARGET) {
              if (found)
                throw new FHIRException("Multiple targets found in map "+map.getUrl());
              found = true;
              res = worker.fetchResource(StructureDefinition.class, uses.getUrl());
              if (res == null)
                throw new FHIRException("Unable to find "+uses.getUrl()+" referenced from map "+map.getUrl());      
            }
          }
          if (res == null)
      throw new FHIRException("No targets found in map "+map.getUrl());
          return res;
        }

        public enum VariableMode {
                INPUT, OUTPUT
        }

        public class Variable {
                private VariableMode mode;
                private String name;
                private Base object;
                public Variable(VariableMode mode, String name, Base object) {
                        super();
                        this.mode = mode;
                        this.name = name;
                        this.object = object;
                }
                public VariableMode getMode() {
                        return mode;
                }
                public String getName() {
                        return name;
                }
                public Base getObject() {
                        return object;
                }
    public String summary() {
      return name+": "+object.fhirType();
    }
        }

        public class Variables {
                private List<Variable> list = new ArrayList<Variable>();

                public void add(VariableMode mode, String name, Base object) {
                        Variable vv = null;
                        for (Variable v : list) 
                                if ((v.mode == mode) && v.getName().equals(name))
                                        vv = v;
                        if (vv != null)
                                list.remove(vv);
                        list.add(new Variable(mode, name, object));
                }

                public Variables copy() {
                        Variables result = new Variables();
                        result.list.addAll(list);
                        return result;
                }

                public Base get(VariableMode mode, String name) {
                        for (Variable v : list) 
                                if ((v.mode == mode) && v.getName().equals(name))
                                        return v.getObject();
                        return null;
                }

    public String summary() {
      CommaSeparatedStringBuilder s = new CommaSeparatedStringBuilder();
      CommaSeparatedStringBuilder t = new CommaSeparatedStringBuilder();
      for (Variable v : list)
        if (v.mode == VariableMode.INPUT)
          s.append(v.summary());
        else
          t.append(v.summary());
      return "source variables ["+s.toString()+"], target variables ["+t.toString()+"]";
    }
        }

        public class TransformContext {
                private Object appInfo;

                public TransformContext(Object appInfo) {
                        super();
                        this.appInfo = appInfo;
                }

                public Object getAppInfo() {
                        return appInfo;
                }

        }

        private void log(String cnt) {
          if (services != null)
            services.log(cnt);
        }

        /**
         * Given an item, return all the children that conform to the pattern described in name
         * 
         * Possible patterns:
         *  - a simple name (which may be the base of a name with [] e.g. value[x])
         *  - a name with a type replacement e.g. valueCodeableConcept
         *  - * which means all children
         *  - ** which means all descendents
         *  
         * @param item
         * @param name
         * @param result
         * @throws FHIRException 
         */
        protected void getChildrenByName(Base item, String name, List<Base> result) throws FHIRException {
                for (Base v : item.listChildrenByName(name, true))
                        if (v != null)
                                result.add(v);
        }

        public void transform(Object appInfo, Base source, StructureMap map, Base target) throws FHIRException {
                TransformContext context = new TransformContext(appInfo);
    log("Start Transform "+map.getUrl());
    StructureMapGroupComponent g = map.getGroup().get(0);

                Variables vars = new Variables();
                vars.add(VariableMode.INPUT, getInputName(g, StructureMapInputMode.SOURCE, "source"), source);
                vars.add(VariableMode.OUTPUT, getInputName(g, StructureMapInputMode.TARGET, "target"), target);

    executeGroup("", context, map, vars, g, true);
    if (target instanceof Element)
      ((Element) target).sort();
        }

        private String getInputName(StructureMapGroupComponent g, StructureMapInputMode mode, String def) throws DefinitionException {
          String name = null;
    for (StructureMapGroupInputComponent inp : g.getInput()) {
      if (inp.getMode() == mode)
        if (name != null)
          throw new DefinitionException("This engine does not support multiple source inputs");
        else
          name = inp.getName();
    }
    return name == null ? def : name;
        }

        private void executeGroup(String indent, TransformContext context, StructureMap map, Variables vars, StructureMapGroupComponent group, boolean atRoot) throws FHIRException {
                log(indent+"Group : "+group.getName());
    // todo: check inputs
                if (group.hasExtends()) {
                  ResolvedGroup rg = resolveGroupReference(map, group, group.getExtends());
                  executeGroup(indent+" ", context, rg.targetMap, vars, rg.target, false); 
                }
                  
                for (StructureMapGroupRuleComponent r : group.getRule()) {
                        executeRule(indent+"  ", context, map, vars, group, r, atRoot);
                }
        }

        private void executeRule(String indent, TransformContext context, StructureMap map, Variables vars, StructureMapGroupComponent group, StructureMapGroupRuleComponent rule, boolean atRoot) throws FHIRException {
                log(indent+"rule : "+rule.getName());
                if (rule.getName().contains("CarePlan.participant-unlink"))
                  System.out.println("debug");
                Variables srcVars = vars.copy();
                if (rule.getSource().size() != 1)
                        throw new FHIRException("Rule \""+rule.getName()+"\": not handled yet");
                List<Variables> source = processSource(rule.getName(), context, srcVars, rule.getSource().get(0), map.getUrl());
                if (source != null) {
                        for (Variables v : source) {
                                for (StructureMapGroupRuleTargetComponent t : rule.getTarget()) {
                                        processTarget(rule.getName(), context, v, map, group, t, rule.getSource().size() == 1 ? rule.getSourceFirstRep().getVariable() : null, atRoot);
                                }
                                if (rule.hasRule()) {
                                        for (StructureMapGroupRuleComponent childrule : rule.getRule()) {
                                                executeRule(indent +"  ", context, map, v, group, childrule, false);
                                        }
                                } else if (rule.hasDependent()) {
                                        for (StructureMapGroupRuleDependentComponent dependent : rule.getDependent()) {
                                                executeDependency(indent+"  ", context, map, v, group, dependent);
                                        }
                                } else if (rule.getSource().size() == 1 && rule.getSourceFirstRep().hasVariable() && rule.getTarget().size() == 1 && rule.getTargetFirstRep().hasVariable() && rule.getTargetFirstRep().getTransform() == StructureMapTransform.CREATE && !rule.getTargetFirstRep().hasParameter()) {
                                  // simple inferred, map by type
                                  Base src = v.get(VariableMode.INPUT, rule.getSourceFirstRep().getVariable());
                                  Base tgt = v.get(VariableMode.OUTPUT, rule.getTargetFirstRep().getVariable());
                                  String srcType = src.fhirType();
                                  String tgtType = tgt.fhirType();
                                  ResolvedGroup defGroup = resolveGroupByTypes(map, rule.getName(), group, srcType, tgtType);
                            Variables vdef = new Variables();
          vdef.add(VariableMode.INPUT, defGroup.target.getInput().get(0).getName(), src);
          vdef.add(VariableMode.OUTPUT, defGroup.target.getInput().get(1).getName(), tgt);
                                  executeGroup(indent+"  ", context, defGroup.targetMap, vdef, defGroup.target, false);
                                }
                        }
                }
        }

        private void executeDependency(String indent, TransformContext context, StructureMap map, Variables vin, StructureMapGroupComponent group, StructureMapGroupRuleDependentComponent dependent) throws FHIRException {
          ResolvedGroup rg = resolveGroupReference(map, group, dependent.getName());

                if (rg.target.getInput().size() != dependent.getVariable().size()) {
                        throw new FHIRException("Rule '"+dependent.getName()+"' has "+Integer.toString(rg.target.getInput().size())+" but the invocation has "+Integer.toString(dependent.getVariable().size())+" variables");
                }
                Variables v = new Variables();
                for (int i = 0; i < rg.target.getInput().size(); i++) {
                        StructureMapGroupInputComponent input = rg.target.getInput().get(i);
                        StringType rdp = dependent.getVariable().get(i);
      String var = rdp.asStringValue();
                        VariableMode mode = input.getMode() == StructureMapInputMode.SOURCE ? VariableMode.INPUT :   VariableMode.OUTPUT; 
                        Base vv = vin.get(mode, var);
      if (vv == null && mode == VariableMode.INPUT) //* once source, always source. but target can be treated as source at user convenient
        vv = vin.get(VariableMode.OUTPUT, var);
                        if (vv == null)
                                throw new FHIRException("Rule '"+dependent.getName()+"' "+mode.toString()+" variable '"+input.getName()+"' named as '"+var+"' has no value");
                        v.add(mode, input.getName(), vv);       
                }
                executeGroup(indent+"  ", context, rg.targetMap, v, rg.target, false);
        }

  private String determineTypeFromSourceType(StructureMap map, StructureMapGroupComponent source, Base base, String[] types) throws FHIRException {
    String type = base.fhirType();
    String kn = "type^"+type;
    if (source.hasUserData(kn))
      return source.getUserString(kn);
    
    ResolvedGroup res = new ResolvedGroup();
    res.targetMap = null;
    res.target = null;
    for (StructureMapGroupComponent grp : map.getGroup()) {
      if (matchesByType(map, grp, type)) {
        if (res.targetMap == null) {
          res.targetMap = map;
          res.target = grp;
        } else 
          throw new FHIRException("Multiple possible matches looking for default rule for '"+type+"'");
      }
    }
    if (res.targetMap != null) {
      String result = getActualType(res.targetMap, res.target.getInput().get(1).getType());
      source.setUserData(kn, result);
      return result;
    }

    for (UriType imp : map.getImport()) {
      List<StructureMap> impMapList = findMatchingMaps(imp.getValue());
      if (impMapList.size() == 0)
        throw new FHIRException("Unable to find map(s) for "+imp.getValue());
      for (StructureMap impMap : impMapList) {
        if (!impMap.getUrl().equals(map.getUrl())) {
          for (StructureMapGroupComponent grp : impMap.getGroup()) {
            if (matchesByType(impMap, grp, type)) {
              if (res.targetMap == null) {
                res.targetMap = impMap;
                res.target = grp;
              } else 
                throw new FHIRException("Multiple possible matches for default rule for '"+type+"' in "+res.targetMap.getUrl()+" ("+res.target.getName()+") and "+impMap.getUrl()+" ("+grp.getName()+")");
            }
          }
        }
      }
    }
    if (res.target == null)
      throw new FHIRException("No matches found for default rule for '"+type+"' from "+map.getUrl());
    String result = getActualType(res.targetMap, res.target.getInput().get(1).getType()); // should be .getType, but R2...
    source.setUserData(kn, result);
    return result;
  }

  private List<StructureMap> findMatchingMaps(String value) {
    List<StructureMap> res = new ArrayList<StructureMap>();
    if (value.contains("*")) {
      for (StructureMap sm : worker.listTransforms()) {
        if (urlMatches(value, sm.getUrl())) {
          res.add(sm); 
        }
      }
    } else {
      StructureMap sm = worker.getTransform(value);
      if (sm != null)
        res.add(sm); 
    }
    Set<String> check = new HashSet<String>();
    for (StructureMap sm : res) {
      if (check.contains(sm.getUrl()))
        throw new Error("duplicate");
      else
        check.add(sm.getUrl());
    }
    return res;
  }

  private boolean urlMatches(String mask, String url) {
    return url.length() > mask.length() && url.startsWith(mask.substring(0, mask.indexOf("*"))) && url.endsWith(mask.substring(mask.indexOf("*")+1)) ;
  }

  private ResolvedGroup resolveGroupByTypes(StructureMap map, String ruleid, StructureMapGroupComponent source, String srcType, String tgtType) throws FHIRException {
    String kn = "types^"+srcType+":"+tgtType;
    if (source.hasUserData(kn))
      return (ResolvedGroup) source.getUserData(kn);
    
    ResolvedGroup res = new ResolvedGroup();
    res.targetMap = null;
    res.target = null;
    for (StructureMapGroupComponent grp : map.getGroup()) {
      if (matchesByType(map, grp, srcType, tgtType)) {
        if (res.targetMap == null) {
          res.targetMap = map;
          res.target = grp;
        } else 
          throw new FHIRException("Multiple possible matches looking for rule for '"+srcType+"/"+tgtType+"', from rule '"+ruleid+"'");
      }
    }
    if (res.targetMap != null) {
      source.setUserData(kn, res);
      return res;
    }

    for (UriType imp : map.getImport()) {
      List<StructureMap> impMapList = findMatchingMaps(imp.getValue());
      if (impMapList.size() == 0)
        throw new FHIRException("Unable to find map(s) for "+imp.getValue());
      for (StructureMap impMap : impMapList) {
        if (!impMap.getUrl().equals(map.getUrl())) {
          for (StructureMapGroupComponent grp : impMap.getGroup()) {
            if (matchesByType(impMap, grp, srcType, tgtType)) {
              if (res.targetMap == null) {
                res.targetMap = impMap;
                res.target = grp;
              } else 
                throw new FHIRException("Multiple possible matches for rule for '"+srcType+"/"+tgtType+"' in "+res.targetMap.getUrl()+" and "+impMap.getUrl()+", from rule '"+ruleid+"'");
            }
          }
        }
      }
    }
    if (res.target == null)
      throw new FHIRException("No matches found for rule for '"+srcType+" to "+tgtType+"' from "+map.getUrl()+", from rule '"+ruleid+"'");
    source.setUserData(kn, res);
    return res;
  }


  private boolean matchesByType(StructureMap map, StructureMapGroupComponent grp, String type) throws FHIRException {
    if (grp.getTypeMode() != StructureMapGroupTypeMode.TYPEANDTYPES)
      return false;
    if (grp.getInput().size() != 2 || grp.getInput().get(0).getMode() != StructureMapInputMode.SOURCE || grp.getInput().get(1).getMode() != StructureMapInputMode.TARGET)
      return false;
    return matchesType(map, type, grp.getInput().get(0).getType());
  }

  private boolean matchesByType(StructureMap map, StructureMapGroupComponent grp, String srcType, String tgtType) throws FHIRException {
    if (grp.getTypeMode() == StructureMapGroupTypeMode.NONE)
      return false;
    if (grp.getInput().size() != 2 || grp.getInput().get(0).getMode() != StructureMapInputMode.SOURCE || grp.getInput().get(1).getMode() != StructureMapInputMode.TARGET)
      return false;
    if (!grp.getInput().get(0).hasType() || !grp.getInput().get(1).hasType())
      return false;
    return matchesType(map, srcType, grp.getInput().get(0).getType()) && matchesType(map, tgtType, grp.getInput().get(1).getType());
  }

  private boolean matchesType(StructureMap map, String actualType, String statedType) throws FHIRException {
    // check the aliases
    for (StructureMapStructureComponent imp : map.getStructure()) {
      if (imp.hasAlias() && statedType.equals(imp.getAlias())) {
        StructureDefinition sd = worker.fetchResource(StructureDefinition.class, imp.getUrl());
        if (sd != null)
          statedType = sd.getType();
        break;
      }
    }
    
    if (Utilities.isAbsoluteUrl(actualType)) {
      StructureDefinition sd = worker.fetchResource(StructureDefinition.class, actualType);
      if (sd != null)
        actualType = sd.getType();
    }
    if (Utilities.isAbsoluteUrl(statedType)) {
      StructureDefinition sd = worker.fetchResource(StructureDefinition.class, statedType);
      if (sd != null)
        statedType = sd.getType();
    }
    return actualType.equals(statedType);
  }

  private String getActualType(StructureMap map, String statedType) throws FHIRException {
    // check the aliases
    for (StructureMapStructureComponent imp : map.getStructure()) {
      if (imp.hasAlias() && statedType.equals(imp.getAlias())) {
        StructureDefinition sd = worker.fetchResource(StructureDefinition.class, imp.getUrl());
        if (sd == null)
          throw new FHIRException("Unable to resolve structure "+imp.getUrl());
        return sd.getId(); // should be sd.getType(), but R2...
      }
    }
    return statedType;
  }


  private ResolvedGroup resolveGroupReference(StructureMap map, StructureMapGroupComponent source, String name) throws FHIRException {
    String kn = "ref^"+name;
    if (source.hasUserData(kn))
      return (ResolvedGroup) source.getUserData(kn);
    
          ResolvedGroup res = new ResolvedGroup();
    res.targetMap = null;
    res.target = null;
    for (StructureMapGroupComponent grp : map.getGroup()) {
      if (grp.getName().equals(name)) {
        if (res.targetMap == null) {
          res.targetMap = map;
          res.target = grp;
        } else 
          throw new FHIRException("Multiple possible matches for rule '"+name+"'");
      }
    }
    if (res.targetMap != null) {
      source.setUserData(kn, res);
      return res;
    }

    for (UriType imp : map.getImport()) {
      List<StructureMap> impMapList = findMatchingMaps(imp.getValue());
      if (impMapList.size() == 0)
        throw new FHIRException("Unable to find map(s) for "+imp.getValue());
      for (StructureMap impMap : impMapList) {
        if (!impMap.getUrl().equals(map.getUrl())) {
          for (StructureMapGroupComponent grp : impMap.getGroup()) {
            if (grp.getName().equals(name)) {
              if (res.targetMap == null) {
                res.targetMap = impMap;
                res.target = grp;
              } else 
                throw new FHIRException("Multiple possible matches for rule '"+name+"' in "+res.targetMap.getUrl()+" and "+impMap.getUrl());
            }
          }
        }
      }
    }
    if (res.target == null)
      throw new FHIRException("No matches found for rule '"+name+"'. Reference found in "+map.getUrl());
    source.setUserData(kn, res);
    return res;
  }

  private List<Variables> processSource(String ruleId, TransformContext context, Variables vars, StructureMapGroupRuleSourceComponent src, String pathForErrors) throws FHIRException {
    List<Base> items;
    if (src.getContext().equals("@search")) {
      ExpressionNode expr = (ExpressionNode) src.getUserData(MAP_SEARCH_EXPRESSION);
      if (expr == null) {
        expr = fpe.parse(src.getElement());
        src.setUserData(MAP_SEARCH_EXPRESSION, expr);
      }
      String search = fpe.evaluateToString(vars, null, new StringType(), expr); // string is a holder of nothing to ensure that variables are processed correctly 
      items = services.performSearch(context.appInfo, search);
    } else {
      items = new ArrayList<Base>();
      Base b = vars.get(VariableMode.INPUT, src.getContext());
      if (b == null)
        throw new FHIRException("Unknown input variable "+src.getContext()+" in "+pathForErrors+" rule "+ruleId+" (vars = "+vars.summary()+")");

      if (!src.hasElement()) 
        items.add(b);
      else { 
        getChildrenByName(b, src.getElement(), items);
        if (items.size() == 0 && src.hasDefaultValue())
          items.add(src.getDefaultValue());
      }
    }
    
                if (src.hasType()) {
            List<Base> remove = new ArrayList<Base>();
            for (Base item : items) {
              if (item != null && !isType(item, src.getType())) {
                remove.add(item);
              }
            }
            items.removeAll(remove);
                }

    if (src.hasCondition()) {
      ExpressionNode expr = (ExpressionNode) src.getUserData(MAP_WHERE_EXPRESSION);
      if (expr == null) {
        expr = fpe.parse(src.getCondition());
        //        fpe.check(context.appInfo, ??, ??, expr)
        src.setUserData(MAP_WHERE_EXPRESSION, expr);
      }
      List<Base> remove = new ArrayList<Base>();
      for (Base item : items) {
        if (!fpe.evaluateToBoolean(vars, null, item, expr))
          remove.add(item);
      }
      items.removeAll(remove);
    }

    if (src.hasCheck()) {
      ExpressionNode expr = (ExpressionNode) src.getUserData(MAP_WHERE_CHECK);
      if (expr == null) {
        expr = fpe.parse(src.getCheck());
        //        fpe.check(context.appInfo, ??, ??, expr)
        src.setUserData(MAP_WHERE_CHECK, expr);
      }
      List<Base> remove = new ArrayList<Base>();
      for (Base item : items) {
        if (!fpe.evaluateToBoolean(vars, null, item, expr))
          throw new FHIRException("Rule \""+ruleId+"\": Check condition failed");
      }
    } 

    if (src.hasLogMessage()) {
      ExpressionNode expr = (ExpressionNode) src.getUserData(MAP_WHERE_LOG);
      if (expr == null) {
        expr = fpe.parse(src.getLogMessage());
        //        fpe.check(context.appInfo, ??, ??, expr)
        src.setUserData(MAP_WHERE_LOG, expr);
      }
      CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
      for (Base item : items) 
        b.appendIfNotNull(fpe.evaluateToString(vars, null, item, expr));
      if (b.length() > 0)
        services.log(b.toString());
    } 

                
                if (src.hasListMode() && !items.isEmpty()) {
                  switch (src.getListMode()) {
                  case FIRST:
                    Base bt = items.get(0);
        items.clear();
        items.add(bt);
                    break;
                  case NOTFIRST: 
        if (items.size() > 0)
          items.remove(0);
        break;
                  case LAST:
        bt = items.get(items.size()-1);
        items.clear();
        items.add(bt);
        break;
                  case NOTLAST: 
        if (items.size() > 0)
          items.remove(items.size()-1);
        break;
                  case ONLYONE:
                    if (items.size() > 1)
          throw new FHIRException("Rule \""+ruleId+"\": Check condition failed: the collection has more than one item");
        break;
      case NULL:
                  }
                }
                List<Variables> result = new ArrayList<Variables>();
                for (Base r : items) {
                        Variables v = vars.copy();
                        if (src.hasVariable())
                                v.add(VariableMode.INPUT, src.getVariable(), r);
                        result.add(v); 
                }
                return result;
        }


        private boolean isType(Base item, String type) {
    if (type.equals(item.fhirType()))
      return true;
    return false;
  }

  private void processTarget(String ruleId, TransformContext context, Variables vars, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, String srcVar, boolean atRoot) throws FHIRException {
          Base dest = null;
          if (tgt.hasContext()) {
                dest = vars.get(VariableMode.OUTPUT, tgt.getContext());
                if (dest == null)
                        throw new FHIRException("Rule \""+ruleId+"\": target context not known: "+tgt.getContext());
                if (!tgt.hasElement())
                        throw new FHIRException("Rule \""+ruleId+"\": Not supported yet");
          }
                Base v = null;
                if (tgt.hasTransform()) {
                        v = runTransform(ruleId, context, map, group, tgt, vars, dest, tgt.getElement(), srcVar, atRoot);
                        if (v != null && dest != null)
                                v = dest.setProperty(tgt.getElement().hashCode(), tgt.getElement(), v); // reset v because some implementations may have to rewrite v when setting the value
                } else if (dest != null) 
                        v = dest.makeProperty(tgt.getElement().hashCode(), tgt.getElement());
                if (tgt.hasVariable() && v != null)
                        vars.add(VariableMode.OUTPUT, tgt.getVariable(), v);
        }

        private Base runTransform(String ruleId, TransformContext context, StructureMap map, StructureMapGroupComponent group, StructureMapGroupRuleTargetComponent tgt, Variables vars, Base dest, String element, String srcVar, boolean root) throws FHIRException {
          try {
            switch (tgt.getTransform()) {
            case CREATE :
              String tn;
              if (tgt.getParameter().isEmpty()) {
                // we have to work out the type. First, we see if there is a single type for the target. If there is, we use that
                String[] types = dest.getTypesForProperty(element.hashCode(), element);
                if (types.length == 1 && !"*".equals(types[0]) && !types[0].equals("Resource"))
                  tn = types[0];
                else if (srcVar != null) {
                  tn = determineTypeFromSourceType(map, group, vars.get(VariableMode.INPUT, srcVar), types);
                } else
                  throw new Error("Cannot determine type implicitly because there is no single input variable");
              } else {
                tn = getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString());
                // ok, now we resolve the type name against the import statements 
                for (StructureMapStructureComponent uses : map.getStructure()) {
                  if (uses.getMode() == StructureMapModelMode.TARGET && uses.hasAlias() && tn.equals(uses.getAlias())) {
                    tn = uses.getUrl();
                    break;
                  }
                }
              }
              Base res = services != null ? services.createType(context.getAppInfo(), tn) : ResourceFactory.createResourceOrType(tn);
              if (res.isResource() && !res.fhirType().equals("Parameters")) {
//              res.setIdBase(tgt.getParameter().size() > 1 ? getParamString(vars, tgt.getParameter().get(0)) : UUID.randomUUID().toString().toLowerCase());
                if (services != null) 
                  res = services.createResource(context.getAppInfo(), res, root);
              }
              if (tgt.hasUserData("profile"))
                res.setUserData("profile", tgt.getUserData("profile"));
              return res;
            case COPY : 
              return getParam(vars, tgt.getParameter().get(0));
            case EVALUATE :
              ExpressionNode expr = (ExpressionNode) tgt.getUserData(MAP_EXPRESSION);
              if (expr == null) {
                expr = fpe.parse(getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString()));
                tgt.setUserData(MAP_WHERE_EXPRESSION, expr);
              }
              List<Base> v = fpe.evaluate(vars, null, tgt.getParameter().size() == 2 ? getParam(vars, tgt.getParameter().get(0)) : new BooleanType(false), expr);
              if (v.size() == 0)
                return null;
              else if (v.size() != 1)
                throw new FHIRException("Rule \""+ruleId+"\": Evaluation of "+expr.toString()+" returned "+Integer.toString(v.size())+" objects");
              else
                return v.get(0);

            case TRUNCATE : 
              String src = getParamString(vars, tgt.getParameter().get(0));
              String len = getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString());
              if (Utilities.isInteger(len)) {
                int l = Integer.parseInt(len);
                if (src.length() > l)
                  src = src.substring(0, l);
              }
              return new StringType(src);
            case ESCAPE : 
              throw new Error("Rule \""+ruleId+"\": Transform "+tgt.getTransform().toCode()+" not supported yet");
            case CAST :
        src = getParamString(vars, tgt.getParameter().get(0));
        if (tgt.getParameter().size() == 1)
          throw new FHIRException("Implicit type parameters on cast not yet supported");
        String t = getParamString(vars, tgt.getParameter().get(1));
        if (t.equals("string"))
          return new StringType(src);
        else
          throw new FHIRException("cast to "+t+" not yet supported");
            case APPEND : 
        StringBuilder sb = new StringBuilder(getParamString(vars, tgt.getParameter().get(0)));
        for (int i = 1; i < tgt.getParameter().size(); i++)
          sb.append(getParamString(vars, tgt.getParameter().get(1)));
        return new StringType(sb.toString());
            case TRANSLATE : 
              return translate(context, map, vars, tgt.getParameter());
            case REFERENCE :
              Base b = getParam(vars, tgt.getParameter().get(0));
              if (b == null)
                throw new FHIRException("Rule \""+ruleId+"\": Unable to find parameter "+((IdType) tgt.getParameter().get(0).getValue()).asStringValue());
              if (!b.isResource())
                throw new FHIRException("Rule \""+ruleId+"\": Transform engine cannot point at an element of type "+b.fhirType());
              else {
                String id = b.getIdBase();
                if (id == null) {
                  id = UUID.randomUUID().toString().toLowerCase();
                  b.setIdBase(id);
                }
                return new Reference().setReference(b.fhirType()+"/"+id);
              }
            case DATEOP :
              throw new Error("Rule \""+ruleId+"\": Transform "+tgt.getTransform().toCode()+" not supported yet");
            case UUID :
              return new IdType(UUID.randomUUID().toString());
            case POINTER :
              b = getParam(vars, tgt.getParameter().get(0));
              if (b instanceof Resource)
                return new UriType("urn:uuid:"+((Resource) b).getId());
              else
                throw new FHIRException("Rule \""+ruleId+"\": Transform engine cannot point at an element of type "+b.fhirType());
            case CC:
              CodeableConcept cc = new CodeableConcept();
              cc.addCoding(buildCoding(getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString()), getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString())));
              return cc;
            case C: 
              Coding c = buildCoding(getParamStringNoNull(vars, tgt.getParameter().get(0), tgt.toString()), getParamStringNoNull(vars, tgt.getParameter().get(1), tgt.toString()));
              return c;
            default:
              throw new Error("Rule \""+ruleId+"\": Transform Unknown: "+tgt.getTransform().toCode());
            }
          } catch (Exception e) {
            throw new FHIRException("Exception executing transform "+tgt.toString()+" on Rule \""+ruleId+"\": "+e.getMessage(), e);
          }
        }


  private Coding buildCoding(String uri, String code) throws FHIRException {
          // if we can get this as a valueSet, we will
          String system = null;
          String display = null;
          ValueSet vs = Utilities.noString(uri) ? null : worker.fetchResourceWithException(ValueSet.class, uri);
          if (vs != null) {
            ValueSetExpansionOutcome vse = worker.expandVS(vs, true, false);
            if (vse.getError() != null)
              throw new FHIRException(vse.getError());
            CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
            for (ValueSetExpansionContainsComponent t : vse.getValueset().getExpansion().getContains()) {
              if (t.hasCode())
                b.append(t.getCode());
              if (code.equals(t.getCode()) && t.hasSystem()) {
                system = t.getSystem();
          display = t.getDisplay();
                break;
              }
        if (code.equalsIgnoreCase(t.getDisplay()) && t.hasSystem()) {
          system = t.getSystem();
          display = t.getDisplay();
          break;
        }
            }
            if (system == null)
              throw new FHIRException("The code '"+code+"' is not in the value set '"+uri+"' (valid codes: "+b.toString()+"; also checked displays)");
          } else
            system = uri;
          ValidationResult vr = worker.validateCode(system, code, null);
          if (vr != null && vr.getDisplay() != null)
            display = vr.getDisplay();
   return new Coding().setSystem(system).setCode(code).setDisplay(display);
  }


  private String getParamStringNoNull(Variables vars, StructureMapGroupRuleTargetParameterComponent parameter, String message) throws FHIRException {
    Base b = getParam(vars, parameter);
    if (b == null)
      throw new FHIRException("Unable to find a value for "+parameter.toString()+". Context: "+message);
    if (!b.hasPrimitiveValue())
      throw new FHIRException("Found a value for "+parameter.toString()+", but it has a type of "+b.fhirType()+" and cannot be treated as a string. Context: "+message);
    return b.primitiveValue();
  }

  private String getParamString(Variables vars, StructureMapGroupRuleTargetParameterComponent parameter) throws DefinitionException {
                Base b = getParam(vars, parameter);
                if (b == null || !b.hasPrimitiveValue())
                        return null;
                return b.primitiveValue();
        }


        private Base getParam(Variables vars, StructureMapGroupRuleTargetParameterComponent parameter) throws DefinitionException {
                Type p = parameter.getValue();
                if (!(p instanceof IdType))
                        return p;
                else { 
                        String n = ((IdType) p).asStringValue();
      Base b = vars.get(VariableMode.INPUT, n);
                        if (b == null)
                                b = vars.get(VariableMode.OUTPUT, n);
                        if (b == null)
        throw new DefinitionException("Variable "+n+" not found ("+vars.summary()+")");
                        return b;
                }
        }


        private Base translate(TransformContext context, StructureMap map, Variables vars, List<StructureMapGroupRuleTargetParameterComponent> parameter) throws FHIRException {
                Base src = getParam(vars, parameter.get(0));
                String id = getParamString(vars, parameter.get(1));
                String fld = parameter.size() > 2 ? getParamString(vars, parameter.get(2)) : null;
                return translate(context, map, src, id, fld);
        }

        private class SourceElementComponentWrapper {
          private ConceptMapGroupComponent group;
    private SourceElementComponent comp;
    public SourceElementComponentWrapper(ConceptMapGroupComponent group, SourceElementComponent comp) {
      super();
      this.group = group;
      this.comp = comp;
    }
        }
        public Base translate(TransformContext context, StructureMap map, Base source, String conceptMapUrl, String fieldToReturn) throws FHIRException {
                Coding src = new Coding();
                if (source.isPrimitive()) {
                        src.setCode(source.primitiveValue());
                } else if ("Coding".equals(source.fhirType())) {
                        Base[] b = source.getProperty("system".hashCode(), "system", true);
                        if (b.length == 1)
                                src.setSystem(b[0].primitiveValue());
                        b = source.getProperty("code".hashCode(), "code", true);
                        if (b.length == 1)
                                src.setCode(b[0].primitiveValue());
                } else if ("CE".equals(source.fhirType())) {
                        Base[] b = source.getProperty("codeSystem".hashCode(), "codeSystem", true);
                        if (b.length == 1)
                                src.setSystem(b[0].primitiveValue());
                        b = source.getProperty("code".hashCode(), "code", true);
                        if (b.length == 1)
                                src.setCode(b[0].primitiveValue());
                } else
                        throw new FHIRException("Unable to translate source "+source.fhirType());

                String su = conceptMapUrl;
                if (conceptMapUrl.equals("http://hl7.org/fhir/ConceptMap/special-oid2uri")) {
                        String uri = worker.oid2Uri(src.getCode());
                        if (uri == null)
                                uri = "urn:oid:"+src.getCode();
                        if ("uri".equals(fieldToReturn))
                                return new UriType(uri);
                        else
                                throw new FHIRException("Error in return code");
                } else {
                        ConceptMap cmap = null;
                        if (conceptMapUrl.startsWith("#")) {
                                for (Resource r : map.getContained()) {
                                        if (r instanceof ConceptMap && ((ConceptMap) r).getId().equals(conceptMapUrl.substring(1))) {
                                                cmap = (ConceptMap) r;
                                                su = map.getUrl()+conceptMapUrl;
                                        }
                                }
                                if (cmap == null)
                      throw new FHIRException("Unable to translate - cannot find map "+conceptMapUrl);
                        } else
                                cmap = worker.fetchResource(ConceptMap.class, conceptMapUrl);
                        Coding outcome = null;
                        boolean done = false;
                        String message = null;
                        if (cmap == null) {
                                if (services == null) 
                                        message = "No map found for "+conceptMapUrl;
                                else {
                                        outcome = services.translate(context.appInfo, src, conceptMapUrl);
                                        done = true;
                                }
                        } else {
                          List<SourceElementComponentWrapper> list = new ArrayList<SourceElementComponentWrapper>();
                          for (ConceptMapGroupComponent g : cmap.getGroup()) {
                            for (SourceElementComponent e : g.getElement()) {
                                                if (!src.hasSystem() && src.getCode().equals(e.getCode())) 
                                list.add(new SourceElementComponentWrapper(g, e));
                              else if (src.hasSystem() && src.getSystem().equals(g.getSource()) && src.getCode().equals(e.getCode()))
                                list.add(new SourceElementComponentWrapper(g, e));
                            }
                                }
                                if (list.size() == 0)
                                        done = true;
                                else if (list.get(0).comp.getTarget().size() == 0)
                                        message = "Concept map "+su+" found no translation for "+src.getCode();
                                else {
                                        for (TargetElementComponent tgt : list.get(0).comp.getTarget()) {
                                                if (tgt.getEquivalence() == null || EnumSet.of( ConceptMapEquivalence.EQUAL , ConceptMapEquivalence.RELATEDTO , ConceptMapEquivalence.EQUIVALENT, ConceptMapEquivalence.WIDER).contains(tgt.getEquivalence())) {
                                                        if (done) {
                                                                message = "Concept map "+su+" found multiple matches for "+src.getCode();
                                                                done = false;
                                                        } else {
                                                                done = true;
                                                                outcome = new Coding().setCode(tgt.getCode()).setSystem(list.get(0).group.getTarget());
                                                        }
                                                } else if (tgt.getEquivalence() == ConceptMapEquivalence.UNMATCHED) {
                                                        done = true;
                                                }
                                        }
                                        if (!done)
                                                message = "Concept map "+su+" found no usable translation for "+src.getCode();
                                }
                        }
                        if (!done) 
                                throw new FHIRException(message);
                        if (outcome == null)
                                return null;
                        if ("code".equals(fieldToReturn))
                                return new CodeType(outcome.getCode());
                        else
                                return outcome; 
                }
        }


        public class PropertyWithType {
    private String path;
    private Property baseProperty;
    private Property profileProperty;
          private TypeDetails types;
    public PropertyWithType(String path, Property baseProperty, Property profileProperty, TypeDetails types) {
      super();
      this.baseProperty = baseProperty;
      this.profileProperty = profileProperty;
      this.path = path;
      this.types = types;
    }

    public TypeDetails getTypes() {
      return types;
    }
    public String getPath() {
      return path;
    }

    public Property getBaseProperty() {
      return baseProperty;
    }

    public void setBaseProperty(Property baseProperty) {
      this.baseProperty = baseProperty;
    }

    public Property getProfileProperty() {
      return profileProperty;
    }

    public void setProfileProperty(Property profileProperty) {
      this.profileProperty = profileProperty;
    }

    public String summary() {
      return path;
    }
    
        }
        
        public class VariableForProfiling {
            private VariableMode mode;
            private String name;
            private PropertyWithType property;
            
            public VariableForProfiling(VariableMode mode, String name, PropertyWithType property) {
              super();
              this.mode = mode;
              this.name = name;
              this.property = property;
            }
            public VariableMode getMode() {
              return mode;
            }
            public String getName() {
              return name;
            }
      public PropertyWithType getProperty() {
        return property;
      }
      public String summary() {
        return name+": "+property.summary();
      }      
          }

  public class VariablesForProfiling {
    private List<VariableForProfiling> list = new ArrayList<VariableForProfiling>();
    private boolean optional;
    private boolean repeating;

    public VariablesForProfiling(boolean optional, boolean repeating) {
      this.optional = optional;
      this.repeating = repeating;
    }

    public void add(VariableMode mode, String name, String path, Property property, TypeDetails types) {
      add(mode, name, new PropertyWithType(path, property, null, types));
    }
    
    public void add(VariableMode mode, String name, String path, Property baseProperty, Property profileProperty, TypeDetails types) {
      add(mode, name, new PropertyWithType(path, baseProperty, profileProperty, types));
    }
    
    public void add(VariableMode mode, String name, PropertyWithType property) {
      VariableForProfiling vv = null;
      for (VariableForProfiling v : list) 
        if ((v.mode == mode) && v.getName().equals(name))
          vv = v;
      if (vv != null)
        list.remove(vv);
      list.add(new VariableForProfiling(mode, name, property));
    }

    public VariablesForProfiling copy(boolean optional, boolean repeating) {
      VariablesForProfiling result = new VariablesForProfiling(optional, repeating);
      result.list.addAll(list);
      return result;
    }

    public VariablesForProfiling copy() {
      VariablesForProfiling result = new VariablesForProfiling(optional, repeating);
      result.list.addAll(list);
      return result;
    }

    public VariableForProfiling get(VariableMode mode, String name) {
      if (mode == null) {
        for (VariableForProfiling v : list) 
          if ((v.mode == VariableMode.OUTPUT) && v.getName().equals(name))
            return v;
        for (VariableForProfiling v : list) 
          if ((v.mode == VariableMode.INPUT) && v.getName().equals(name))
            return v;
      }
      for (VariableForProfiling v : list) 
        if ((v.mode == mode) && v.getName().equals(name))
          return v;
      return null;
    }

    public String summary() {
      CommaSeparatedStringBuilder s = new CommaSeparatedStringBuilder();
      CommaSeparatedStringBuilder t = new CommaSeparatedStringBuilder();
      for (VariableForProfiling v : list)
        if (v.mode == VariableMode.INPUT)
          s.append(v.summary());
        else
          t.append(v.summary());
      return "source variables ["+s.toString()+"], target variables ["+t.toString()+"]";
    }
  }

  public class StructureMapAnalysis {
    private List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
    private XhtmlNode summary;
    public List<StructureDefinition> getProfiles() {
      return profiles;
    }
    public XhtmlNode getSummary() {
      return summary;
    }
    
  }

        /**
         * Given a structure map, return a set of analyses on it. 
         * 
         * Returned:
         *   - a list or profiles for what it will create. First profile is the target
         *   - a table with a summary (in xhtml) for easy human undertanding of the mapping
         *   
         * 
         * @param appInfo
         * @param map
         * @return
         * @throws Exception
         */
  public StructureMapAnalysis analyse(Object appInfo, StructureMap map) throws Exception {
    ids.clear();
    StructureMapAnalysis result = new StructureMapAnalysis(); 
    TransformContext context = new TransformContext(appInfo);
    VariablesForProfiling vars = new VariablesForProfiling(false, false);
    StructureMapGroupComponent start = map.getGroup().get(0);
    for (StructureMapGroupInputComponent t : start.getInput()) {
      PropertyWithType ti = resolveType(map, t.getType(), t.getMode());
      if (t.getMode() == StructureMapInputMode.SOURCE)
       vars.add(VariableMode.INPUT, t.getName(), ti);
      else 
        vars.add(VariableMode.OUTPUT, t.getName(), createProfile(map, result.profiles, ti, start.getName(), start));
    }

    result.summary = new XhtmlNode(NodeType.Element, "table").setAttribute("class", "grid");
    XhtmlNode tr = result.summary.addTag("tr");
    tr.addTag("td").addTag("b").addText("Source");
    tr.addTag("td").addTag("b").addText("Target");
    
    log("Start Profiling Transform "+map.getUrl());
    analyseGroup("", context, map, vars, start, result);
    ProfileUtilities pu = new ProfileUtilities(worker, null, pkp);
    for (StructureDefinition sd : result.getProfiles())
      pu.cleanUpDifferential(sd);
    return result;
  }


  private void analyseGroup(String indent, TransformContext context, StructureMap map, VariablesForProfiling vars, StructureMapGroupComponent group, StructureMapAnalysis result) throws Exception {
    log(indent+"Analyse Group : "+group.getName());
    // todo: extends
    // todo: check inputs
    XhtmlNode tr = result.summary.addTag("tr").setAttribute("class", "diff-title");
    XhtmlNode xs = tr.addTag("td");
    XhtmlNode xt = tr.addTag("td");
    for (StructureMapGroupInputComponent inp : group.getInput()) {
      if (inp.getMode() == StructureMapInputMode.SOURCE) 
        noteInput(vars, inp, VariableMode.INPUT, xs);
      if (inp.getMode() == StructureMapInputMode.TARGET) 
        noteInput(vars, inp, VariableMode.OUTPUT, xt);
    }
    for (StructureMapGroupRuleComponent r : group.getRule()) {
      analyseRule(indent+"  ", context, map, vars, group, r, result);
    }    
  }


  private void noteInput(VariablesForProfiling vars, StructureMapGroupInputComponent inp, VariableMode mode, XhtmlNode xs) {
    VariableForProfiling v = vars.get(mode, inp.getName());
    if (v != null)
      xs.addText("Input: "+v.property.getPath());
  }

  private void analyseRule(String indent, TransformContext context, StructureMap map, VariablesForProfiling vars, StructureMapGroupComponent group, StructureMapGroupRuleComponent rule, StructureMapAnalysis result) throws Exception {
    log(indent+"Analyse rule : "+rule.getName());
    XhtmlNode tr = result.summary.addTag("tr");
    XhtmlNode xs = tr.addTag("td");
    XhtmlNode xt = tr.addTag("td");

    VariablesForProfiling srcVars = vars.copy();
    if (rule.getSource().size() != 1)
      throw new Exception("Rule \""+rule.getName()+"\": not handled yet");
    VariablesForProfiling source = analyseSource(rule.getName(), context, srcVars, rule.getSourceFirstRep(), xs);

    TargetWriter tw = new TargetWriter();
      for (StructureMapGroupRuleTargetComponent t : rule.getTarget()) {
      analyseTarget(rule.getName(), context, source, map, t, rule.getSourceFirstRep().getVariable(), tw, result.profiles, rule.getName());
      }
    tw.commit(xt);

          for (StructureMapGroupRuleComponent childrule : rule.getRule()) {
      analyseRule(indent+"  ", context, map, source, group, childrule, result);
          }
//    for (StructureMapGroupRuleDependentComponent dependent : rule.getDependent()) {
//      executeDependency(indent+"  ", context, map, v, group, dependent); // do we need group here?
//    }
          }

  public class StringPair {
    private String var;
    private String desc;
    public StringPair(String var, String desc) {
      super();
      this.var = var;
      this.desc = desc;
        }
    public String getVar() {
      return var;
      }
    public String getDesc() {
      return desc;
    }
  }
  public class TargetWriter {
    private Map<String, String> newResources = new HashMap<String, String>();
    private List<StringPair> assignments = new ArrayList<StringPair>();
    private List<StringPair> keyProps = new ArrayList<StringPair>();
    private CommaSeparatedStringBuilder txt = new CommaSeparatedStringBuilder();

    public void newResource(String var, String name) {
      newResources.put(var, name);
      txt.append("new "+name);
    }

    public void valueAssignment(String context, String desc) {
      assignments.add(new StringPair(context, desc));      
      txt.append(desc);
        }

    public void keyAssignment(String context, String desc) {
      keyProps.add(new StringPair(context, desc));      
      txt.append(desc);
    }
    public void commit(XhtmlNode xt) {
      if (newResources.size() == 1 && assignments.size() == 1 && newResources.containsKey(assignments.get(0).getVar()) && keyProps.size() == 1 && newResources.containsKey(keyProps.get(0).getVar()) ) {
        xt.addText("new "+assignments.get(0).desc+" ("+keyProps.get(0).desc.substring(keyProps.get(0).desc.indexOf(".")+1)+")");
      } else if (newResources.size() == 1 && assignments.size() == 1 && newResources.containsKey(assignments.get(0).getVar()) && keyProps.size() == 0) {
        xt.addText("new "+assignments.get(0).desc);
      } else {
        xt.addText(txt.toString());        
    }
    }
  }

  private VariablesForProfiling analyseSource(String ruleId, TransformContext context, VariablesForProfiling vars, StructureMapGroupRuleSourceComponent src, XhtmlNode td) throws Exception {
    VariableForProfiling var = vars.get(VariableMode.INPUT, src.getContext());
    if (var == null)
      throw new FHIRException("Rule \""+ruleId+"\": Unknown input variable "+src.getContext());
    PropertyWithType prop = var.getProperty();

    boolean optional = false;
    boolean repeating = false;

    if (src.hasCondition()) {
      optional = true;
    }

    if (src.hasElement()) {
      Property element = prop.getBaseProperty().getChild(prop.types.getType(), src.getElement());
      if (element == null)
        throw new Exception("Rule \""+ruleId+"\": Unknown element name "+src.getElement());
      if (element.getDefinition().getMin() == 0)
        optional = true;
      if (element.getDefinition().getMax().equals("*"))
        repeating = true;
      VariablesForProfiling result = vars.copy(optional, repeating);
      TypeDetails type = new TypeDetails(CollectionStatus.SINGLETON);
      for (TypeRefComponent tr : element.getDefinition().getType()) {
        if (!tr.hasCode())
          throw new Error("Rule \""+ruleId+"\": Element has no type");
        ProfiledType pt = new ProfiledType(tr.getCode());
        if (tr.hasProfile())
          pt.addProfiles(tr.getProfile());
        if (element.getDefinition().hasBinding())
          pt.addBinding(element.getDefinition().getBinding());
        type.addType(pt);
    } 
      td.addText(prop.getPath()+"."+src.getElement()); 
      if (src.hasVariable())
        result.add(VariableMode.INPUT, src.getVariable(), new PropertyWithType(prop.getPath()+"."+src.getElement(), element, null, type));
    return result;
    } else {
      td.addText(prop.getPath()); // ditto!
      return vars.copy(optional, repeating);
    }
  }


  private void analyseTarget(String ruleId, TransformContext context, VariablesForProfiling vars, StructureMap map, StructureMapGroupRuleTargetComponent tgt, String tv, TargetWriter tw, List<StructureDefinition> profiles, String sliceName) throws Exception {
    VariableForProfiling var = null;
    if (tgt.hasContext()) {
      var = vars.get(VariableMode.OUTPUT, tgt.getContext());
      if (var == null)
        throw new Exception("Rule \""+ruleId+"\": target context not known: "+tgt.getContext());
      if (!tgt.hasElement())
        throw new Exception("Rule \""+ruleId+"\": Not supported yet");
    }

    
    TypeDetails type = null;
    if (tgt.hasTransform()) {
      type = analyseTransform(context, map, tgt, var, vars);
        // profiling: dest.setProperty(tgt.getElement().hashCode(), tgt.getElement(), v);
    } else {
      Property vp = var.property.baseProperty.getChild(tgt.getElement(),  tgt.getElement());
      if (vp == null)
        throw new Exception("Unknown Property "+tgt.getElement()+" on "+var.property.path);
      
      type = new TypeDetails(CollectionStatus.SINGLETON, vp.getType(tgt.getElement()));
    }

    if (tgt.getTransform() == StructureMapTransform.CREATE) {
      String s = getParamString(vars, tgt.getParameter().get(0));
      if (worker.getResourceNames().contains(s))
        tw.newResource(tgt.getVariable(), s);
    } else { 
      boolean mapsSrc = false;
      for (StructureMapGroupRuleTargetParameterComponent p : tgt.getParameter()) {
        Type pr = p.getValue();
        if (pr instanceof IdType && ((IdType) pr).asStringValue().equals(tv)) 
          mapsSrc = true;
      }
      if (mapsSrc) { 
        if (var == null)
          throw new Error("Rule \""+ruleId+"\": Attempt to assign with no context");
        tw.valueAssignment(tgt.getContext(), var.property.getPath()+"."+tgt.getElement()+getTransformSuffix(tgt.getTransform()));
      } else if (tgt.hasContext()) {
        if (isSignificantElement(var.property, tgt.getElement())) {
          String td = describeTransform(tgt);
          if (td != null)
            tw.keyAssignment(tgt.getContext(), var.property.getPath()+"."+tgt.getElement()+" = "+td);
        }
      }
    }
    Type fixed = generateFixedValue(tgt);
    
    PropertyWithType prop = updateProfile(var, tgt.getElement(), type, map, profiles, sliceName, fixed, tgt);
    if (tgt.hasVariable())
      if (tgt.hasElement())
        vars.add(VariableMode.OUTPUT, tgt.getVariable(), prop); 
      else
        vars.add(VariableMode.OUTPUT, tgt.getVariable(), prop); 
  }
  
  private Type generateFixedValue(StructureMapGroupRuleTargetComponent tgt) {
    if (!allParametersFixed(tgt))
      return null;
    if (!tgt.hasTransform())
      return null;
    switch (tgt.getTransform()) {
    case COPY: return tgt.getParameter().get(0).getValue(); 
    case TRUNCATE: return null; 
    //case ESCAPE: 
    //case CAST: 
    //case APPEND: 
    case TRANSLATE: return null; 
  //case DATEOP, 
  //case UUID, 
  //case POINTER, 
  //case EVALUATE, 
    case CC: 
      CodeableConcept cc = new CodeableConcept();
      cc.addCoding(buildCoding(tgt.getParameter().get(0).getValue(), tgt.getParameter().get(1).getValue()));
      return cc;
    case C: 
      return buildCoding(tgt.getParameter().get(0).getValue(), tgt.getParameter().get(1).getValue());
    case QTY: return null; 
  //case ID, 
  //case CP, 
    default:
      return null;
    }
  }

  @SuppressWarnings("rawtypes")
  private Coding buildCoding(Type value1, Type value2) {
    return new Coding().setSystem(((PrimitiveType) value1).asStringValue()).setCode(((PrimitiveType) value2).asStringValue()) ;
  }

  private boolean allParametersFixed(StructureMapGroupRuleTargetComponent tgt) {
    for (StructureMapGroupRuleTargetParameterComponent p : tgt.getParameter()) {
      Type pr = p.getValue();
      if (pr instanceof IdType)
        return false;
    }
    return true;
  }

  private String describeTransform(StructureMapGroupRuleTargetComponent tgt) throws FHIRException {
    switch (tgt.getTransform()) {
    case COPY: return null; 
    case TRUNCATE: return null; 
    //case ESCAPE: 
    //case CAST: 
    //case APPEND: 
    case TRANSLATE: return null; 
  //case DATEOP, 
  //case UUID, 
  //case POINTER, 
  //case EVALUATE, 
    case CC: return describeTransformCCorC(tgt); 
    case C: return describeTransformCCorC(tgt); 
    case QTY: return null; 
  //case ID, 
  //case CP, 
    default:
      return null;
    }
  }

  @SuppressWarnings("rawtypes")
  private String describeTransformCCorC(StructureMapGroupRuleTargetComponent tgt) throws FHIRException {
    if (tgt.getParameter().size() < 2)
      return null;
    Type p1 = tgt.getParameter().get(0).getValue();
    Type p2 = tgt.getParameter().get(1).getValue();
    if (p1 instanceof IdType || p2 instanceof IdType)
      return null;
    if (!(p1 instanceof PrimitiveType) || !(p2 instanceof PrimitiveType))
      return null;
    String uri = ((PrimitiveType) p1).asStringValue();
    String code = ((PrimitiveType) p2).asStringValue();
    if (Utilities.noString(uri))
      throw new FHIRException("Describe Transform, but the uri is blank");
    if (Utilities.noString(code))
      throw new FHIRException("Describe Transform, but the code is blank");
    Coding c = buildCoding(uri, code);
    return NarrativeGenerator.describeSystem(c.getSystem())+"#"+c.getCode()+(c.hasDisplay() ? "("+c.getDisplay()+")" : "");
  }


  private boolean isSignificantElement(PropertyWithType property, String element) {
    if ("Observation".equals(property.getPath()))
      return "code".equals(element);
    else if ("Bundle".equals(property.getPath()))
      return "type".equals(element);
    else
      return false;
  }

  private String getTransformSuffix(StructureMapTransform transform) {
    switch (transform) {
    case COPY: return ""; 
    case TRUNCATE: return " (truncated)"; 
    //case ESCAPE: 
    //case CAST: 
    //case APPEND: 
    case TRANSLATE: return " (translated)"; 
  //case DATEOP, 
  //case UUID, 
  //case POINTER, 
  //case EVALUATE, 
    case CC: return " (--> CodeableConcept)"; 
    case C: return " (--> Coding)"; 
    case QTY: return " (--> Quantity)"; 
  //case ID, 
  //case CP, 
    default:
      return " {??)";
    }
  }

  private PropertyWithType updateProfile(VariableForProfiling var, String element, TypeDetails type, StructureMap map, List<StructureDefinition> profiles, String sliceName, Type fixed, StructureMapGroupRuleTargetComponent tgt) throws FHIRException {
    if (var == null) {
      assert (Utilities.noString(element));
      // 1. start the new structure definition
      StructureDefinition sdn = worker.fetchResource(StructureDefinition.class, type.getType());
      if (sdn == null)
        throw new FHIRException("Unable to find definition for "+type.getType());
      ElementDefinition edn = sdn.getSnapshot().getElementFirstRep();
      PropertyWithType pn = createProfile(map, profiles, new PropertyWithType(sdn.getId(), new Property(worker, edn, sdn), null, type), sliceName, tgt);

//      // 2. hook it into the base bundle
//      if (type.getType().startsWith("http://hl7.org/fhir/StructureDefinition/") && worker.getResourceNames().contains(type.getType().substring(40))) {
//        StructureDefinition sd = var.getProperty().profileProperty.getStructure();
//        ElementDefinition ed = sd.getDifferential().addElement();
//        ed.setPath("Bundle.entry");
//        ed.setName(sliceName);
//        ed.setMax("1"); // well, it is for now...
//        ed = sd.getDifferential().addElement();
//        ed.setPath("Bundle.entry.fullUrl");
//        ed.setMin(1);
//        ed = sd.getDifferential().addElement();
//        ed.setPath("Bundle.entry.resource");
//        ed.setMin(1);
//        ed.addType().setCode(pn.getProfileProperty().getStructure().getType()).setProfile(pn.getProfileProperty().getStructure().getUrl());
//      }
      return pn; 
    } else {
      assert (!Utilities.noString(element));
      Property pvb = var.getProperty().getBaseProperty();
      Property pvd = var.getProperty().getProfileProperty();
      Property pc = pvb.getChild(element, var.property.types);
      if (pc == null)
        throw new DefinitionException("Unable to find a definition for "+pvb.getDefinition().getPath()+"."+element);
      
      // the profile structure definition (derived)
      StructureDefinition sd = var.getProperty().profileProperty.getStructure();
      ElementDefinition ednew = sd.getDifferential().addElement();
      ednew.setPath(var.getProperty().profileProperty.getDefinition().getPath()+"."+pc.getName());
      ednew.setUserData("slice-name", sliceName);
      ednew.setFixed(fixed);
      for (ProfiledType pt : type.getProfiledTypes()) {
        if (pt.hasBindings())
          ednew.setBinding(pt.getBindings().get(0));
        if (pt.getUri().startsWith("http://hl7.org/fhir/StructureDefinition/")) {
          String t = pt.getUri().substring(40);
          t = checkType(t, pc, pt.getProfiles());
          if (t != null) {
            if (pt.hasProfiles()) {
              for (String p : pt.getProfiles())
                if (t.equals("Reference"))
                  ednew.getType(t).addTargetProfile(p);
                else
                  ednew.getType(t).addProfile(p);
            } else 
            ednew.getType(t);
      }
        }
      }
      
      return new PropertyWithType(var.property.path+"."+element, pc, new Property(worker, ednew, sd), type);
    }
  }
  


  private String checkType(String t, Property pvb, List<String> profiles) throws FHIRException {
    if (pvb.getDefinition().getType().size() == 1 && isCompatibleType(t, pvb.getDefinition().getType().get(0).getCode()) && profilesMatch(profiles, pvb.getDefinition().getType().get(0).getProfile())) 
      return null;
    for (TypeRefComponent tr : pvb.getDefinition().getType()) {
      if (isCompatibleType(t, tr.getCode()))
        return tr.getCode(); // note what is returned - the base type, not the inferred mapping type
    }
    throw new FHIRException("The type "+t+" is not compatible with the allowed types for "+pvb.getDefinition().getPath());
  }

  private boolean profilesMatch(List<String> profiles, List<CanonicalType> profile) {
    return profiles == null || profiles.size() == 0 || profile.size() == 0 || (profiles.size() == 1 && profiles.get(0).equals(profile.get(0).getValue()));
  }

  private boolean isCompatibleType(String t, String code) {
    if (t.equals(code))
      return true;
    if (t.equals("string")) {
      StructureDefinition sd = worker.fetchTypeDefinition(code);
      if (sd != null && sd.getBaseDefinition().equals("http://hl7.org/fhir/StructureDefinition/string"))
        return true;
    }
    return false;
  }

  private TypeDetails analyseTransform(TransformContext context, StructureMap map, StructureMapGroupRuleTargetComponent tgt, VariableForProfiling var, VariablesForProfiling vars) throws FHIRException {
    switch (tgt.getTransform()) {
    case CREATE :
      String p = getParamString(vars, tgt.getParameter().get(0));
      return new TypeDetails(CollectionStatus.SINGLETON, p);
    case COPY : 
      return getParam(vars, tgt.getParameter().get(0));
    case EVALUATE :
      ExpressionNode expr = (ExpressionNode) tgt.getUserData(MAP_EXPRESSION);
      if (expr == null) {
        expr = fpe.parse(getParamString(vars, tgt.getParameter().get(tgt.getParameter().size()-1)));
        tgt.setUserData(MAP_WHERE_EXPRESSION, expr);
      }
      return fpe.check(vars, null, expr);

////case TRUNCATE : 
////  String src = getParamString(vars, tgt.getParameter().get(0));
////  String len = getParamString(vars, tgt.getParameter().get(1));
////  if (Utilities.isInteger(len)) {
////    int l = Integer.parseInt(len);
////    if (src.length() > l)
////      src = src.substring(0, l);
////  }
////  return new StringType(src);
////case ESCAPE : 
////  throw new Error("Transform "+tgt.getTransform().toCode()+" not supported yet");
////case CAST :
////  throw new Error("Transform "+tgt.getTransform().toCode()+" not supported yet");
////case APPEND : 
////  throw new Error("Transform "+tgt.getTransform().toCode()+" not supported yet");
    case TRANSLATE : 
      return new TypeDetails(CollectionStatus.SINGLETON, "CodeableConcept");
   case CC:
     ProfiledType res = new ProfiledType("CodeableConcept");
     if (tgt.getParameter().size() >= 2  && isParamId(vars, tgt.getParameter().get(1))) {
       TypeDetails td = vars.get(null, getParamId(vars, tgt.getParameter().get(1))).property.types;
       if (td != null && td.hasBinding())
         // todo: do we need to check that there's no implicit translation her? I don't think we do...
         res.addBinding(td.getBinding());
     }
     return new TypeDetails(CollectionStatus.SINGLETON, res);
   case C:
     return new TypeDetails(CollectionStatus.SINGLETON, "Coding");
   case QTY:
     return new TypeDetails(CollectionStatus.SINGLETON, "Quantity");
   case REFERENCE :
      VariableForProfiling vrs = vars.get(VariableMode.OUTPUT, getParamId(vars, tgt.getParameterFirstRep()));
      if (vrs == null)
        throw new FHIRException("Unable to resolve variable \""+getParamId(vars, tgt.getParameterFirstRep())+"\"");
      String profile = vrs.property.getProfileProperty().getStructure().getUrl();
     TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON);
     td.addType("Reference", profile);
     return td;  
////case DATEOP :
////  throw new Error("Transform "+tgt.getTransform().toCode()+" not supported yet");
////case UUID :
////  return new IdType(UUID.randomUUID().toString());
////case POINTER :
////  Base b = getParam(vars, tgt.getParameter().get(0));
////  if (b instanceof Resource)
////    return new UriType("urn:uuid:"+((Resource) b).getId());
////  else
////    throw new FHIRException("Transform engine cannot point at an element of type "+b.fhirType());
    default:
      throw new Error("Transform Unknown or not handled yet: "+tgt.getTransform().toCode());
    }
  }
  private String getParamString(VariablesForProfiling vars, StructureMapGroupRuleTargetParameterComponent parameter) {
    Type p = parameter.getValue();
    if (p == null || p instanceof IdType)
      return null;
    if (!p.hasPrimitiveValue())
      return null;
    return p.primitiveValue();
  }

  private String getParamId(VariablesForProfiling vars, StructureMapGroupRuleTargetParameterComponent parameter) {
    Type p = parameter.getValue();
    if (p == null || !(p instanceof IdType))
      return null;
    return p.primitiveValue();
  }

  private boolean isParamId(VariablesForProfiling vars, StructureMapGroupRuleTargetParameterComponent parameter) {
    Type p = parameter.getValue();
    if (p == null || !(p instanceof IdType))
      return false;
    return vars.get(null, p.primitiveValue()) != null;
  }

  private TypeDetails getParam(VariablesForProfiling vars, StructureMapGroupRuleTargetParameterComponent parameter) throws DefinitionException {
    Type p = parameter.getValue();
    if (!(p instanceof IdType))
      return new TypeDetails(CollectionStatus.SINGLETON, ProfileUtilities.sdNs(p.fhirType(), worker.getOverrideVersionNs()));
    else { 
      String n = ((IdType) p).asStringValue();
      VariableForProfiling b = vars.get(VariableMode.INPUT, n);
      if (b == null)
        b = vars.get(VariableMode.OUTPUT, n);
      if (b == null)
        throw new DefinitionException("Variable "+n+" not found ("+vars.summary()+")");
      return b.getProperty().getTypes();
    }
  }

  private PropertyWithType createProfile(StructureMap map, List<StructureDefinition> profiles, PropertyWithType prop, String sliceName, Base ctxt) throws DefinitionException {
    if (prop.getBaseProperty().getDefinition().getPath().contains(".")) 
      throw new DefinitionException("Unable to process entry point");

    String type = prop.getBaseProperty().getDefinition().getPath();
    String suffix = "";
    if (ids.containsKey(type)) {
      int id = ids.get(type);
      id++;
      ids.put(type, id);
      suffix = "-"+Integer.toString(id);
    } else
      ids.put(type, 0);
    
    StructureDefinition profile = new StructureDefinition();
    profiles.add(profile);
    profile.setDerivation(TypeDerivationRule.CONSTRAINT);
    profile.setType(type);
    profile.setBaseDefinition(prop.getBaseProperty().getStructure().getUrl());
    profile.setName("Profile for "+profile.getType()+" for "+sliceName);
    profile.setUrl(map.getUrl().replace("StructureMap", "StructureDefinition")+"-"+profile.getType()+suffix);
    ctxt.setUserData("profile", profile.getUrl()); // then we can easily assign this profile url for validation later when we actually transform
    profile.setId(map.getId()+"-"+profile.getType()+suffix);
    profile.setStatus(map.getStatus());
    profile.setExperimental(map.getExperimental());
    profile.setDescription("Generated automatically from the mapping by the Java Reference Implementation");
    for (ContactDetail c : map.getContact()) {
      ContactDetail p = profile.addContact();
      p.setName(c.getName());
      for (ContactPoint cc : c.getTelecom()) 
        p.addTelecom(cc);
    }
    profile.setDate(map.getDate());
    profile.setCopyright(map.getCopyright());
    profile.setFhirVersion(Constants.VERSION);
    profile.setKind(prop.getBaseProperty().getStructure().getKind());
    profile.setAbstract(false);
    ElementDefinition ed = profile.getDifferential().addElement();
    ed.setPath(profile.getType());
    prop.profileProperty = new Property(worker, ed, profile);
    return prop;
  }

  private PropertyWithType resolveType(StructureMap map, String type, StructureMapInputMode mode) throws Exception {
    for (StructureMapStructureComponent imp : map.getStructure()) {
      if ((imp.getMode() == StructureMapModelMode.SOURCE && mode == StructureMapInputMode.SOURCE) || 
          (imp.getMode() == StructureMapModelMode.TARGET && mode == StructureMapInputMode.TARGET)) {
        StructureDefinition sd = worker.fetchResource(StructureDefinition.class, imp.getUrl());
        if (sd == null)
          throw new Exception("Import "+imp.getUrl()+" cannot be resolved");
        if (sd.getId().equals(type)) {
          return new PropertyWithType(sd.getType(), new Property(worker, sd.getSnapshot().getElement().get(0), sd), null, new TypeDetails(CollectionStatus.SINGLETON, sd.getUrl()));
        }
      }
    }
    throw new Exception("Unable to find structure definition for "+type+" in imports");
  }


  public StructureMap generateMapFromMappings(StructureDefinition sd) throws IOException, FHIRException {
    String id = getLogicalMappingId(sd);
    if (id == null) 
        return null;
    String prefix = ToolingExtensions.readStringExtension(sd,  ToolingExtensions.EXT_MAPPING_PREFIX);
    String suffix = ToolingExtensions.readStringExtension(sd,  ToolingExtensions.EXT_MAPPING_SUFFIX);
    if (prefix == null || suffix == null)
      return null;
    // we build this by text. Any element that has a mapping, we put it's mappings inside it....
    StringBuilder b = new StringBuilder();
    b.append(prefix);

    ElementDefinition root = sd.getSnapshot().getElementFirstRep();
    String m = getMapping(root, id);
    if (m != null)
      b.append(m+"\r\n");
    addChildMappings(b, id, "", sd, root, false);
    b.append("\r\n");
    b.append(suffix);
    b.append("\r\n");
    StructureMap map = parse(b.toString());
    map.setId(tail(map.getUrl()));
    if (!map.hasStatus())
      map.setStatus(PublicationStatus.DRAFT);
    map.getText().setStatus(NarrativeStatus.GENERATED);
    map.getText().setDiv(new XhtmlNode(NodeType.Element, "div"));
    map.getText().getDiv().addTag("pre").addText(render(map));
    return map;
  }


  private String tail(String url) {
    return url.substring(url.lastIndexOf("/")+1);
  }


  private void addChildMappings(StringBuilder b, String id, String indent, StructureDefinition sd, ElementDefinition ed, boolean inner) throws DefinitionException {
    boolean first = true;
    List<ElementDefinition> children = ProfileUtilities.getChildMap(sd, ed);
    for (ElementDefinition child : children) {
      if (first && inner) {
        b.append(" then {\r\n");
        first = false;
      }
      String map = getMapping(child, id);
      if (map != null) {
        b.append(indent+"  "+child.getPath()+": "+map);
        addChildMappings(b, id, indent+"  ", sd, child, true);
        b.append("\r\n");
      }
    }
    if (!first && inner)
      b.append(indent+"}");
    
  }


  private String getMapping(ElementDefinition ed, String id) {
    for (ElementDefinitionMappingComponent map : ed.getMapping())
      if (id.equals(map.getIdentity()))
        return map.getMap();
    return null;
  }


  private String getLogicalMappingId(StructureDefinition sd) {
    String id = null;
    for (StructureDefinitionMappingComponent map : sd.getMapping()) {
      if ("http://hl7.org/fhir/logical".equals(map.getUri()))
        return map.getIdentity();
    }
    return null;
  }
        
}