Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core

org.hl7.fhir.convertors/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.8.24-SNAPSHOT</version>
+        <version>4.0.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>3.8.24-SNAPSHOT</version>
+		<version>4.0.1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu2016may/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>3.8.24-SNAPSHOT</version>
+		<version>4.0.1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu3/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.8.24-SNAPSHOT</version>
+        <version>4.0.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/Property.java

@@ -82,7 +82,8 @@ public class Property {
 	  this.definition = definition;
 	  this.minCardinality = minCardinality;
 	  this.maxCardinality = maxCardinality;
-	  this.values.add(value);
+    if (value != null)
+  	  this.values.add(value);
   }
 
 	/**
@@ -156,6 +157,8 @@ public class Property {
     this.structure = structure;
   }
 
+  public boolean isList() {
+    return maxCardinality > 1;
+  }
 
-	
 }

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/GraphQLEngine.java

@@ -0,0 +1,964 @@
+package org.hl7.fhir.dstu3.utils;
+
+/*-
+ * #%L
+ * org.hl7.fhir.dstu3
+ * %%
+ * Copyright (C) 2014 - 2019 Health Level 7
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+
+import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.dstu3.context.IWorkerContext;
+import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.dstu3.model.Bundle.BundleLinkComponent;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.graphql.*;
+import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
+import org.hl7.fhir.utilities.graphql.Package;
+import org.hl7.fhir.utilities.graphql.Operation.OperationType;
+
+import java.io.UnsupportedEncodingException;
+import java.net.URLDecoder;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static org.hl7.fhir.utilities.graphql.IGraphQLStorageServices.ReferenceResolution;
+
+public class GraphQLEngine implements IGraphQLEngine {
+  
+  public static class SearchEdge extends Base {
+
+    private BundleEntryComponent be;
+    private String type;
+    
+    SearchEdge(String type, BundleEntryComponent be) {
+      this.type = type;
+      this.be = be;
+    }
+    @Override
+    public String fhirType() {
+      return type;
+    }
+
+    @Override
+    protected void listChildren(List<Property> result) {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public String getIdBase() {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public void setIdBase(String value) {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
+      switch (_hash) {
+      case 3357091:    /*mode*/     return new Property(_name, "string",   "n/a", 0, 1, be.getSearch().hasMode() ? be.getSearch().getModeElement() : null);
+      case 109264530:  /*score*/    return new Property(_name, "string",   "n/a", 0, 1, be.getSearch().hasScore() ? be.getSearch().getScoreElement() : null);
+      case -341064690: /*resource*/ return new Property(_name, "resource",  "n/a", 0, 1, be.hasResource() ? be.getResource() : null);
+      default: return super.getNamedProperty(_hash, _name, _checkValid);
+      }
+    }
+  }
+
+  public static class SearchWrapper extends Base {
+
+    private Bundle bnd;
+    private String type;
+    private Map<String, String> map;
+
+    SearchWrapper(String type, Bundle bnd) throws FHIRException {
+      this.type = type;
+      this.bnd = bnd;
+      for (BundleLinkComponent bl : bnd.getLink()) 
+        if (bl.getRelation().equals("self"))
+          map = parseURL(bl.getUrl());
+    }
+
+    @Override
+    public String fhirType() {
+      return type;
+    }
+
+    @Override
+    protected void listChildren(List<Property> result) {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public String getIdBase() {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public void setIdBase(String value) {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
+      switch (_hash) {
+      case 97440432:   /*first*/     return new Property(_name, "string",  "n/a", 0, 1, extractLink(_name));
+      case -1273775369: /*previous*/  return new Property(_name, "string",  "n/a", 0, 1, extractLink(_name));
+      case 3377907:    /*next*/      return new Property(_name, "string",  "n/a", 0, 1, extractLink(_name));
+      case 3314326:    /*last*/      return new Property(_name, "string",  "n/a", 0, 1, extractLink(_name));
+      case 94851343:   /*count*/     return new Property(_name, "integer", "n/a", 0, 1, bnd.getTotalElement());
+      case -1019779949:/*offset*/    return new Property(_name, "integer", "n/a", 0, 1, extractParam("search-offset"));
+      case 860381968:  /*pagesize*/  return new Property(_name, "integer", "n/a", 0, 1, extractParam("_count"));
+      case 96356950:  /*edges*/      return new Property(_name, "edge",    "n/a", 0, Integer.MAX_VALUE, getEdges());
+      default: return super.getNamedProperty(_hash, _name, _checkValid);
+      }
+    }
+
+    private List<Base> getEdges() {
+      List<Base> list = new ArrayList<>();
+      for (BundleEntryComponent be : bnd.getEntry())
+        list.add(new SearchEdge(type.substring(0, type.length() - 10) + "Edge", be));
+      return list;
+    }
+
+    private Base extractParam(String name) throws FHIRException {
+      return map != null ? new IntegerType(map.get(name)) : null;
+    }
+
+    private Map<String, String> parseURL(String url) throws FHIRException {
+      try {
+        Map<String, String> map = new HashMap<String, String>();
+        String[] pairs = url.split("&");
+        for (String pair : pairs) {
+          int idx = pair.indexOf("=");
+          String key;
+          key = idx > 0 ? URLDecoder.decode(pair.substring(0, idx), "UTF-8") : pair;
+          String value = idx > 0 && pair.length() > idx + 1 ? URLDecoder.decode(pair.substring(idx + 1), "UTF-8") : null;
+          map.put(key, value);
+        }
+        return map;
+      } catch (UnsupportedEncodingException e) {
+        throw new FHIRException(e);
+      }
+    }
+
+    private Base extractLink(String _name) throws FHIRException {
+      for (BundleLinkComponent bl : bnd.getLink()) {
+        if (bl.getRelation().equals(_name)) {
+          Map<String, String> map = parseURL(bl.getUrl());
+          return new StringType(map.get("search-id")+':'+map.get("search-offset"));
+        }
+      }
+      return null;
+    }
+
+  }
+  
+  private IWorkerContext context;
+  
+  public GraphQLEngine(IWorkerContext context) {
+    super();
+    this.context = context;
+  }
+
+  /**
+   *  for the host to pass context into and get back on the reference resolution interface
+   */
+  private Object appInfo;
+
+  /**
+   *  the focus resource - if (there instanceof one. if (there isn"t,) there instanceof no focus
+   */
+  private Resource focus;
+
+  /**
+   * The package that describes the graphQL to be executed, operation name, and variables
+   */
+  private Package graphQL;
+
+  /**
+   * where the output from executing the query instanceof going to go
+   */
+  private ObjectValue output;
+
+  /** 
+   * Application provided reference resolution services 
+   */
+  private IGraphQLStorageServices services;
+
+  // internal stuff 
+  private Map<String, Argument> workingVariables = new HashMap<String, Argument>();
+
+  private FHIRPathEngine fpe;
+
+  private ExpressionNode magicExpression;
+  
+  public void execute() throws EGraphEngine, EGraphQLException, FHIRException {
+    if (graphQL == null)
+      throw new EGraphEngine("Unable to process graphql - graphql document missing");
+    fpe = new FHIRPathEngine(this.context);
+    magicExpression = new ExpressionNode(0);
+
+    output = new ObjectValue();
+
+    Operation op = null;
+    // todo: initial conditions
+    if (!Utilities.noString(graphQL.getOperationName())) {
+      op = graphQL.getDocument().operation(graphQL.getOperationName());
+      if (op == null)
+        throw new EGraphEngine("Unable to find operation \""+graphQL.getOperationName()+"\"");
+    } else if ((graphQL.getDocument().getOperations().size() == 1))
+      op = graphQL.getDocument().getOperations().get(0);
+    else
+      throw new EGraphQLException("No operation name provided, so expected to find a single operation");
+
+    if (op.getOperationType() == OperationType.qglotMutation)
+      throw new EGraphQLException("Mutation operations are not supported (yet)");
+
+    checkNoDirectives(op.getDirectives());
+    processVariables(op);
+    if (focus == null)
+      processSearch(output, op.getSelectionSet(), false, "");
+    else
+      processObject(focus, focus, output, op.getSelectionSet(), false, "");
+  }
+
+  private boolean checkBooleanDirective(Directive dir) throws EGraphQLException {
+    if (dir.getArguments().size() != 1)
+      throw new EGraphQLException("Unable to process @"+dir.getName()+": expected a single argument \"if\"");
+    if (!dir.getArguments().get(0).getName().equals("if"))
+      throw new EGraphQLException("Unable to process @"+dir.getName()+": expected a single argument \"if\"");
+    List<Value> vl = resolveValues(dir.getArguments().get(0), 1);
+    return vl.get(0).toString().equals("true");
+  }
+
+  private boolean checkDirectives(List<Directive> directives) throws EGraphQLException {
+    Directive skip = null;
+    Directive include = null;
+    for (Directive dir : directives) {
+      if (dir.getName().equals("skip")) {
+        if ((skip == null))
+          skip = dir;
+        else
+          throw new EGraphQLException("Duplicate @skip directives");
+      } else if (dir.getName().equals("include")) {
+        if ((include == null))
+          include = dir;
+        else
+          throw new EGraphQLException("Duplicate @include directives");
+      }
+      else if (!Utilities.existsInList(dir.getName(), "flatten", "first", "singleton", "slice"))
+        throw new EGraphQLException("Directive \""+dir.getName()+"\" instanceof not recognised");
+    }
+    if ((skip != null && include != null))
+      throw new EGraphQLException("Cannot mix @skip and @include directives");
+    if (skip != null)
+      return !checkBooleanDirective(skip);
+    else if (include != null)
+      return checkBooleanDirective(include);
+    else
+      return true;
+  }
+
+  private void checkNoDirectives(List<Directive> directives) {
+
+  }
+
+  private boolean targetTypeOk(List<Argument> arguments, IBaseResource dest) throws EGraphQLException {
+    List<String> list = new ArrayList<String>();
+    for (Argument arg : arguments) {
+      if ((arg.getName().equals("type"))) {
+        List<Value> vl = resolveValues(arg);
+        for (Value v : vl)
+          list.add(v.toString());
+      }
+    }
+    if (list.size() == 0)
+      return true;
+    else
+      return list.indexOf(dest.fhirType()) > -1;
+  }
+
+  private boolean hasExtensions(Base obj) {
+    if (obj instanceof BackboneElement)
+      return ((BackboneElement) obj).getExtension().size() > 0 || ((BackboneElement) obj).getModifierExtension().size() > 0;
+      else if (obj instanceof DomainResource)
+        return ((DomainResource)obj).getExtension().size() > 0 || ((DomainResource)obj).getModifierExtension().size() > 0;
+        else if (obj instanceof Element)
+          return ((Element)obj).getExtension().size() > 0;
+          else
+            return false;
+  }
+
+  private boolean passesExtensionMode(Base obj, boolean extensionMode) {
+    if (!obj.isPrimitive())
+      return !extensionMode;
+    else if (extensionMode)
+      return !Utilities.noString(obj.getIdBase()) || hasExtensions(obj);
+    else
+      return obj.primitiveValue() != "";
+  }
+
+  private List<Base> filter(Resource context, Property prop, List<Argument> arguments, List<Base> values, boolean extensionMode) throws FHIRException, EGraphQLException {
+    List<Base> result = new ArrayList<Base>();
+    if (values.size() > 0) {
+      int count = Integer.MAX_VALUE;
+      int offset = 0;
+      StringBuilder fp = new StringBuilder();
+      for (Argument arg : arguments) {
+        List<Value> vl = resolveValues(arg);
+        if ((vl.size() != 1))
+          throw new EGraphQLException("Incorrect number of arguments");
+        if (values.get(0).isPrimitive())
+          throw new EGraphQLException("Attempt to use a filter ("+arg.getName()+") on a primtive type ("+prop.getTypeCode()+")");
+        if ((arg.getName().equals("fhirpath")))
+          fp.append(" and "+vl.get(0).toString());
+        else if ((arg.getName().equals("_count")))
+          count = Integer.valueOf(vl.get(0).toString());
+        else if ((arg.getName().equals("_offset")))
+          offset = Integer.valueOf(vl.get(0).toString());
+        else {
+          Property p = values.get(0).getNamedProperty(arg.getName());
+          if (p == null)
+            throw new EGraphQLException("Attempt to use an unknown filter ("+arg.getName()+") on a type ("+prop.getTypeCode()+")");
+          fp.append(" and "+arg.getName()+" = '"+vl.get(0).toString()+"'");
+        }
+      }
+      int i = 0;
+      int t = 0;
+      if (fp.length() == 0)
+        for (Base v : values) {
+          if ((i >= offset) && passesExtensionMode(v, extensionMode)) {
+            result.add(v);
+            t++;
+            if (t >= count)
+              break;
+          }
+          i++;
+        } else {
+          ExpressionNode node = fpe.parse(fp.toString().substring(5));
+          for (Base v : values) {
+            if ((i >= offset) && passesExtensionMode(v, extensionMode) && fpe.evaluateToBoolean(null, context, v, node)) {
+              result.add(v);
+              t++;
+              if (t >= count)
+                break;
+            }
+            i++;
+          }
+        }
+    }
+    return result;
+  }
+
+  private List<Resource> filterResources(Argument fhirpath, Bundle bnd) throws EGraphQLException, FHIRException {
+    List<Resource> result = new ArrayList<Resource>();
+    if (bnd.getEntry().size() > 0) {
+      if ((fhirpath == null))
+        for (BundleEntryComponent be : bnd.getEntry())
+          result.add(be.getResource());
+      else {
+        FHIRPathEngine fpe = new FHIRPathEngine(context);
+        ExpressionNode node = fpe.parse(getSingleValue(fhirpath));
+        for (BundleEntryComponent be : bnd.getEntry())
+          if (fpe.evaluateToBoolean(null, be.getResource(), be.getResource(), node))
+            result.add(be.getResource());
+      }
+    }
+    return result;
+  }
+
+  private List<Resource> filterResources(Argument fhirpath, List<IBaseResource> list) throws EGraphQLException, FHIRException {
+    List<Resource> result = new ArrayList<>();
+    if (list.size() > 0) {
+      if ((fhirpath == null))
+        for (IBaseResource v : list)
+          result.add((Resource) v);
+      else {
+        FHIRPathEngine fpe = new FHIRPathEngine(context);
+        ExpressionNode node = fpe.parse(getSingleValue(fhirpath));
+        for (IBaseResource v : list)
+          if (fpe.evaluateToBoolean(null, (Resource)v, (Resource)v, node))
+            result.add((Resource) v);
+      }
+    }
+    return result;
+  }
+
+  private boolean hasArgument(List<Argument> arguments, String name, String value) {
+    for (Argument arg : arguments)
+      if ((arg.getName().equals(name)) && arg.hasValue(value))
+        return true;
+    return false;
+  }
+
+  private void processValues(Resource context, Selection sel, Property prop, ObjectValue target, List<Base> values, boolean extensionMode, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    boolean il = false;
+    Argument arg = null;
+    ExpressionNode expression = null;
+    if (sel.getField().hasDirective("slice")) {
+      Directive dir = sel.getField().directive("slice");
+      String s = ((StringValue) dir.getArguments().get(0).getValues().get(0)).getValue();
+      if (s.equals("$index"))
+        expression = magicExpression;
+      else
+        expression = fpe.parse(s);
+    }
+    if (sel.getField().hasDirective("flatten")) // special: instruction to drop this node...
+      il = prop.isList() && !sel.getField().hasDirective("first");
+    else if (sel.getField().hasDirective("first")) {
+      if (expression != null) 
+        throw new FHIRException("You cannot mix @slice and @first");
+      arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), inheritedList));
+    } else if (expression == null)
+      arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
+
+    
+    int index = 0;
+    for (Base value : values) {
+      String ss = "";
+      if (expression != null) {
+        if (expression == magicExpression)
+          ss = suffix+'.'+Integer.toString(index);
+        else
+          ss = suffix+'.'+fpe.evaluateToString(null, null, value, expression);
+        if (!sel.getField().hasDirective("flatten"))
+          arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
+      }
+
+      if (value.isPrimitive() && !extensionMode) {
+        if (!sel.getField().getSelectionSet().isEmpty())
+          throw new EGraphQLException("Encountered a selection set on a scalar field type");
+        processPrimitive(arg, value);
+      } else {
+        if (sel.getField().getSelectionSet().isEmpty())
+          throw new EGraphQLException("No Fields selected on a complex object");
+        if (arg == null)
+          processObject(context, value, target, sel.getField().getSelectionSet(), il, ss);
+        else {
+          ObjectValue n = new ObjectValue();
+          arg.addValue(n);
+          processObject(context, value, n, sel.getField().getSelectionSet(), il, ss);
+        }
+      }
+      if (sel.getField().hasDirective("first"))
+        return;
+      index++;
+    }
+  }
+
+  private void processVariables(Operation op) throws EGraphQLException {
+    for (Variable varRef : op.getVariables()) {
+      Argument varDef = null;
+      for (Argument v : graphQL.getVariables()) 
+        if (v.getName().equals(varRef.getName()))
+          varDef = v;
+      if (varDef != null)
+        workingVariables.put(varRef.getName(), varDef); // todo: check type?
+      else if (varRef.getDefaultValue() != null)
+        workingVariables.put(varRef.getName(), new Argument(varRef.getName(), varRef.getDefaultValue()));
+      else
+        throw new EGraphQLException("No value found for variable ");
+    }
+  }
+
+  private boolean isPrimitive(String typename) {
+    return Utilities.existsInList(typename, "boolean", "integer", "string", "decimal", "uri", "base64Binary", "instant", "date", "dateTime", "time", "code", "oid", "id", "markdown", "unsignedInt", "positiveInt", "url", "canonical");
+  }
+
+  private boolean isResourceName(String name, String suffix) {
+    if (!name.endsWith(suffix))
+      return false;
+    name = name.substring(0, name.length()-suffix.length());
+    return context.getResourceNamesAsSet().contains(name);
+  }
+
+  private void processObject(Resource context, Base source, ObjectValue target, List<Selection> selection, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    for (Selection sel : selection) {
+      if (sel.getField() != null) {
+        if (checkDirectives(sel.getField().getDirectives())) {
+          Property prop = source.getNamedProperty(sel.getField().getName());
+          if ((prop == null) && sel.getField().getName().startsWith("_"))
+            prop = source.getNamedProperty(sel.getField().getName().substring(1));
+          if (prop == null) {
+            if ((sel.getField().getName().equals("resourceType") && source instanceof Resource))
+              target.addField("resourceType", listStatus(sel.getField(), false)).addValue(new StringValue(source.fhirType()));
+            else if ((sel.getField().getName().equals("resource") && source.fhirType().equals("Reference")))
+              processReference(context, source, sel.getField(), target, inheritedList, suffix);
+            else if ((sel.getField().getName().equals("resource") && source.fhirType().equals("canonical")))
+              processCanonicalReference(context, source, sel.getField(), target, inheritedList, suffix);
+            else if (isResourceName(sel.getField().getName(), "List") && (source instanceof Resource))
+              processReverseReferenceList((Resource) source, sel.getField(), target, inheritedList, suffix);
+            else if (isResourceName(sel.getField().getName(), "Connection") && (source instanceof Resource))
+              processReverseReferenceSearch((Resource) source, sel.getField(), target, inheritedList, suffix);
+            else
+              throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType());
+          } else {
+            if (!isPrimitive(prop.getTypeCode()) && sel.getField().getName().startsWith("_"))
+              throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType());
+
+            List<Base> vl = filter(context, prop, sel.getField().getArguments(), prop.getValues(), sel.getField().getName().startsWith("_"));
+            if (!vl.isEmpty())
+              processValues(context, sel, prop, target, vl, sel.getField().getName().startsWith("_"), inheritedList, suffix);
+          }
+        }
+      } else if (sel.getInlineFragment() != null) {
+        if (checkDirectives(sel.getInlineFragment().getDirectives())) {
+          if (Utilities.noString(sel.getInlineFragment().getTypeCondition()))
+            throw new EGraphQLException("Not done yet - inline fragment with no type condition"); // cause why? why instanceof it even valid?
+          if (source.fhirType().equals(sel.getInlineFragment().getTypeCondition())) 
+            processObject(context, source, target, sel.getInlineFragment().getSelectionSet(), inheritedList, suffix);
+        }
+      } else if (checkDirectives(sel.getFragmentSpread().getDirectives())) {
+        Fragment fragment = graphQL.getDocument().fragment(sel.getFragmentSpread().getName());
+        if (fragment == null)
+          throw new EGraphQLException("Unable to resolve fragment "+sel.getFragmentSpread().getName());
+
+        if (Utilities.noString(fragment.getTypeCondition()))
+          throw new EGraphQLException("Not done yet - inline fragment with no type condition"); // cause why? why instanceof it even valid?
+        if (source.fhirType().equals(fragment.getTypeCondition()))
+          processObject(context, source, target, fragment.getSelectionSet(), inheritedList, suffix);
+      }
+    }
+  }
+
+  private void processPrimitive(Argument arg, Base value) {
+    String s = value.fhirType();
+    if (s.equals("integer") || s.equals("decimal") || s.equals("unsignedInt") || s.equals("positiveInt"))
+      arg.addValue(new NumberValue(value.primitiveValue()));
+    else if (s.equals("boolean"))
+      arg.addValue(new NameValue(value.primitiveValue()));
+    else
+      arg.addValue(new StringValue(value.primitiveValue()));
+  }
+
+  private void processReference(Resource context, Base source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    if (!(source instanceof Reference))
+      throw new EGraphQLException("Not done yet");
+    if (services == null)
+      throw new EGraphQLException("Resource Referencing services not provided");
+
+    Reference ref = (Reference) source;
+    ReferenceResolution res = services.lookup(appInfo, context, ref);
+    if (res != null) {
+      if (targetTypeOk(field.getArguments(), res.getTarget())) {
+        Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
+        ObjectValue obj = new ObjectValue();
+        arg.addValue(obj);
+        processObject((Resource)res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
+      }
+    }
+    else if (!hasArgument(field.getArguments(), "optional", "true"))
+      throw new EGraphQLException("Unable to resolve reference to "+ref.getReference());
+  }
+
+  private void processCanonicalReference(Resource context, Base source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    if (services == null)
+      throw new EGraphQLException("Resource Referencing services not provided");
+
+    Reference ref = new Reference(source.primitiveValue());
+    ReferenceResolution res = services.lookup(appInfo, context, ref);
+    if (res != null) {
+      if (targetTypeOk(field.getArguments(), res.getTarget())) {
+        Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
+        ObjectValue obj = new ObjectValue();
+        arg.addValue(obj);
+        processObject((Resource)res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
+      }
+    }
+    else if (!hasArgument(field.getArguments(), "optional", "true"))
+      throw new EGraphQLException("Unable to resolve reference to "+ref.getReference());
+  }
+
+  private ArgumentListStatus listStatus(Field field, boolean isList) {
+    if (field.hasDirective("singleton"))
+      return ArgumentListStatus.SINGLETON;
+    else if (isList)
+      return ArgumentListStatus.REPEATING;
+    else
+      return ArgumentListStatus.NOT_SPECIFIED;
+  }
+
+  private void processReverseReferenceList(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    if (services == null)
+      throw new EGraphQLException("Resource Referencing services not provided");
+    List<IBaseResource> list = new ArrayList<>();
+    List<Argument> params = new ArrayList<>();
+    Argument parg = null;
+    for (Argument a : field.getArguments())
+      if (!(a.getName().equals("_reference")))
+        params.add(a);
+      else if ((parg == null))
+        parg = a;
+      else
+        throw new EGraphQLException("Duplicate parameter _reference");
+    if (parg == null)
+      throw new EGraphQLException("Missing parameter _reference");
+    Argument arg = new Argument();
+    params.add(arg);
+    arg.setName(getSingleValue(parg));
+    arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
+    services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), params, list);
+    arg = null;
+    ObjectValue obj = null;
+
+    List<Resource> vl = filterResources(field.argument("fhirpath"), list);
+    if (!vl.isEmpty()) {
+      arg = target.addField(field.getAlias()+suffix, listStatus(field, true));
+      for (Resource v : vl) {
+        obj = new ObjectValue();
+        arg.addValue(obj);
+        processObject(v, v, obj, field.getSelectionSet(), inheritedList, suffix);
+      }
+    }
+  }
+  
+  private void processReverseReferenceSearch(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    if (services == null)
+      throw new EGraphQLException("Resource Referencing services not provided");
+    List<Argument> params = new ArrayList<Argument>();
+    Argument parg = null;
+    for (Argument a : field.getArguments())
+      if (!(a.getName().equals("_reference")))
+        params.add(a);
+      else if ((parg == null))
+        parg = a;
+      else
+        throw new EGraphQLException("Duplicate parameter _reference");
+    if (parg == null)
+      throw new EGraphQLException("Missing parameter _reference");
+    Argument arg = new Argument();
+    params.add(arg);
+    arg.setName(getSingleValue(parg));
+    arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
+    Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
+    Base bndWrapper = new SearchWrapper(field.getName(), bnd);
+    arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
+    ObjectValue obj = new ObjectValue();
+    arg.addValue(obj);
+    processObject(null, bndWrapper, obj, field.getSelectionSet(), inheritedList, suffix);
+  }
+
+  private void processSearch(ObjectValue target, List<Selection> selection, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    for (Selection sel : selection) {
+      if ((sel.getField() == null))
+        throw new EGraphQLException("Only field selections are allowed in this context");
+      checkNoDirectives(sel.getField().getDirectives());
+
+      if ((isResourceName(sel.getField().getName(), "")))
+        processSearchSingle(target, sel.getField(), inheritedList, suffix);
+      else if ((isResourceName(sel.getField().getName(), "List")))
+        processSearchSimple(target, sel.getField(), inheritedList, suffix);
+      else if ((isResourceName(sel.getField().getName(), "Connection")))
+        processSearchFull(target, sel.getField(), inheritedList, suffix);
+    }
+  }
+
+  private void processSearchSingle(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    if (services == null)
+      throw new EGraphQLException("Resource Referencing services not provided");
+    String id = "";
+    for (Argument arg : field.getArguments())
+      if ((arg.getName().equals("id")))
+        id = getSingleValue(arg);
+      else
+        throw new EGraphQLException("Unknown/invalid parameter "+arg.getName());
+    if (Utilities.noString(id))
+      throw new EGraphQLException("No id found");
+    Resource res = (Resource) services.lookup(appInfo, field.getName(), id);
+    if (res == null)
+      throw new EGraphQLException("Resource "+field.getName()+"/"+id+" not found");
+    Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
+    ObjectValue obj = new ObjectValue();
+    arg.addValue(obj);
+    processObject(res, res, obj, field.getSelectionSet(), inheritedList, suffix);
+  }
+
+  private void processSearchSimple(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    if (services == null)
+      throw new EGraphQLException("Resource Referencing services not provided");
+    List<IBaseResource> list = new ArrayList<>();
+    services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), field.getArguments(), list);
+    Argument arg = null;
+    ObjectValue obj = null;
+
+    List<Resource> vl = filterResources(field.argument("fhirpath"), list);
+    if (!vl.isEmpty()) {
+      arg = target.addField(field.getAlias()+suffix, listStatus(field, true));
+      for (Resource v : vl) {
+        obj = new ObjectValue();
+        arg.addValue(obj);
+        processObject(v, v, obj, field.getSelectionSet(), inheritedList, suffix);
+      }
+    }
+  }
+  
+  private void processSearchFull(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
+    if (services == null)
+      throw new EGraphQLException("Resource Referencing services not provided");
+    List<Argument> params = new ArrayList<Argument>();
+    Argument carg = null;
+    for ( Argument arg : field.getArguments())
+      if (arg.getName().equals("cursor"))
+        carg = arg;
+      else
+        params.add(arg);
+    if ((carg != null)) {
+      params.clear();;
+      String[] parts = getSingleValue(carg).split(":");
+      params.add(new Argument("search-id", new StringValue(parts[0])));
+      params.add(new Argument("search-offset", new StringValue(parts[1])));
+    }
+
+    Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
+    SearchWrapper bndWrapper = new SearchWrapper(field.getName(), bnd);
+    Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
+    ObjectValue obj = new ObjectValue();
+    arg.addValue(obj);
+    processObject(null, bndWrapper, obj, field.getSelectionSet(), inheritedList, suffix);
+  }
+
+  private String getSingleValue(Argument arg) throws EGraphQLException {
+    List<Value> vl = resolveValues(arg, 1);
+    if (vl.size() == 0)
+      return "";
+    return vl.get(0).toString();
+  }
+
+  private List<Value> resolveValues(Argument arg) throws EGraphQLException {
+    return resolveValues(arg, -1, "");
+  }
+  
+  private List<Value> resolveValues(Argument arg, int max) throws EGraphQLException {
+    return resolveValues(arg, max, "");
+  }
+  
+  private List<Value> resolveValues(Argument arg, int max, String vars) throws EGraphQLException {
+    List<Value> result = new ArrayList<Value>();
+    for (Value v : arg.getValues()) {
+      if (! (v instanceof VariableValue))
+        result.add(v);
+      else {
+        if (vars.contains(":"+v.toString()+":"))
+          throw new EGraphQLException("Recursive reference to variable "+v.toString());
+        Argument a = workingVariables.get(v.toString());
+        if (a == null)
+          throw new EGraphQLException("No value found for variable \""+v.toString()+"\" in \""+arg.getName()+"\"");
+        List<Value> vl = resolveValues(a, -1, vars+":"+v.toString()+":");
+        result.addAll(vl);
+      }
+    }
+    if ((max != -1 && result.size() > max))
+      throw new EGraphQLException("Only "+Integer.toString(max)+" values are allowed for \""+arg.getName()+"\", but "+Integer.toString(result.size())+" enoucntered");
+    return result;
+  }
+
+
+  
+  
+  public Object getAppInfo() {
+    return appInfo;
+  }
+
+  public void setAppInfo(Object appInfo) {
+    this.appInfo = appInfo;
+  }
+
+  public Resource getFocus() {
+    return focus;
+  }
+
+  @Override
+  public void setFocus(IBaseResource focus) {
+    this.focus = (Resource) focus;
+  }
+
+  public Package getGraphQL() {
+    return graphQL;
+  }
+
+  @Override
+  public void setGraphQL(Package graphQL) {
+    this.graphQL = graphQL;
+  }
+
+  public ObjectValue getOutput() {
+    return output;
+  }
+
+  public IGraphQLStorageServices getServices() {
+    return services;
+  }
+
+  @Override
+  public void setServices(IGraphQLStorageServices services) {
+    this.services = services;
+  }
+
+
+  //
+//{ GraphQLSearchWrapper }
+//
+//constructor GraphQLSearchWrapper.Create(bundle : Bundle);
+//var
+//  s : String;
+//{
+//  inherited Create;
+//  FBundle = bundle;
+//  s = bundle_List.Matches["self"];
+//  FParseMap = TParseMap.create(s.Substring(s.IndexOf("?")+1));
+//}
+//
+//destructor GraphQLSearchWrapper.Destroy;
+//{
+//  FParseMap.free;
+//  FBundle.Free;
+//  inherited;
+//}
+//
+//function GraphQLSearchWrapper.extractLink(name: String): String;
+//var
+//  s : String;
+//  pm : TParseMap;
+//{
+//  s = FBundle_List.Matches[name];
+//  if (s == "")
+//    result = null
+//  else
+//  {
+//    pm = TParseMap.create(s.Substring(s.IndexOf("?")+1));
+//    try
+//      result = String.Create(pm.GetVar("search-id")+":"+pm.GetVar("search-offset"));
+//    finally
+//      pm.Free;
+//    }
+//  }
+//}
+//
+//function GraphQLSearchWrapper.extractParam(name: String; int : boolean): Base;
+//var
+//  s : String;
+//{
+//  s = FParseMap.GetVar(name);
+//  if (s == "")
+//    result = null
+//  else if (int)
+//    result = Integer.Create(s)
+//  else
+//    result = String.Create(s);
+//}
+//
+//function GraphQLSearchWrapper.fhirType(): String;
+//{
+//  result = "*Connection";
+//}
+//
+//  // http://test.fhir.org/r4/Patient?_format==text/xhtml&search-id==77c97e03-8a6c-415f-a63d-11c80cf73f&&active==true&_sort==_id&search-offset==50&_count==50
+//
+//function GraphQLSearchWrapper.getPropertyValue(propName: string): Property;
+//var
+//  list : List<GraphQLSearchEdge>;
+//  be : BundleEntry;
+//{
+//  if (propName == "first")
+//    result = Property.Create(self, propname, "string", false, String, extractLink("first"))
+//  else if (propName == "previous")
+//    result = Property.Create(self, propname, "string", false, String, extractLink("previous"))
+//  else if (propName == "next")
+//    result = Property.Create(self, propname, "string", false, String, extractLink("next"))
+//  else if (propName == "last")
+//    result = Property.Create(self, propname, "string", false, String, extractLink("last"))
+//  else if (propName == "count")
+//    result = Property.Create(self, propname, "integer", false, String, FBundle.totalElement)
+//  else if (propName == "offset")
+//    result = Property.Create(self, propname, "integer", false, Integer, extractParam("search-offset", true))
+//  else if (propName == "pagesize")
+//    result = Property.Create(self, propname, "integer", false, Integer, extractParam("_count", true))
+//  else if (propName == "edges")
+//  {
+//    list = ArrayList<GraphQLSearchEdge>();
+//    try
+//      for be in FBundle.getEntry() do
+//        list.add(GraphQLSearchEdge.create(be));
+//      result = Property.Create(self, propname, "integer", true, Integer, List<Base>(list));
+//    finally
+//      list.Free;
+//    }
+//  }
+//  else
+//    result = null;
+//}
+//
+//private void GraphQLSearchWrapper.SetBundle(const Value: Bundle);
+//{
+//  FBundle.Free;
+//  FBundle = Value;
+//}
+//
+//{ GraphQLSearchEdge }
+//
+//constructor GraphQLSearchEdge.Create(entry: BundleEntry);
+//{
+//  inherited Create;
+//  FEntry = entry;
+//}
+//
+//destructor GraphQLSearchEdge.Destroy;
+//{
+//  FEntry.Free;
+//  inherited;
+//}
+//
+//function GraphQLSearchEdge.fhirType(): String;
+//{
+//  result = "*Edge";
+//}
+//
+//function GraphQLSearchEdge.getPropertyValue(propName: string): Property;
+//{
+//  if (propName == "mode")
+//  {
+//    if (FEntry.search != null)
+//      result = Property.Create(self, propname, "code", false, Enum, FEntry.search.modeElement)
+//    else
+//      result = Property.Create(self, propname, "code", false, Enum, Base(null));
+//  }
+//  else if (propName == "score")
+//  {
+//    if (FEntry.search != null)
+//      result = Property.Create(self, propname, "decimal", false, Decimal, FEntry.search.scoreElement)
+//    else
+//      result = Property.Create(self, propname, "decimal", false, Decimal, Base(null));
+//  }
+//  else if (propName == "resource")
+//    result = Property.Create(self, propname, "resource", false, Resource, FEntry.getResource())
+//  else
+//    result = null;
+//}
+//
+//private void GraphQLSearchEdge.SetEntry(const Value: BundleEntry);
+//{
+//  FEntry.Free;
+//  FEntry = value;
+//}
+//
+}

org.hl7.fhir.r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>3.8.24-SNAPSHOT</version>
+		<version>4.0.1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/GraphQLEngine.java

@@ -21,6 +21,18 @@ package org.hl7.fhir.r4.utils;
  */
 
 
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.context.IWorkerContext;
+import org.hl7.fhir.r4.model.*;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Bundle.BundleLinkComponent;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.graphql.*;
+import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
+import org.hl7.fhir.utilities.graphql.Package;
+import org.hl7.fhir.utilities.graphql.Operation.OperationType;
+
 import java.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
 import java.util.ArrayList;
@@ -28,239 +40,41 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.hl7.fhir.exceptions.FHIRException;
+import static org.hl7.fhir.utilities.graphql.IGraphQLStorageServices.ReferenceResolution;
-import org.hl7.fhir.r4.context.IWorkerContext;
-import org.hl7.fhir.r4.model.BackboneElement;
-import org.hl7.fhir.r4.model.Base;
-import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.r4.model.Bundle.BundleLinkComponent;
-import org.hl7.fhir.r4.model.CanonicalType;
-import org.hl7.fhir.r4.model.DomainResource;
-import org.hl7.fhir.r4.model.Element;
-import org.hl7.fhir.r4.model.ExpressionNode;
-import org.hl7.fhir.r4.model.IntegerType;
-import org.hl7.fhir.r4.model.Property;
-import org.hl7.fhir.r4.model.Reference;
-import org.hl7.fhir.r4.model.Resource;
-import org.hl7.fhir.r4.model.StringType;
-import org.hl7.fhir.r4.utils.GraphQLEngine.IGraphQLStorageServices.ReferenceResolution;
-import org.hl7.fhir.utilities.Utilities;
-import org.hl7.fhir.utilities.graphql.Argument;
-import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
-import org.hl7.fhir.utilities.graphql.Directive;
-import org.hl7.fhir.utilities.graphql.EGraphEngine;
-import org.hl7.fhir.utilities.graphql.EGraphQLException;
-import org.hl7.fhir.utilities.graphql.Field;
-import org.hl7.fhir.utilities.graphql.Fragment;
-import org.hl7.fhir.utilities.graphql.NameValue;
-import org.hl7.fhir.utilities.graphql.NumberValue;
-import org.hl7.fhir.utilities.graphql.ObjectValue;
-import org.hl7.fhir.utilities.graphql.Operation;
-import org.hl7.fhir.utilities.graphql.Operation.OperationType;
-import org.hl7.fhir.utilities.graphql.Package;
-import org.hl7.fhir.utilities.graphql.Selection;
-import org.hl7.fhir.utilities.graphql.StringValue;
-import org.hl7.fhir.utilities.graphql.Value;
-import org.hl7.fhir.utilities.graphql.Variable;
-import org.hl7.fhir.utilities.graphql.VariableValue;
 
-public class GraphQLEngine {
+public class GraphQLEngine implements IGraphQLEngine {
-  
-  public class SearchEdge extends Base {
 
-    private BundleEntryComponent be;
-    private String type;
-    
-    public SearchEdge(String type, BundleEntryComponent be) {
-      this.type = type;
-      this.be = be;
-    }
-    @Override
-    public String fhirType() {
-      return type;
-    }
-
-    @Override
-    protected void listChildren(List<Property> result) {
-      throw new Error("Not Implemented");
-    }
-
-    @Override
-    public String getIdBase() {
-      throw new Error("Not Implemented");
-    }
-
-    @Override
-    public void setIdBase(String value) {
-      throw new Error("Not Implemented");
-    }
-
-    @Override
-    public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
-      switch (_hash) {
-      case 3357091:    /*mode*/     return new Property(_name, "string",   "n/a", 0, 1, be.getSearch().hasMode() ? be.getSearch().getModeElement() : null);
-      case 109264530:  /*score*/    return new Property(_name, "string",   "n/a", 0, 1, be.getSearch().hasScore() ? be.getSearch().getScoreElement() : null);
-      case -341064690: /*resource*/ return new Property(_name, "resource",  "n/a", 0, 1, be.hasResource() ? be.getResource() : null);
-      default: return super.getNamedProperty(_hash, _name, _checkValid);
-      }
-    }
-  }
-
-  public class SearchWrapper extends Base {
-
-    private Bundle bnd;
-    private String type;
-    private Map<String, String> map;
-
-    public SearchWrapper(String type, Bundle bnd) throws FHIRException {
-      this.type = type;
-      this.bnd = bnd;
-      for (BundleLinkComponent bl : bnd.getLink()) 
-        if (bl.getRelation().equals("self"))
-          map = parseURL(bl.getUrl());
-    }
-
-    @Override
-    public String fhirType() {
-      return type;
-    }
-
-    @Override
-    protected void listChildren(List<Property> result) {
-      throw new Error("Not Implemented");
-    }
-
-    @Override
-    public String getIdBase() {
-      throw new Error("Not Implemented");
-    }
-
-    @Override
-    public void setIdBase(String value) {
-      throw new Error("Not Implemented");
-    }
-
-    @Override
-    public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
-      switch (_hash) {
-      case 97440432:   /*first*/     return new Property(_name, "string",  "n/a", 0, 1, extractLink(_name));
-      case -1273775369: /*previous*/  return new Property(_name, "string",  "n/a", 0, 1, extractLink(_name));
-      case 3377907:    /*next*/      return new Property(_name, "string",  "n/a", 0, 1, extractLink(_name));
-      case 3314326:    /*last*/      return new Property(_name, "string",  "n/a", 0, 1, extractLink(_name));
-      case 94851343:   /*count*/     return new Property(_name, "integer", "n/a", 0, 1, bnd.getTotalElement());
-      case -1019779949:/*offset*/    return new Property(_name, "integer", "n/a", 0, 1, extractParam("search-offset"));
-      case 860381968:  /*pagesize*/  return new Property(_name, "integer", "n/a", 0, 1, extractParam("_count"));
-      case 96356950:  /*edges*/      return new Property(_name, "edge",    "n/a", 0, Integer.MAX_VALUE, getEdges());
-      default: return super.getNamedProperty(_hash, _name, _checkValid);
-      }
-    }
-
-    private List<Base> getEdges() {
-      List<Base> list = new ArrayList<>();
-      for (BundleEntryComponent be : bnd.getEntry())
-        list.add(new SearchEdge(type.substring(0, type.length()-10)+"Edge", be));
-      return list;
-    }
-
-    private Base extractParam(String name) throws FHIRException {
-      return map != null ? new IntegerType(map.get(name)) : null;
-    }
-
-    private Map<String, String> parseURL(String url) throws FHIRException {
-      try {
-        Map<String, String> map = new HashMap<String, String>();
-        String[] pairs = url.split("&");
-        for (String pair : pairs) {
-          int idx = pair.indexOf("=");
-          String key;
-          key = idx > 0 ? URLDecoder.decode(pair.substring(0, idx), "UTF-8") : pair;
-          String value = idx > 0 && pair.length() > idx + 1 ? URLDecoder.decode(pair.substring(idx + 1), "UTF-8") : null;
-          map.put(key, value);
-        }
-        return map;
-      } catch (UnsupportedEncodingException e) {
-        throw new FHIRException(e);
-      }
-    }
-
-    private Base extractLink(String _name) throws FHIRException {
-      for (BundleLinkComponent bl : bnd.getLink()) {
-        if (bl.getRelation().equals(_name)) {
-          Map<String, String> map = parseURL(bl.getUrl());
-          return new StringType(map.get("search-id")+':'+map.get("search-offset"));
-        }
-      }
-      return null;
-    }
-
-  }
-
-  public interface IGraphQLStorageServices {
-    public class ReferenceResolution {
-      private Resource targetContext;
-      private Resource target;
-      public ReferenceResolution(Resource targetContext, Resource target) {
-        super();
-        this.targetContext = targetContext;
-        this.target = target;
-      }
-      
-      
-    }
-    // given a reference inside a context, return what it references (including resolving internal references (e.g. start with #)
-    public ReferenceResolution lookup(Object appInfo, Resource context, Reference reference) throws FHIRException;
-    
-    // just get the identified resource
-    public Resource lookup(Object appInfo, String type, String id) throws FHIRException;
-
-    // list the matching resources. searchParams are the standard search params. 
-    // this instanceof different to search because the server returns all matching resources, or an error. There instanceof no paging on this search   
-    public void listResources(Object appInfo, String type, List<Argument> searchParams, List<Resource> matches) throws FHIRException;
-
-    // just perform a standard search, and return the bundle as you return to the client  
-    public Bundle search(Object appInfo, String type, List<Argument> searchParams) throws FHIRException;
-  }
-  
   private IWorkerContext context;
-  
+  /**
+   * for the host to pass context into and get back on the reference resolution interface
+   */
+  private Object appInfo;
+  /**
+   * the focus resource - if (there instanceof one. if (there isn"t,) there instanceof no focus
+   */
+  private Resource focus;
+  /**
+   * The package that describes the graphQL to be executed, operation name, and variables
+   */
+  private Package graphQL;
+  /**
+   * where the output from executing the query instanceof going to go
+   */
+  private ObjectValue output;
+  /**
+   * Application provided reference resolution services
+   */
+  private IGraphQLStorageServices services;
+  // internal stuff
+  private Map<String, Argument> workingVariables = new HashMap<String, Argument>();
+  private FHIRPathEngine fpe;
+  private ExpressionNode magicExpression;
+
   public GraphQLEngine(IWorkerContext context) {
     super();
     this.context = context;
   }
 
-  /**
-   *  for the host to pass context into and get back on the reference resolution interface
-   */
-  private Object appInfo;
-
-  /**
-   *  the focus resource - if (there instanceof one. if (there isn"t,) there instanceof no focus
-   */
-  private Resource focus;
-
-  /**
-   * The package that describes the graphQL to be executed, operation name, and variables
-   */
-  private Package graphQL;
-
-  /**
-   * where the output from executing the query instanceof going to go
-   */
-  private ObjectValue output;
-
-  /** 
-   * Application provided reference resolution services 
-   */
-  private IGraphQLStorageServices services;
-
-  // internal stuff 
-  private Map<String, Argument> workingVariables = new HashMap<String, Argument>();
-
-  private FHIRPathEngine fpe;
-
-  private ExpressionNode magicExpression;
-  
   public void execute() throws EGraphEngine, EGraphQLException, FHIRException {
     if (graphQL == null)
       throw new EGraphEngine("Unable to process graphql - graphql document missing");
@@ -274,7 +88,7 @@ public class GraphQLEngine {
     if (!Utilities.noString(graphQL.getOperationName())) {
       op = graphQL.getDocument().operation(graphQL.getOperationName());
       if (op == null)
-        throw new EGraphEngine("Unable to find operation \""+graphQL.getOperationName()+"\"");
+        throw new EGraphEngine("Unable to find operation \"" + graphQL.getOperationName() + "\"");
     } else if ((graphQL.getDocument().getOperations().size() == 1))
       op = graphQL.getDocument().getOperations().get(0);
     else
@@ -293,9 +107,9 @@ public class GraphQLEngine {
 
   private boolean checkBooleanDirective(Directive dir) throws EGraphQLException {
     if (dir.getArguments().size() != 1)
-      throw new EGraphQLException("Unable to process @"+dir.getName()+": expected a single argument \"if\"");
+      throw new EGraphQLException("Unable to process @" + dir.getName() + ": expected a single argument \"if\"");
     if (!dir.getArguments().get(0).getName().equals("if"))
-      throw new EGraphQLException("Unable to process @"+dir.getName()+": expected a single argument \"if\"");
+      throw new EGraphQLException("Unable to process @" + dir.getName() + ": expected a single argument \"if\"");
     List<Value> vl = resolveValues(dir.getArguments().get(0), 1);
     return vl.get(0).toString().equals("true");
   }
@@ -314,9 +128,8 @@ public class GraphQLEngine {
           include = dir;
         else
           throw new EGraphQLException("Duplicate @include directives");
-      }
+      } else if (!Utilities.existsInList(dir.getName(), "flatten", "first", "singleton", "slice"))
-      else if (!Utilities.existsInList(dir.getName(), "flatten", "first", "singleton", "slice"))
+        throw new EGraphQLException("Directive \"" + dir.getName() + "\" instanceof not recognised");
-        throw new EGraphQLException("Directive \""+dir.getName()+"\" instanceof not recognised");
     }
     if ((skip != null && include != null))
       throw new EGraphQLException("Cannot mix @skip and @include directives");
@@ -332,7 +145,7 @@ public class GraphQLEngine {
 
   }
 
-  private boolean targetTypeOk(List<Argument> arguments, Resource dest) throws EGraphQLException {
+  private boolean targetTypeOk(List<Argument> arguments, IBaseResource dest) throws EGraphQLException {
     List<String> list = new ArrayList<String>();
     for (Argument arg : arguments) {
       if ((arg.getName().equals("type"))) {
@@ -350,12 +163,12 @@ public class GraphQLEngine {
   private boolean hasExtensions(Base obj) {
     if (obj instanceof BackboneElement)
       return ((BackboneElement) obj).getExtension().size() > 0 || ((BackboneElement) obj).getModifierExtension().size() > 0;
-      else if (obj instanceof DomainResource)
+    else if (obj instanceof DomainResource)
-        return ((DomainResource)obj).getExtension().size() > 0 || ((DomainResource)obj).getModifierExtension().size() > 0;
+      return ((DomainResource) obj).getExtension().size() > 0 || ((DomainResource) obj).getModifierExtension().size() > 0;
-        else if (obj instanceof Element)
+    else if (obj instanceof Element)
-          return ((Element)obj).getExtension().size() > 0;
+      return ((Element) obj).getExtension().size() > 0;
-          else
+    else
-            return false;
+      return false;
   }
 
   private boolean passesExtensionMode(Base obj, boolean extensionMode) {
@@ -378,9 +191,9 @@ public class GraphQLEngine {
         if ((vl.size() != 1))
           throw new EGraphQLException("Incorrect number of arguments");
         if (values.get(0).isPrimitive())
-          throw new EGraphQLException("Attempt to use a filter ("+arg.getName()+") on a primtive type ("+prop.getTypeCode()+")");
+          throw new EGraphQLException("Attempt to use a filter (" + arg.getName() + ") on a primtive type (" + prop.getTypeCode() + ")");
         if ((arg.getName().equals("fhirpath")))
-          fp.append(" and "+vl.get(0).toString());
+          fp.append(" and " + vl.get(0).toString());
         else if ((arg.getName().equals("_count")))
           count = Integer.valueOf(vl.get(0).toString());
         else if ((arg.getName().equals("_offset")))
@@ -388,8 +201,8 @@ public class GraphQLEngine {
         else {
           Property p = values.get(0).getNamedProperty(arg.getName());
           if (p == null)
-            throw new EGraphQLException("Attempt to use an unknown filter ("+arg.getName()+") on a type ("+prop.getTypeCode()+")");
+            throw new EGraphQLException("Attempt to use an unknown filter (" + arg.getName() + ") on a type (" + prop.getTypeCode() + ")");
-          fp.append(" and "+arg.getName()+" = '"+vl.get(0).toString()+"'");
+          fp.append(" and " + arg.getName() + " = '" + vl.get(0).toString() + "'");
         }
       }
       int i = 0;
@@ -403,18 +216,19 @@ public class GraphQLEngine {
               break;
           }
           i++;
-        } else {
-          ExpressionNode node = fpe.parse(fp.toString().substring(5));
-          for (Base v : values) {
-            if ((i >= offset) && passesExtensionMode(v, extensionMode) && fpe.evaluateToBoolean(null, context, v, node)) {
-              result.add(v);
-              t++;
-              if (t >= count)
-                break;
-            }
-            i++;
-          }
         }
+      else {
+        ExpressionNode node = fpe.parse(fp.toString().substring(5));
+        for (Base v : values) {
+          if ((i >= offset) && passesExtensionMode(v, extensionMode) && fpe.evaluateToBoolean(null, context, v, node)) {
+            result.add(v);
+            t++;
+            if (t >= count)
+              break;
+          }
+          i++;
+        }
+      }
     }
     return result;
   }
@@ -436,18 +250,18 @@ public class GraphQLEngine {
     return result;
   }
 
-  private List<Resource> filterResources(Argument fhirpath, List<Resource> list) throws EGraphQLException, FHIRException {
+  private List<Resource> filterResources(Argument fhirpath, List<IBaseResource> list) throws EGraphQLException, FHIRException {
     List<Resource> result = new ArrayList<Resource>();
     if (list.size() > 0) {
       if ((fhirpath == null))
-        for (Resource v : list)
+        for (IBaseResource v : list)
-          result.add(v);
+          result.add((Resource) v);
       else {
         FHIRPathEngine fpe = new FHIRPathEngine(context);
         ExpressionNode node = fpe.parse(getSingleValue(fhirpath));
-        for (Resource v : list)
+        for (IBaseResource v : list)
-          if (fpe.evaluateToBoolean(null, v, v, node))
+          if (fpe.evaluateToBoolean(null, (Resource) v, (Base) v, node))
-            result.add(v);
+            result.add((Resource) v);
       }
     }
     return result;
@@ -475,23 +289,23 @@ public class GraphQLEngine {
     if (sel.getField().hasDirective("flatten")) // special: instruction to drop this node...
       il = prop.isList() && !sel.getField().hasDirective("first");
     else if (sel.getField().hasDirective("first")) {
-      if (expression != null) 
+      if (expression != null)
         throw new FHIRException("You cannot mix @slice and @first");
-      arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), inheritedList));
+      arg = target.addField(sel.getField().getAlias() + suffix, listStatus(sel.getField(), inheritedList));
     } else if (expression == null)
-      arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
+      arg = target.addField(sel.getField().getAlias() + suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
+
 
-    
     int index = 0;
     for (Base value : values) {
       String ss = "";
       if (expression != null) {
         if (expression == magicExpression)
-          ss = suffix+'.'+Integer.toString(index);
+          ss = suffix + '.' + Integer.toString(index);
         else
           ss = suffix+'.'+fpe.evaluateToString(null, null, null, value, expression);
         if (!sel.getField().hasDirective("flatten"))
-          arg = target.addField(sel.getField().getAlias()+suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
+          arg = target.addField(sel.getField().getAlias() + suffix, listStatus(sel.getField(), prop.isList() || inheritedList));
       }
 
       if (value.isPrimitive() && !extensionMode) {
@@ -518,7 +332,7 @@ public class GraphQLEngine {
   private void processVariables(Operation op) throws EGraphQLException {
     for (Variable varRef : op.getVariables()) {
       Argument varDef = null;
-      for (Argument v : graphQL.getVariables()) 
+      for (Argument v : graphQL.getVariables())
         if (v.getName().equals(varRef.getName()))
           varDef = v;
       if (varDef != null)
@@ -537,7 +351,7 @@ public class GraphQLEngine {
   private boolean isResourceName(String name, String suffix) {
     if (!name.endsWith(suffix))
       return false;
-    name = name.substring(0, name.length()-suffix.length());
+    name = name.substring(0, name.length() - suffix.length());
     return context.getResourceNamesAsSet().contains(name);
   }
 
@@ -560,10 +374,10 @@ public class GraphQLEngine {
             else if (isResourceName(sel.getField().getName(), "Connection") && (source instanceof Resource))
               processReverseReferenceSearch((Resource) source, sel.getField(), target, inheritedList, suffix);
             else
-              throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType());
+              throw new EGraphQLException("Unknown property " + sel.getField().getName() + " on " + source.fhirType());
           } else {
             if (!isPrimitive(prop.getTypeCode()) && sel.getField().getName().startsWith("_"))
-              throw new EGraphQLException("Unknown property "+sel.getField().getName()+" on "+source.fhirType());
+              throw new EGraphQLException("Unknown property " + sel.getField().getName() + " on " + source.fhirType());
 
             List<Base> vl = filter(context, prop, sel.getField().getArguments(), prop.getValues(), sel.getField().getName().startsWith("_"));
             if (!vl.isEmpty())
@@ -574,13 +388,13 @@ public class GraphQLEngine {
         if (checkDirectives(sel.getInlineFragment().getDirectives())) {
           if (Utilities.noString(sel.getInlineFragment().getTypeCondition()))
             throw new EGraphQLException("Not done yet - inline fragment with no type condition"); // cause why? why instanceof it even valid?
-          if (source.fhirType().equals(sel.getInlineFragment().getTypeCondition())) 
+          if (source.fhirType().equals(sel.getInlineFragment().getTypeCondition()))
             processObject(context, source, target, sel.getInlineFragment().getSelectionSet(), inheritedList, suffix);
         }
       } else if (checkDirectives(sel.getFragmentSpread().getDirectives())) {
         Fragment fragment = graphQL.getDocument().fragment(sel.getFragmentSpread().getName());
         if (fragment == null)
-          throw new EGraphQLException("Unable to resolve fragment "+sel.getFragmentSpread().getName());
+          throw new EGraphQLException("Unable to resolve fragment " + sel.getFragmentSpread().getName());
 
         if (Utilities.noString(fragment.getTypeCondition()))
           throw new EGraphQLException("Not done yet - inline fragment with no type condition"); // cause why? why instanceof it even valid?
@@ -609,15 +423,14 @@ public class GraphQLEngine {
     Reference ref = (Reference) source;
     ReferenceResolution res = services.lookup(appInfo, context, ref);
     if (res != null) {
-      if (targetTypeOk(field.getArguments(), res.target)) {
+      if (targetTypeOk(field.getArguments(), res.getTarget())) {
         Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
         ObjectValue obj = new ObjectValue();
         arg.addValue(obj);
-        processObject(res.targetContext, res.target, obj, field.getSelectionSet(), inheritedList, suffix);
+        processObject((Resource) res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
       }
-    }
+    } else if (!hasArgument(field.getArguments(), "optional", "true"))
-    else if (!hasArgument(field.getArguments(), "optional", "true"))
+      throw new EGraphQLException("Unable to resolve reference to " + ref.getReference());
-      throw new EGraphQLException("Unable to resolve reference to "+ref.getReference());
   }
 
   private void processCanonicalReference(Resource context, Base source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
@@ -629,15 +442,14 @@ public class GraphQLEngine {
     Reference ref = new Reference(source.primitiveValue());
     ReferenceResolution res = services.lookup(appInfo, context, ref);
     if (res != null) {
-      if (targetTypeOk(field.getArguments(), res.target)) {
+      if (targetTypeOk(field.getArguments(), res.getTarget())) {
         Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
         ObjectValue obj = new ObjectValue();
         arg.addValue(obj);
-        processObject(res.targetContext, res.target, obj, field.getSelectionSet(), inheritedList, suffix);
+        processObject((Resource) res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
       }
-    }
+    } else if (!hasArgument(field.getArguments(), "optional", "true"))
-    else if (!hasArgument(field.getArguments(), "optional", "true"))
+      throw new EGraphQLException("Unable to resolve reference to " + ref.getReference());
-      throw new EGraphQLException("Unable to resolve reference to "+ref.getReference());
   }
 
   private ArgumentListStatus listStatus(Field field, boolean isList) {
@@ -652,7 +464,7 @@ public class GraphQLEngine {
   private void processReverseReferenceList(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
     if (services == null)
       throw new EGraphQLException("Resource Referencing services not provided");
-    List<Resource> list = new ArrayList<Resource>();
+    List<IBaseResource> list = new ArrayList<>();
     List<Argument> params = new ArrayList<Argument>();
     Argument parg = null;
     for (Argument a : field.getArguments())
@@ -667,14 +479,14 @@ public class GraphQLEngine {
     Argument arg = new Argument();
     params.add(arg);
     arg.setName(getSingleValue(parg));
-    arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
+    arg.addValue(new StringValue(source.fhirType() + "/" + source.getId()));
     services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), params, list);
     arg = null;
     ObjectValue obj = null;
 
     List<Resource> vl = filterResources(field.argument("fhirpath"), list);
     if (!vl.isEmpty()) {
-      arg = target.addField(field.getAlias()+suffix, listStatus(field, true));
+      arg = target.addField(field.getAlias() + suffix, listStatus(field, true));
       for (Resource v : vl) {
         obj = new ObjectValue();
         arg.addValue(obj);
@@ -682,7 +494,7 @@ public class GraphQLEngine {
       }
     }
   }
-  
+
   private void processReverseReferenceSearch(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
     if (services == null)
       throw new EGraphQLException("Resource Referencing services not provided");
@@ -700,10 +512,10 @@ public class GraphQLEngine {
     Argument arg = new Argument();
     params.add(arg);
     arg.setName(getSingleValue(parg));
-    arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
+    arg.addValue(new StringValue(source.fhirType() + "/" + source.getId()));
-    Bundle bnd = services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
+    Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length() - 10), params);
     Base bndWrapper = new SearchWrapper(field.getName(), bnd);
-    arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
+    arg = target.addField(field.getAlias() + suffix, listStatus(field, false));
     ObjectValue obj = new ObjectValue();
     arg.addValue(obj);
     processObject(null, bndWrapper, obj, field.getSelectionSet(), inheritedList, suffix);
@@ -732,13 +544,13 @@ public class GraphQLEngine {
       if ((arg.getName().equals("id")))
         id = getSingleValue(arg);
       else
-        throw new EGraphQLException("Unknown/invalid parameter "+arg.getName());
+        throw new EGraphQLException("Unknown/invalid parameter " + arg.getName());
     if (Utilities.noString(id))
       throw new EGraphQLException("No id found");
-    Resource res = services.lookup(appInfo, field.getName(), id);
+    Resource res = (Resource) services.lookup(appInfo, field.getName(), id);
     if (res == null)
-      throw new EGraphQLException("Resource "+field.getName()+"/"+id+" not found");
+      throw new EGraphQLException("Resource " + field.getName() + "/" + id + " not found");
-    Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
+    Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, false));
     ObjectValue obj = new ObjectValue();
     arg.addValue(obj);
     processObject(res, res, obj, field.getSelectionSet(), inheritedList, suffix);
@@ -747,14 +559,14 @@ public class GraphQLEngine {
   private void processSearchSimple(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
     if (services == null)
       throw new EGraphQLException("Resource Referencing services not provided");
-    List<Resource> list = new ArrayList<Resource>();
+    List<IBaseResource> list = new ArrayList<>();
     services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), field.getArguments(), list);
     Argument arg = null;
     ObjectValue obj = null;
 
     List<Resource> vl = filterResources(field.argument("fhirpath"), list);
     if (!vl.isEmpty()) {
-      arg = target.addField(field.getAlias()+suffix, listStatus(field, true));
+      arg = target.addField(field.getAlias() + suffix, listStatus(field, true));
       for (Resource v : vl) {
         obj = new ObjectValue();
         arg.addValue(obj);
@@ -762,27 +574,28 @@ public class GraphQLEngine {
       }
     }
   }
-  
+
   private void processSearchFull(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
     if (services == null)
       throw new EGraphQLException("Resource Referencing services not provided");
     List<Argument> params = new ArrayList<Argument>();
     Argument carg = null;
-    for ( Argument arg : field.getArguments())
+    for (Argument arg : field.getArguments())
       if (arg.getName().equals("cursor"))
         carg = arg;
       else
         params.add(arg);
     if ((carg != null)) {
-      params.clear();;
+      params.clear();
+      ;
       String[] parts = getSingleValue(carg).split(":");
       params.add(new Argument("search-id", new StringValue(parts[0])));
       params.add(new Argument("search-offset", new StringValue(parts[1])));
     }
 
-    Bundle bnd = services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
+    Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length() - 10), params);
     SearchWrapper bndWrapper = new SearchWrapper(field.getName(), bnd);
-    Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
+    Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, false));
     ObjectValue obj = new ObjectValue();
     arg.addValue(obj);
     processObject(null, bndWrapper, obj, field.getSelectionSet(), inheritedList, suffix);
@@ -798,34 +611,31 @@ public class GraphQLEngine {
   private List<Value> resolveValues(Argument arg) throws EGraphQLException {
     return resolveValues(arg, -1, "");
   }
-  
+
   private List<Value> resolveValues(Argument arg, int max) throws EGraphQLException {
     return resolveValues(arg, max, "");
   }
-  
+
   private List<Value> resolveValues(Argument arg, int max, String vars) throws EGraphQLException {
     List<Value> result = new ArrayList<Value>();
     for (Value v : arg.getValues()) {
-      if (! (v instanceof VariableValue))
+      if (!(v instanceof VariableValue))
         result.add(v);
       else {
-        if (vars.contains(":"+v.toString()+":"))
+        if (vars.contains(":" + v.toString() + ":"))
-          throw new EGraphQLException("Recursive reference to variable "+v.toString());
+          throw new EGraphQLException("Recursive reference to variable " + v.toString());
         Argument a = workingVariables.get(v.toString());
         if (a == null)
-          throw new EGraphQLException("No value found for variable \""+v.toString()+"\" in \""+arg.getName()+"\"");
+          throw new EGraphQLException("No value found for variable \"" + v.toString() + "\" in \"" + arg.getName() + "\"");
-        List<Value> vl = resolveValues(a, -1, vars+":"+v.toString()+":");
+        List<Value> vl = resolveValues(a, -1, vars + ":" + v.toString() + ":");
         result.addAll(vl);
       }
     }
     if ((max != -1 && result.size() > max))
-      throw new EGraphQLException("Only "+Integer.toString(max)+" values are allowed for \""+arg.getName()+"\", but "+Integer.toString(result.size())+" enoucntered");
+      throw new EGraphQLException("Only " + Integer.toString(max) + " values are allowed for \"" + arg.getName() + "\", but " + Integer.toString(result.size()) + " enoucntered");
     return result;
   }
 
-
-  
-  
   public Object getAppInfo() {
     return appInfo;
   }
@@ -838,14 +648,16 @@ public class GraphQLEngine {
     return focus;
   }
 
-  public void setFocus(Resource focus) {
+  @Override
-    this.focus = focus;
+  public void setFocus(IBaseResource focus) {
+    this.focus = (Resource) focus;
   }
 
   public Package getGraphQL() {
     return graphQL;
   }
 
+  @Override
   public void setGraphQL(Package graphQL) {
     this.graphQL = graphQL;
   }
@@ -858,10 +670,154 @@ public class GraphQLEngine {
     return services;
   }
 
+  @Override
   public void setServices(IGraphQLStorageServices services) {
     this.services = services;
   }
 
+  public static class SearchEdge extends Base {
+
+    private BundleEntryComponent be;
+    private String type;
+
+    SearchEdge(String type, BundleEntryComponent be) {
+      this.type = type;
+      this.be = be;
+    }
+
+    @Override
+    public String fhirType() {
+      return type;
+    }
+
+    @Override
+    protected void listChildren(List<Property> result) {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public String getIdBase() {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public void setIdBase(String value) {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
+      switch (_hash) {
+        case 3357091:    /*mode*/
+          return new Property(_name, "string", "n/a", 0, 1, be.getSearch().hasMode() ? be.getSearch().getModeElement() : null);
+        case 109264530:  /*score*/
+          return new Property(_name, "string", "n/a", 0, 1, be.getSearch().hasScore() ? be.getSearch().getScoreElement() : null);
+        case -341064690: /*resource*/
+          return new Property(_name, "resource", "n/a", 0, 1, be.hasResource() ? be.getResource() : null);
+        default:
+          return super.getNamedProperty(_hash, _name, _checkValid);
+      }
+    }
+  }
+
+  public static class SearchWrapper extends Base {
+
+    private Bundle bnd;
+    private String type;
+    private Map<String, String> map;
+
+    SearchWrapper(String type, Bundle bnd) throws FHIRException {
+      this.type = type;
+      this.bnd = bnd;
+      for (BundleLinkComponent bl : bnd.getLink())
+        if (bl.getRelation().equals("self"))
+          map = parseURL(bl.getUrl());
+    }
+
+    @Override
+    public String fhirType() {
+      return type;
+    }
+
+    @Override
+    protected void listChildren(List<Property> result) {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public String getIdBase() {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public void setIdBase(String value) {
+      throw new Error("Not Implemented");
+    }
+
+    @Override
+    public Property getNamedProperty(int _hash, String _name, boolean _checkValid) throws FHIRException {
+      switch (_hash) {
+        case 97440432:   /*first*/
+          return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
+        case -1273775369: /*previous*/
+          return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
+        case 3377907:    /*next*/
+          return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
+        case 3314326:    /*last*/
+          return new Property(_name, "string", "n/a", 0, 1, extractLink(_name));
+        case 94851343:   /*count*/
+          return new Property(_name, "integer", "n/a", 0, 1, bnd.getTotalElement());
+        case -1019779949:/*offset*/
+          return new Property(_name, "integer", "n/a", 0, 1, extractParam("search-offset"));
+        case 860381968:  /*pagesize*/
+          return new Property(_name, "integer", "n/a", 0, 1, extractParam("_count"));
+        case 96356950:  /*edges*/
+          return new Property(_name, "edge", "n/a", 0, Integer.MAX_VALUE, getEdges());
+        default:
+          return super.getNamedProperty(_hash, _name, _checkValid);
+      }
+    }
+
+    private List<Base> getEdges() {
+      List<Base> list = new ArrayList<>();
+      for (BundleEntryComponent be : bnd.getEntry())
+        list.add(new SearchEdge(type.substring(0, type.length() - 10) + "Edge", be));
+      return list;
+    }
+
+    private Base extractParam(String name) throws FHIRException {
+      return map != null ? new IntegerType(map.get(name)) : null;
+    }
+
+    private Map<String, String> parseURL(String url) throws FHIRException {
+      try {
+        Map<String, String> map = new HashMap<String, String>();
+        String[] pairs = url.split("&");
+        for (String pair : pairs) {
+          int idx = pair.indexOf("=");
+          String key;
+          key = idx > 0 ? URLDecoder.decode(pair.substring(0, idx), "UTF-8") : pair;
+          String value = idx > 0 && pair.length() > idx + 1 ? URLDecoder.decode(pair.substring(idx + 1), "UTF-8") : null;
+          map.put(key, value);
+        }
+        return map;
+      } catch (UnsupportedEncodingException e) {
+        throw new FHIRException(e);
+      }
+    }
+
+    private Base extractLink(String _name) throws FHIRException {
+      for (BundleLinkComponent bl : bnd.getLink()) {
+        if (bl.getRelation().equals(_name)) {
+          Map<String, String> map = parseURL(bl.getUrl());
+          return new StringType(map.get("search-id") + ':' + map.get("search-offset"));
+        }
+      }
+      return null;
+    }
+
+  }
+
 
   //
 //{ GraphQLSearchWrapper }

org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/GraphQLEngineTests.java

@@ -1,32 +1,22 @@
 package org.hl7.fhir.r4.test;
 
-import static org.junit.Assert.assertTrue;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.parsers.ParserConfigurationException;
-
 import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.r4.context.SimpleWorkerContext;
+import org.hl7.fhir.instance.model.api.IBaseReference;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.formats.XmlParser;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.Bundle.BundleLinkComponent;
 import org.hl7.fhir.r4.model.Bundle.SearchEntryMode;
-import org.hl7.fhir.r4.test.utils.TestingUtilities;
 import org.hl7.fhir.r4.model.DomainResource;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.Resource;
+import org.hl7.fhir.r4.test.utils.TestingUtilities;
 import org.hl7.fhir.r4.utils.GraphQLEngine;
-import org.hl7.fhir.r4.utils.GraphQLEngine.IGraphQLStorageServices;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.graphql.Argument;
+import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.hl7.fhir.utilities.graphql.NameValue;
 import org.hl7.fhir.utilities.graphql.Parser;
 import org.hl7.fhir.utilities.xml.XMLUtil;
@@ -38,6 +28,16 @@ import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.xml.sax.SAXException;
 
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.Assert.assertTrue;
+
 @RunWith(Parameterized.class)
 public class GraphQLEngineTests implements IGraphQLStorageServices {
 
@@ -127,18 +127,18 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
   }
 
   @Override
-  public ReferenceResolution lookup(Object appInfo, Resource context, Reference reference) throws FHIRException {
+  public ReferenceResolution lookup(Object appInfo, IBaseResource context, IBaseReference reference) throws FHIRException {
     try {
-      if (reference.getReference().startsWith("#")) {
+      if (reference.getReferenceElement().isLocal()) {
-        if (!(context instanceof DomainResource)) 
+        if (!(context instanceof DomainResource))
           return null;
         for (Resource r : ((DomainResource)context).getContained()) {
-          if (('#'+r.getId()).equals(reference.getReference())) {
+          if (('#'+r.getId()).equals(reference.getReferenceElement().getValue())) {
             return new ReferenceResolution(context, r);
           }
         }
       } else {
-        String[] parts = reference.getReference().split("/");
+        String[] parts = reference.getReferenceElement().getValue().split("/");
         String filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase()+'-'+parts[1].toLowerCase()+".xml");
         if (new File(filename).exists())
           return new ReferenceResolution(null, new XmlParser().parse(new FileInputStream(filename)));
@@ -150,7 +150,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
   }
 
   @Override
-  public void listResources(Object appInfo, String type, List<Argument> searchParams, List<Resource> matches) throws FHIRException {
+  public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
     try {
       if (type.equals("Condition")) 
         matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("condition-example.xml"))));

org.hl7.fhir.r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>3.8.24-SNAPSHOT</version>
+		<version>4.0.1-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

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

@@ -21,6 +21,18 @@ package org.hl7.fhir.r5.utils;
  */
 
 
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.model.*;
+import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.graphql.*;
+import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
+import org.hl7.fhir.utilities.graphql.Package;
+import org.hl7.fhir.utilities.graphql.Operation.OperationType;
+
 import java.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
 import java.util.ArrayList;
@@ -28,51 +40,16 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import org.hl7.fhir.exceptions.FHIRException;
+import static org.hl7.fhir.utilities.graphql.IGraphQLStorageServices.ReferenceResolution;
-import org.hl7.fhir.r5.context.IWorkerContext;
-import org.hl7.fhir.r5.model.BackboneElement;
-import org.hl7.fhir.r5.model.Base;
-import org.hl7.fhir.r5.model.Bundle;
-import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent;
-import org.hl7.fhir.r5.model.CanonicalType;
-import org.hl7.fhir.r5.model.DomainResource;
-import org.hl7.fhir.r5.model.Element;
-import org.hl7.fhir.r5.model.ExpressionNode;
-import org.hl7.fhir.r5.model.IntegerType;
-import org.hl7.fhir.r5.model.Property;
-import org.hl7.fhir.r5.model.Reference;
-import org.hl7.fhir.r5.model.Resource;
-import org.hl7.fhir.r5.model.StringType;
-import org.hl7.fhir.r5.utils.GraphQLEngine.IGraphQLStorageServices.ReferenceResolution;
-import org.hl7.fhir.utilities.Utilities;
-import org.hl7.fhir.utilities.graphql.Argument;
-import org.hl7.fhir.utilities.graphql.Argument.ArgumentListStatus;
-import org.hl7.fhir.utilities.graphql.Directive;
-import org.hl7.fhir.utilities.graphql.EGraphEngine;
-import org.hl7.fhir.utilities.graphql.EGraphQLException;
-import org.hl7.fhir.utilities.graphql.Field;
-import org.hl7.fhir.utilities.graphql.Fragment;
-import org.hl7.fhir.utilities.graphql.NameValue;
-import org.hl7.fhir.utilities.graphql.NumberValue;
-import org.hl7.fhir.utilities.graphql.ObjectValue;
-import org.hl7.fhir.utilities.graphql.Operation;
-import org.hl7.fhir.utilities.graphql.Operation.OperationType;
-import org.hl7.fhir.utilities.graphql.Package;
-import org.hl7.fhir.utilities.graphql.Selection;
-import org.hl7.fhir.utilities.graphql.StringValue;
-import org.hl7.fhir.utilities.graphql.Value;
-import org.hl7.fhir.utilities.graphql.Variable;
-import org.hl7.fhir.utilities.graphql.VariableValue;
 
-public class GraphQLEngine {
+public class GraphQLEngine implements IGraphQLEngine {
   
-  public class SearchEdge extends Base {
+  public static class SearchEdge extends Base {
 
     private BundleEntryComponent be;
     private String type;
     
-    public SearchEdge(String type, BundleEntryComponent be) {
+    SearchEdge(String type, BundleEntryComponent be) {
       this.type = type;
       this.be = be;
     }
@@ -107,13 +84,13 @@ public class GraphQLEngine {
     }
   }
 
-  public class SearchWrapper extends Base {
+  public static class SearchWrapper extends Base {
 
     private Bundle bnd;
     private String type;
     private Map<String, String> map;
 
-    public SearchWrapper(String type, Bundle bnd) throws FHIRException {
+    SearchWrapper(String type, Bundle bnd) throws FHIRException {
       this.type = type;
       this.bnd = bnd;
       for (BundleLinkComponent bl : bnd.getLink()) 
@@ -159,7 +136,7 @@ public class GraphQLEngine {
     private List<Base> getEdges() {
       List<Base> list = new ArrayList<>();
       for (BundleEntryComponent be : bnd.getEntry())
-        list.add(new SearchEdge(type.substring(0, type.length()-10)+"Edge", be));
+        list.add(new SearchEdge(type.substring(0, type.length() - 10) + "Edge", be));
       return list;
     }
 
@@ -195,32 +172,6 @@ public class GraphQLEngine {
     }
 
   }
-
-  public interface IGraphQLStorageServices {
-    public class ReferenceResolution {
-      private Resource targetContext;
-      private Resource target;
-      public ReferenceResolution(Resource targetContext, Resource target) {
-        super();
-        this.targetContext = targetContext;
-        this.target = target;
-      }
-      
-      
-    }
-    // given a reference inside a context, return what it references (including resolving internal references (e.g. start with #)
-    public ReferenceResolution lookup(Object appInfo, Resource context, Reference reference) throws FHIRException;
-    
-    // just get the identified resource
-    public Resource lookup(Object appInfo, String type, String id) throws FHIRException;
-
-    // list the matching resources. searchParams are the standard search params. 
-    // this instanceof different to search because the server returns all matching resources, or an error. There instanceof no paging on this search   
-    public void listResources(Object appInfo, String type, List<Argument> searchParams, List<Resource> matches) throws FHIRException;
-
-    // just perform a standard search, and return the bundle as you return to the client  
-    public Bundle search(Object appInfo, String type, List<Argument> searchParams) throws FHIRException;
-  }
   
   private IWorkerContext context;
   
@@ -260,7 +211,8 @@ public class GraphQLEngine {
   private FHIRPathEngine fpe;
 
   private ExpressionNode magicExpression;
-  
+
+  @Override
   public void execute() throws EGraphEngine, EGraphQLException, FHIRException {
     if (graphQL == null)
       throw new EGraphEngine("Unable to process graphql - graphql document missing");
@@ -332,7 +284,7 @@ public class GraphQLEngine {
 
   }
 
-  private boolean targetTypeOk(List<Argument> arguments, Resource dest) throws EGraphQLException {
+  private boolean targetTypeOk(List<Argument> arguments, IBaseResource dest) throws EGraphQLException {
     List<String> list = new ArrayList<String>();
     for (Argument arg : arguments) {
       if ((arg.getName().equals("type"))) {
@@ -436,18 +388,18 @@ public class GraphQLEngine {
     return result;
   }
 
-  private List<Resource> filterResources(Argument fhirpath, List<Resource> list) throws EGraphQLException, FHIRException {
+  private List<Resource> filterResources(Argument fhirpath, List<IBaseResource> list) throws EGraphQLException, FHIRException {
     List<Resource> result = new ArrayList<Resource>();
     if (list.size() > 0) {
       if ((fhirpath == null))
-        for (Resource v : list)
+        for (IBaseResource v : list)
-          result.add(v);
+          result.add((Resource) v);
       else {
         FHIRPathEngine fpe = new FHIRPathEngine(context);
         ExpressionNode node = fpe.parse(getSingleValue(fhirpath));
-        for (Resource v : list)
+        for (IBaseResource v : list)
-          if (fpe.evaluateToBoolean(null, v, v, node))
+          if (fpe.evaluateToBoolean(null, (Resource)v, (Base) v, node))
-            result.add(v);
+            result.add((Resource) v);
       }
     }
     return result;
@@ -609,11 +561,11 @@ public class GraphQLEngine {
     Reference ref = (Reference) source;
     ReferenceResolution res = services.lookup(appInfo, context, ref);
     if (res != null) {
-      if (targetTypeOk(field.getArguments(), res.target)) {
+      if (targetTypeOk(field.getArguments(), res.getTarget())) {
         Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
         ObjectValue obj = new ObjectValue();
         arg.addValue(obj);
-        processObject(res.targetContext, res.target, obj, field.getSelectionSet(), inheritedList, suffix);
+        processObject((Resource)res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
       }
     }
     else if (!hasArgument(field.getArguments(), "optional", "true"))
@@ -629,11 +581,11 @@ public class GraphQLEngine {
     Reference ref = new Reference(source.primitiveValue());
     ReferenceResolution res = services.lookup(appInfo, context, ref);
     if (res != null) {
-      if (targetTypeOk(field.getArguments(), res.target)) {
+      if (targetTypeOk(field.getArguments(), res.getTarget())) {
         Argument arg = target.addField(field.getAlias() + suffix, listStatus(field, inheritedList));
         ObjectValue obj = new ObjectValue();
         arg.addValue(obj);
-        processObject(res.targetContext, res.target, obj, field.getSelectionSet(), inheritedList, suffix);
+        processObject((Resource)res.getTargetContext(), (Base) res.getTarget(), obj, field.getSelectionSet(), inheritedList, suffix);
       }
     }
     else if (!hasArgument(field.getArguments(), "optional", "true"))
@@ -652,8 +604,8 @@ public class GraphQLEngine {
   private void processReverseReferenceList(Resource source, Field field, ObjectValue target, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
     if (services == null)
       throw new EGraphQLException("Resource Referencing services not provided");
-    List<Resource> list = new ArrayList<Resource>();
+    List<IBaseResource> list = new ArrayList<>();
-    List<Argument> params = new ArrayList<Argument>();
+    List<Argument> params = new ArrayList<>();
     Argument parg = null;
     for (Argument a : field.getArguments())
       if (!(a.getName().equals("_reference")))
@@ -701,7 +653,7 @@ public class GraphQLEngine {
     params.add(arg);
     arg.setName(getSingleValue(parg));
     arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
-    Bundle bnd = services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
+    Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
     Base bndWrapper = new SearchWrapper(field.getName(), bnd);
     arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
     ObjectValue obj = new ObjectValue();
@@ -735,7 +687,7 @@ public class GraphQLEngine {
         throw new EGraphQLException("Unknown/invalid parameter "+arg.getName());
     if (Utilities.noString(id))
       throw new EGraphQLException("No id found");
-    Resource res = services.lookup(appInfo, field.getName(), id);
+    Resource res = (Resource) services.lookup(appInfo, field.getName(), id);
     if (res == null)
       throw new EGraphQLException("Resource "+field.getName()+"/"+id+" not found");
     Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
@@ -747,7 +699,7 @@ public class GraphQLEngine {
   private void processSearchSimple(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
     if (services == null)
       throw new EGraphQLException("Resource Referencing services not provided");
-    List<Resource> list = new ArrayList<Resource>();
+    List<IBaseResource> list = new ArrayList<>();
     services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), field.getArguments(), list);
     Argument arg = null;
     ObjectValue obj = null;
@@ -780,7 +732,7 @@ public class GraphQLEngine {
       params.add(new Argument("search-offset", new StringValue(parts[1])));
     }
 
-    Bundle bnd = services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
+    Bundle bnd = (Bundle) services.search(appInfo, field.getName().substring(0, field.getName().length()-10), params);
     SearchWrapper bndWrapper = new SearchWrapper(field.getName(), bnd);
     Argument arg = target.addField(field.getAlias()+suffix, listStatus(field, false));
     ObjectValue obj = new ObjectValue();
@@ -830,6 +782,7 @@ public class GraphQLEngine {
     return appInfo;
   }
 
+  @Override
   public void setAppInfo(Object appInfo) {
     this.appInfo = appInfo;
   }
@@ -838,18 +791,21 @@ public class GraphQLEngine {
     return focus;
   }
 
-  public void setFocus(Resource focus) {
+  @Override
-    this.focus = focus;
+  public void setFocus(IBaseResource focus) {
+    this.focus = (Resource) focus;
   }
 
   public Package getGraphQL() {
     return graphQL;
   }
 
+  @Override
   public void setGraphQL(Package graphQL) {
     this.graphQL = graphQL;
   }
 
+  @Override
   public ObjectValue getOutput() {
     return output;
   }
@@ -858,6 +814,7 @@ public class GraphQLEngine {
     return services;
   }
 
+  @Override
   public void setServices(IGraphQLStorageServices services) {
     this.services = services;
   }

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/GraphQLEngineTests.java

@@ -1,32 +1,21 @@
 package org.hl7.fhir.r5.test;
 
-import static org.junit.Assert.assertTrue;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.parsers.ParserConfigurationException;
-
 import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.r5.context.SimpleWorkerContext;
+import org.hl7.fhir.instance.model.api.IBaseReference;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r5.model.Bundle.BundleLinkComponent;
 import org.hl7.fhir.r5.model.Bundle.SearchEntryMode;
-import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.model.DomainResource;
-import org.hl7.fhir.r5.model.Reference;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.GraphQLEngine;
-import org.hl7.fhir.r5.utils.GraphQLEngine.IGraphQLStorageServices;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.graphql.Argument;
+import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
 import org.hl7.fhir.utilities.graphql.NameValue;
 import org.hl7.fhir.utilities.graphql.Parser;
 import org.hl7.fhir.utilities.xml.XMLUtil;
@@ -38,6 +27,16 @@ import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.xml.sax.SAXException;
 
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.Assert.assertTrue;
+
 @RunWith(Parameterized.class)
 public class GraphQLEngineTests implements IGraphQLStorageServices {
 
@@ -127,18 +126,18 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
   }
 
   @Override
-  public ReferenceResolution lookup(Object appInfo, Resource context, Reference reference) throws FHIRException {
+  public ReferenceResolution lookup(Object appInfo, IBaseResource context, IBaseReference reference) throws FHIRException {
     try {
-      if (reference.getReference().startsWith("#")) {
+      if (reference.getReferenceElement().isLocal()) {
         if (!(context instanceof DomainResource)) 
           return null;
         for (Resource r : ((DomainResource)context).getContained()) {
-          if (('#'+r.getId()).equals(reference.getReference())) {
+          if (('#'+r.getId()).equals(reference.getReferenceElement().getValue())) {
             return new ReferenceResolution(context, r);
           }
         }
       } else {
-        String[] parts = reference.getReference().split("/");
+        String[] parts = reference.getReferenceElement().getValue().split("/");
         String filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase()+'-'+parts[1].toLowerCase()+".xml");
         if (new File(filename).exists())
           return new ReferenceResolution(null, new XmlParser().parse(new FileInputStream(filename)));
@@ -150,7 +149,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
   }
 
   @Override
-  public void listResources(Object appInfo, String type, List<Argument> searchParams, List<Resource> matches) throws FHIRException {
+  public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
     try {
       if (type.equals("Condition")) 
         matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("condition-example.xml"))));

org.hl7.fhir.utilities/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.8.24-SNAPSHOT</version>
+        <version>4.0.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/graphql/IGraphQLEngine.java

@@ -0,0 +1,39 @@
+package org.hl7.fhir.utilities.graphql;
+
+/*-
+ * #%L
+ * org.hl7.fhir.utilities
+ * %%
+ * Copyright (C) 2014 - 2019 Health Level 7
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+public interface IGraphQLEngine {
+
+  void execute() throws EGraphEngine, EGraphQLException, FHIRException;
+
+  ObjectValue getOutput();
+
+  void setAppInfo(Object appInfo);
+
+  void setFocus(IBaseResource focus);
+
+  void setGraphQL(Package graphQL);
+
+  void setServices(IGraphQLStorageServices services);
+}

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/graphql/IGraphQLStorageServices.java

@@ -0,0 +1,73 @@
+package org.hl7.fhir.utilities.graphql;
+
+/*-
+ * #%L
+ * org.hl7.fhir.utilities
+ * %%
+ * Copyright (C) 2014 - 2019 Health Level 7
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.instance.model.api.IBaseReference;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import java.util.List;
+
+public interface IGraphQLStorageServices {
+
+  /**
+   * given a reference inside a context, return what it references (including resolving internal references (e.g. start with #)
+   */
+  ReferenceResolution lookup(Object appInfo, IBaseResource context, IBaseReference reference) throws FHIRException;
+
+  /**
+   * just get the identified resource
+   */
+  IBaseResource lookup(Object appInfo, String type, String id) throws FHIRException;
+
+  /**
+   * list the matching resources. searchParams are the standard search params.
+   * this instanceof different to search because the server returns all matching resources, or an error. There instanceof no paging on this search
+   */
+  void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException;
+
+  /**
+   * just perform a standard search, and return the bundle as you return to the client
+   */
+  IBaseBundle search(Object appInfo, String type, List<Argument> searchParams) throws FHIRException;
+
+  class ReferenceResolution {
+    private IBaseResource targetContext;
+    private IBaseResource target;
+
+    public ReferenceResolution(IBaseResource targetContext, IBaseResource target) {
+      super();
+      this.targetContext = targetContext;
+      this.target = target;
+    }
+
+    public IBaseResource getTargetContext() {
+      return targetContext;
+    }
+
+    public IBaseResource getTarget() {
+      return target;
+    }
+
+
+  }
+}

org.hl7.fhir.validation.cli/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.8.24-SNAPSHOT</version>
+        <version>4.0.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.validation.cli/src/main/java/Marker.java

@@ -0,0 +1,22 @@
+/*-
+ * #%L
+ * org.hl7.fhir.validation.cli
+ * %%
+ * Copyright (C) 2014 - 2019 Health Level 7
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+public class Marker {
+  // This class is just here to force a javadoc build in order to satisfy maven central
+}

org.hl7.fhir.validation/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>3.8.24-SNAPSHOT</version>
+        <version>4.0.1-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>hapi-deployable-pom</artifactId>
-		<version>3.8.0-SNAPSHOT</version>
+		<version>4.0.0</version>
 	</parent>
 
 	<!--
@@ -13,10 +13,10 @@
 	each other. It is fine to bump the point version of this POM without affecting
 	HAPI FHIR.
 	-->
-	<version>3.8.24-SNAPSHOT</version>
+	<version>4.0.1-SNAPSHOT</version>
 
 	<properties>
-		<hapi_fhir_version>4.0.0-SNAPSHOT</hapi_fhir_version>
+		<hapi_fhir_version>4.0.0</hapi_fhir_version>
 	</properties>
 
 	<artifactId>org.hl7.fhir.core</artifactId>