Merge branch 'custom_jpa_search_params'

HELPWANTED.md

@@ -0,0 +1,8 @@
+# Help Wanted
+
+This page is a work in progress!
+
+It serves as a place to list potential help a new volunteer could offer.
+
+* Investigate adding support for FHIR's RDF (Turtle) encoding to HAPI
+

example-projects/hapi-fhir-base-example-embedded-ws/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

example-projects/hapi-fhir-standalone-overlay-example/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.8

hapi-fhir-android-realm/.project

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>hapi-fhir-android-realm</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java

@@ -82,87 +82,22 @@ public class FhirContext {
 	private Map<String, Class<? extends IBaseResource>> myDefaultTypeForProfile = new HashMap<String, Class<? extends IBaseResource>>();
 	private volatile Map<String, RuntimeResourceDefinition> myIdToResourceDefinition = Collections.emptyMap();
 	private boolean myInitialized;
+	private boolean myInitializing;
 	private HapiLocalizer myLocalizer = new HapiLocalizer();
 	private volatile Map<String, BaseRuntimeElementDefinition<?>> myNameToElementDefinition = Collections.emptyMap();
 	private volatile Map<String, RuntimeResourceDefinition> myNameToResourceDefinition = Collections.emptyMap();
 	private volatile Map<String, Class<? extends IBaseResource>> myNameToResourceType;
 	private volatile INarrativeGenerator myNarrativeGenerator;
 	private volatile IParserErrorHandler myParserErrorHandler = new LenientErrorHandler();
+	private ParserOptions myParserOptions = new ParserOptions();
 	private Set<PerformanceOptionsEnum> myPerformanceOptions = new HashSet<PerformanceOptionsEnum>();
 	private Collection<Class<? extends IBaseResource>> myResourceTypesToScan;
 	private volatile IRestfulClientFactory myRestfulClientFactory;
 	private volatile RuntimeChildUndeclaredExtensionDefinition myRuntimeChildUndeclaredExtensionDefinition;
-	private final IFhirVersion myVersion;
-	private Map<FhirVersionEnum, Map<String, Class<? extends IBaseResource>>> myVersionToNameToResourceType = Collections.emptyMap();
-	private boolean myInitializing;
 	private IContextValidationSupport<?, ?, ?, ?, ?, ?> myValidationSupport;
+	private final IFhirVersion myVersion;
 	
-	/**
+	private Map<FhirVersionEnum, Map<String, Class<? extends IBaseResource>>> myVersionToNameToResourceType = Collections.emptyMap();
-	 * Returns the validation support module configured for this context, creating a default
-	 * implementation if no module has been passed in via the {@link #setValidationSupport(IContextValidationSupport)}
-	 * method
-	 * @see #setValidationSupport(IContextValidationSupport)
-	 */
-	public IContextValidationSupport<?, ?, ?, ?, ?, ?> getValidationSupport() {
-		if (myValidationSupport == null) {
-			myValidationSupport = myVersion.createValidationSupport();
-		}
-		return myValidationSupport;
-	}
-
-	/**
-	 * Creates a new FluentPath engine which can be used to exvaluate
-	 * path expressions over FHIR resources. Note that this engine will use the
-	 * {@link IContextValidationSupport context validation support} module which is 
-	 * configured on the context at the time this method is called.
-	 * <p>
-	 * In other words, call {@link #setValidationSupport(IContextValidationSupport)} before
-	 * calling {@link #newFluentPath()}
-	 * </p>
-	 * <p>
-	 * Note that this feature was added for FHIR DSTU3 and is not available
-	 * for contexts configured to use an older version of FHIR. Calling this method
-	 * on a context for a previous version of fhir will result in an
-	 * {@link UnsupportedOperationException}
-	 * </p>
-	 * 
-	 * @since 2.2
-	 */
-	public IFluentPath newFluentPath() {
-		return myVersion.createFluentPathExecutor(this);
-	}
-	
-	/**
-	 * Sets the validation support module to use for this context. The validation support module
-	 * is used to supply underlying infrastructure such as conformance resources (StructureDefinition, ValueSet, etc)
-	 * as well as to provide terminology services to modules such as the validator and FluentPath executor 
-	 */
-	public void setValidationSupport(IContextValidationSupport<?, ?, ?, ?, ?, ?> theValidationSupport) {
-		myValidationSupport = theValidationSupport;
-	}
-
-	private ParserOptions myParserOptions = new ParserOptions();
-
-	/**
-	 * Returns the parser options object which will be used to supply default
-	 * options to newly created parsers
-	 * 
-	 * @return The parser options - Will not return <code>null</code>
-	 */
-	public ParserOptions getParserOptions() {
-		return myParserOptions;
-	}
-
-	/**
-	 * Sets the parser options object which will be used to supply default
-	 * options to newly created parsers
-	 *  
-	 * @param theParserOptions The parser options object - Must not be <code>null</code>
-	 */
-	public void setParserOptions(ParserOptions theParserOptions) {
-		Validate.notNull(theParserOptions, "theParserOptions must not be null");
-		myParserOptions = theParserOptions;
-	}
 
 	/**
 	 * @deprecated It is recommended that you use one of the static initializer methods instead
@@ -172,7 +107,7 @@ public class FhirContext {
 	public FhirContext() {
 		this(EMPTY_LIST);
 	}
-
+	
 	/**
 	 * @deprecated It is recommended that you use one of the static initializer methods instead
 	 *             of this method, e.g. {@link #forDstu2()} or {@link #forDstu3()}
@@ -282,7 +217,7 @@ public class FhirContext {
 		validateInitialized();
 		return myNameToResourceDefinition.values();
 	}
-	
+
 	/**
 	 * Returns the default resource type for the given profile
 	 * 
@@ -332,7 +267,7 @@ public class FhirContext {
 		validateInitialized();
 		return Collections.unmodifiableCollection(myClassToElementDefinition.values());
 	}
-
+	
 	/**
 	 * This feature is not yet in its final state and should be considered an internal part of HAPI for now - use with
 	 * caution
@@ -348,6 +283,16 @@ public class FhirContext {
 		return myNarrativeGenerator;
 	}
 
+	/**
+	 * Returns the parser options object which will be used to supply default
+	 * options to newly created parsers
+	 * 
+	 * @return The parser options - Will not return <code>null</code>
+	 */
+	public ParserOptions getParserOptions() {
+		return myParserOptions;
+	}
+
 	/**
 	 * Get the configured performance options
 	 */
@@ -449,6 +394,20 @@ public class FhirContext {
 		return myIdToResourceDefinition.get(theId);
 	}
 
+//	/**
+//	 * Return an unmodifiable collection containing all known resource definitions
+//	 */
+//	public Collection<RuntimeResourceDefinition> getResourceDefinitions() {
+//		
+//		Set<Class<? extends IBase>> datatypes = Collections.emptySet();
+//		Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> existing = Collections.emptyMap();
+//		HashMap<String, Class<? extends IBaseResource>> types = new HashMap<String, Class<? extends IBaseResource>>();
+//		ModelScanner.scanVersionPropertyFile(datatypes, types, myVersion.getVersion(), existing);
+//		for (int next : types.)
+//		
+//		return Collections.unmodifiableCollection(myIdToResourceDefinition.values());
+//	}
+
 	/**
 	 * Returns the scanned runtime models. This is an advanced feature which is generally only needed for extending the
 	 * core library.
@@ -476,6 +435,19 @@ public class FhirContext {
 		return myRuntimeChildUndeclaredExtensionDefinition;
 	}
 
+	/**
+	 * Returns the validation support module configured for this context, creating a default
+	 * implementation if no module has been passed in via the {@link #setValidationSupport(IContextValidationSupport)}
+	 * method
+	 * @see #setValidationSupport(IContextValidationSupport)
+	 */
+	public IContextValidationSupport<?, ?, ?, ?, ?, ?> getValidationSupport() {
+		if (myValidationSupport == null) {
+			myValidationSupport = myVersion.createValidationSupport();
+		}
+		return myValidationSupport;
+	}
+
 	public IFhirVersion getVersion() {
 		return myVersion;
 	}
@@ -500,6 +472,28 @@ public class FhirContext {
 		return myVersion.newBundleFactory(this);
 	}
 
+	/**
+	 * Creates a new FluentPath engine which can be used to exvaluate
+	 * path expressions over FHIR resources. Note that this engine will use the
+	 * {@link IContextValidationSupport context validation support} module which is 
+	 * configured on the context at the time this method is called.
+	 * <p>
+	 * In other words, call {@link #setValidationSupport(IContextValidationSupport)} before
+	 * calling {@link #newFluentPath()}
+	 * </p>
+	 * <p>
+	 * Note that this feature was added for FHIR DSTU3 and is not available
+	 * for contexts configured to use an older version of FHIR. Calling this method
+	 * on a context for a previous version of fhir will result in an
+	 * {@link UnsupportedOperationException}
+	 * </p>
+	 * 
+	 * @since 2.2
+	 */
+	public IFluentPath newFluentPath() {
+		return myVersion.createFluentPathExecutor(this);
+	}
+
 	/**
 	 * Create and return a new JSON parser.
 	 * 
@@ -783,6 +777,17 @@ public class FhirContext {
 		myParserErrorHandler = theParserErrorHandler;
 	}
 
+	/**
+	 * Sets the parser options object which will be used to supply default
+	 * options to newly created parsers
+	 *  
+	 * @param theParserOptions The parser options object - Must not be <code>null</code>
+	 */
+	public void setParserOptions(ParserOptions theParserOptions) {
+		Validate.notNull(theParserOptions, "theParserOptions must not be null");
+		myParserOptions = theParserOptions;
+	}
+
 	/**
 	 * Sets the configured performance options
 	 * 
@@ -818,6 +823,15 @@ public class FhirContext {
 		this.myRestfulClientFactory = theRestfulClientFactory;
 	}
 
+	/**
+	 * Sets the validation support module to use for this context. The validation support module
+	 * is used to supply underlying infrastructure such as conformance resources (StructureDefinition, ValueSet, etc)
+	 * as well as to provide terminology services to modules such as the validator and FluentPath executor 
+	 */
+	public void setValidationSupport(IContextValidationSupport<?, ?, ?, ?, ?, ?> theValidationSupport) {
+		myValidationSupport = theValidationSupport;
+	}
+
 	@SuppressWarnings({ "cast" })
 	private List<Class<? extends IElement>> toElementList(Collection<Class<? extends IBaseResource>> theResourceTypes) {
 		if (theResourceTypes == null) {
@@ -850,6 +864,13 @@ public class FhirContext {
 		return new FhirContext(FhirVersionEnum.DSTU2);
 	}
 
+	/**
+	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2 DSTU2} (2016 May DSTU3 Snapshot)
+	 */
+	public static FhirContext forDstu2_1() {
+		return new FhirContext(FhirVersionEnum.DSTU2_1);
+	}
+
 	/**
 	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2_HL7ORG DSTU2} (using the Reference
 	 * Implementation Structures)
@@ -885,11 +906,4 @@ public class FhirContext {
 		return retVal;
 	}
 
-	/**
-	 * Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2 DSTU2} (2016 May DSTU3 Snapshot)
-	 */
-	public static FhirContext forDstu2_1() {
-		return new FhirContext(FhirVersionEnum.DSTU2_1);
-	}
-
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/ModelScanner.java

@@ -34,6 +34,7 @@ import java.util.Map.Entry;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.*;
 
+import ca.uhn.fhir.context.RuntimeSearchParam.RuntimeSearchParamStatusEnum;
 import ca.uhn.fhir.model.api.ExtensionDt;
 import ca.uhn.fhir.model.api.IDatatype;
 import ca.uhn.fhir.model.api.IElement;
@@ -437,7 +438,7 @@ class ModelScanner {
 				}
 
 
-				RuntimeSearchParam param = new RuntimeSearchParam(searchParam.name(), searchParam.description(), searchParam.path(), paramType, providesMembershipInCompartments, toTargetList(searchParam.target()));
+				RuntimeSearchParam param = new RuntimeSearchParam(searchParam.name(), searchParam.description(), searchParam.path(), paramType, providesMembershipInCompartments, toTargetList(searchParam.target()), RuntimeSearchParamStatusEnum.ACTIVE);
 				theResourceDef.addSearchParam(param);
 				nameToParam.put(param.getName(), param);
 			}
@@ -457,7 +458,7 @@ class ModelScanner {
 				compositeOf.add(param);
 			}
 
-			RuntimeSearchParam param = new RuntimeSearchParam(searchParam.name(), searchParam.description(), searchParam.path(), RestSearchParameterTypeEnum.COMPOSITE, compositeOf, null, toTargetList(searchParam.target()));
+			RuntimeSearchParam param = new RuntimeSearchParam(null, null, searchParam.name(), searchParam.description(), searchParam.path(), RestSearchParameterTypeEnum.COMPOSITE, compositeOf, null, toTargetList(searchParam.target()), RuntimeSearchParamStatusEnum.ACTIVE);
 			theResourceDef.addSearchParam(param);
 		}
 	}

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeSearchParam.java

@@ -6,6 +6,8 @@ import java.util.List;
 import java.util.Set;
 import java.util.StringTokenizer;
 
+import org.hl7.fhir.instance.model.api.IIdType;
+
 import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
 
 /*
@@ -29,7 +31,7 @@ import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
  */
 
 public class RuntimeSearchParam {
-
+	private final IIdType myId;
 	private final List<RuntimeSearchParam> myCompositeOf;
 	private final String myDescription;
 	private final String myName;
@@ -37,15 +39,28 @@ public class RuntimeSearchParam {
 	private final String myPath;
 	private final Set<String> myTargets;
 	private final Set<String> myProvidesMembershipInCompartments;
+	private final RuntimeSearchParamStatusEnum myStatus;
+	private final String myUri;
 
-	public RuntimeSearchParam(String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, List<RuntimeSearchParam> theCompositeOf,
+	public IIdType getId() {
-			Set<String> theProvidesMembershipInCompartments, Set<String> theTargets) {
+		return myId;
+	}
+
+	public String getUri() {
+		return myUri;
+	}
+
+	public RuntimeSearchParam(IIdType theId, String theUri, String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, List<RuntimeSearchParam> theCompositeOf,
+			Set<String> theProvidesMembershipInCompartments, Set<String> theTargets, RuntimeSearchParamStatusEnum theStatus) {
 		super();
+		myId = theId;
+		myUri = theUri;
 		myName = theName;
 		myDescription = theDescription;
 		myPath = thePath;
 		myParamType = theParamType;
 		myCompositeOf = theCompositeOf;
+		myStatus = theStatus;
 		if (theProvidesMembershipInCompartments != null && !theProvidesMembershipInCompartments.isEmpty()) {
 			myProvidesMembershipInCompartments = Collections.unmodifiableSet(theProvidesMembershipInCompartments);
 		} else {
@@ -62,8 +77,12 @@ public class RuntimeSearchParam {
 		return myTargets;
 	}
 
-	public RuntimeSearchParam(String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, Set<String> theProvidesMembershipInCompartments, Set<String> theTargets) {
+	public RuntimeSearchParamStatusEnum getStatus() {
-		this(theName, theDescription, thePath, theParamType, null, theProvidesMembershipInCompartments, theTargets);
+		return myStatus;
+	}
+
+	public RuntimeSearchParam(String theName, String theDescription, String thePath, RestSearchParameterTypeEnum theParamType, Set<String> theProvidesMembershipInCompartments, Set<String> theTargets, RuntimeSearchParamStatusEnum theStatus) {
+		this(null, null, theName, theDescription, thePath, theParamType, null, theProvidesMembershipInCompartments, theTargets, theStatus);
 	}
 
 	public List<RuntimeSearchParam> getCompositeOf() {
@@ -108,4 +127,10 @@ public class RuntimeSearchParam {
 		return myProvidesMembershipInCompartments;
 	}
 
+	public enum RuntimeSearchParamStatusEnum {
+		ACTIVE,
+		DRAFT,
+		RETIRED
+	}
+	
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/OptionalParam.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.rest.annotation;
 
+import java.lang.annotation.ElementType;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -10,7 +12,7 @@ package ca.uhn.fhir.rest.annotation;
  * 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
+ * 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,
@@ -22,19 +24,19 @@ package ca.uhn.fhir.rest.annotation;
 
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
 
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.CompositeParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
-//import ca.uhn.fhir.testmodel.Patient; // TODO: qualify this correctly
-
 
 /**
- * Parameter annotation which specifies a search parameter for a {@link Search} method. 
+ * Parameter annotation which specifies a search parameter for a {@link Search} method.
  */
 @Retention(RetentionPolicy.RUNTIME)
+@Target(value=ElementType.PARAMETER)
 public @interface OptionalParam {
 
 	public static final String ALLOW_CHAIN_ANY = "*";
@@ -42,63 +44,63 @@ public @interface OptionalParam {
 	public static final String ALLOW_CHAIN_NOTCHAINED = "";
 
 	/**
-     * For reference parameters ({@link ReferenceParam}) this value may be
+	 * For reference parameters ({@link ReferenceParam}) this value may be
-     * used to indicate which chain values (if any) are <b>not</b> valid 
+	 * used to indicate which chain values (if any) are <b>not</b> valid
-     * for the given parameter. Values here will supercede any values specified
+	 * for the given parameter. Values here will supercede any values specified
-     * in {@link #chainWhitelist()}  
+	 * in {@link #chainWhitelist()}
-     * <p>
+	 * <p>
-     * If the parameter annotated with this annotation is not a {@link ReferenceParam},
+	 * If the parameter annotated with this annotation is not a {@link ReferenceParam},
-     * this value must not be populated.
+	 * this value must not be populated.
-     * </p>
+	 * </p>
-     */
+	 */
 	String[] chainBlacklist() default {};
-    
-    /**
-     * For reference parameters ({@link ReferenceParam}) this value may be
-     * used to indicate which chain values (if any) are valid for the given 
-     * parameter. If the list contains the value {@link #ALLOW_CHAIN_ANY}, all values are valid.  (this is the default)
-     * If the list contains the value {@link #ALLOW_CHAIN_NOTCHAINED}
-     * then the reference param only supports the empty chain (i.e. the resource
-     * ID). 
-     * <p>
-     * Valid values for this parameter include:
-     * </p>
-     * <ul>
-     * <li><code>chainWhitelist={ OptionalParam.ALLOW_CHAIN_NOTCHAINED }</code> - Only allow resource reference (no chaining allowed for this parameter)</li>
-     * <li><code>chainWhitelist={ OptionalParam.ALLOW_CHAIN_ANY }</code> - Allow any chaining at all (including a non chained value, <b>this is the default</b>)</li>
-     * <li><code>chainWhitelist={ "foo", "bar" }</code> - Allow property.foo and property.bar</li>
-     * </ul>
-     * <p>
-     * Any values specified in 
-     * {@link #chainBlacklist()} will supercede (have priority over) values
-     * here.
-     * </p>
-     * <p>
-     * If the parameter annotated with this annotation is not a {@link ReferenceParam},
-     * this value must not be populated.
-     * </p>
-     */
-	String[] chainWhitelist() default {ALLOW_CHAIN_ANY};
-    
-    /**
-     * For composite parameters ({@link CompositeParam}) this value may be
-     * used to indicate the parameter type(s) which may be referenced by this param.
-     * <p>
-     * If the parameter annotated with this annotation is not a {@link CompositeParam},
-     * this value must not be populated.
-     * </p>
-     */
-    Class<? extends IQueryParameterType>[] compositeTypes() default {};
 
-    /**
+	/**
-	 * This is the name for the parameter. Generally this should be a 
+	 * For reference parameters ({@link ReferenceParam}) this value may be
+	 * used to indicate which chain values (if any) are valid for the given
+	 * parameter. If the list contains the value {@link #ALLOW_CHAIN_ANY}, all values are valid. (this is the default)
+	 * If the list contains the value {@link #ALLOW_CHAIN_NOTCHAINED}
+	 * then the reference param only supports the empty chain (i.e. the resource
+	 * ID).
+	 * <p>
+	 * Valid values for this parameter include:
+	 * </p>
+	 * <ul>
+	 * <li><code>chainWhitelist={ OptionalParam.ALLOW_CHAIN_NOTCHAINED }</code> - Only allow resource reference (no chaining allowed for this parameter)</li>
+	 * <li><code>chainWhitelist={ OptionalParam.ALLOW_CHAIN_ANY }</code> - Allow any chaining at all (including a non chained value, <b>this is the default</b>)</li>
+	 * <li><code>chainWhitelist={ "foo", "bar" }</code> - Allow property.foo and property.bar</li>
+	 * </ul>
+	 * <p>
+	 * Any values specified in
+	 * {@link #chainBlacklist()} will supercede (have priority over) values
+	 * here.
+	 * </p>
+	 * <p>
+	 * If the parameter annotated with this annotation is not a {@link ReferenceParam},
+	 * this value must not be populated.
+	 * </p>
+	 */
+	String[] chainWhitelist() default { ALLOW_CHAIN_ANY };
+
+	/**
+	 * For composite parameters ({@link CompositeParam}) this value may be
+	 * used to indicate the parameter type(s) which may be referenced by this param.
+	 * <p>
+	 * If the parameter annotated with this annotation is not a {@link CompositeParam},
+	 * this value must not be populated.
+	 * </p>
+	 */
+	Class<? extends IQueryParameterType>[] compositeTypes() default {};
+
+	/**
+	 * This is the name for the parameter. Generally this should be a
 	 * simple string (e.g. "name", or "identifier") which will be the name
 	 * of the URL parameter used to populate this method parameter.
 	 * <p>
 	 * Most resource model classes have constants which may be used to
 	 * supply values for this field, e.g. <code>Patient.SP_NAME</code> or
 	 * <code>Observation.SP_DATE</code>
-	 * </p>  
+	 * </p>
 	 * <p>
 	 * If you wish to specify a parameter for a resource reference which
 	 * only accepts a specific chained value, it is also valid to supply
@@ -109,13 +111,13 @@ public @interface OptionalParam {
 	 */
 	String name();
 
-    /**
+	/**
-     * For resource reference parameters ({@link ReferenceParam}) this value may be
+	 * For resource reference parameters ({@link ReferenceParam}) this value may be
-     * used to indicate the resource type(s) which may be referenced by this param.
+	 * used to indicate the resource type(s) which may be referenced by this param.
-     * <p>
+	 * <p>
-     * If the parameter annotated with this annotation is not a {@link ReferenceParam},
+	 * If the parameter annotated with this annotation is not a {@link ReferenceParam},
-     * this value must not be populated.
+	 * this value must not be populated.
-     * </p>
+	 * </p>
-     */
+	 */
-    Class<? extends IBaseResource>[] targetTypes() default {};
+	Class<? extends IBaseResource>[] targetTypes() default {};
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/RawParam.java

@@ -0,0 +1,20 @@
+package ca.uhn.fhir.rest.annotation;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * On a {@link Search} method, a parameter marked with this annotation 
+ * will receive search parameters not captured by other parameters. 
+ * <p>
+ * Parameters with this annotation must be of type
+ * {@code Map<String, List<String>>}
+ * </p>
+ */
+@Retention(RetentionPolicy.RUNTIME)
+@Target(value=ElementType.PARAMETER)
+public @interface RawParam {
+	// nothing
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/RequiredParam.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.rest.annotation;
 
+import java.lang.annotation.ElementType;
+
 /*
  * #%L
  * HAPI FHIR - Core Library
@@ -10,7 +12,7 @@ package ca.uhn.fhir.rest.annotation;
  * 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
+ * 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,
@@ -22,18 +24,19 @@ package ca.uhn.fhir.rest.annotation;
 
 import java.lang.annotation.Retention;
 import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
 
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.rest.param.CompositeParam;
 import ca.uhn.fhir.rest.param.ReferenceParam;
-//import ca.uhn.fhir.testmodel.Patient; // TODO: qualify this correctly
 
-@Retention(RetentionPolicy.RUNTIME)
 /**
- * Parameter annotation which specifies a search parameter for a {@link Search} method. 
+ * Parameter annotation which specifies a search parameter for a {@link Search} method.
  */
+@Retention(RetentionPolicy.RUNTIME)
+@Target(value=ElementType.PARAMETER)
 public @interface RequiredParam {
 
 	/**
@@ -45,32 +48,32 @@ public @interface RequiredParam {
 	 */
 	String[] chainBlacklist() default {};
 
-    /**
+	/**
-     * For reference parameters ({@link ReferenceParam}) this value may be
+	 * For reference parameters ({@link ReferenceParam}) this value may be
-     * used to indicate which chain values (if any) are valid for the given 
+	 * used to indicate which chain values (if any) are valid for the given
-     * parameter. If the list contains the value {@link OptionalParam#ALLOW_CHAIN_ANY}, all values are valid.  (this is the default)
+	 * parameter. If the list contains the value {@link OptionalParam#ALLOW_CHAIN_ANY}, all values are valid. (this is the default)
-     * If the list contains the value {@link OptionalParam#ALLOW_CHAIN_NOTCHAINED}
+	 * If the list contains the value {@link OptionalParam#ALLOW_CHAIN_NOTCHAINED}
-     * then the reference param only supports the empty chain (i.e. the resource
+	 * then the reference param only supports the empty chain (i.e. the resource
-     * ID). 
+	 * ID).
-     * <p>
+	 * <p>
-     * Valid values for this parameter include:
+	 * Valid values for this parameter include:
-     * </p>
+	 * </p>
-     * <ul>
+	 * <ul>
-     * <li><code>chainWhitelist={ OptionalParam.ALLOW_CHAIN_NOTCHAINED }</code> - Only allow resource reference (no chaining allowed for this parameter)</li>
+	 * <li><code>chainWhitelist={ OptionalParam.ALLOW_CHAIN_NOTCHAINED }</code> - Only allow resource reference (no chaining allowed for this parameter)</li>
-     * <li><code>chainWhitelist={ OptionalParam.ALLOW_CHAIN_ANY }</code> - Allow any chaining at all (including a non chained value, <b>this is the default</b>)</li>
+	 * <li><code>chainWhitelist={ OptionalParam.ALLOW_CHAIN_ANY }</code> - Allow any chaining at all (including a non chained value, <b>this is the default</b>)</li>
-     * <li><code>chainWhitelist={ "foo", "bar" }</code> - Allow property.foo and property.bar</li>
+	 * <li><code>chainWhitelist={ "foo", "bar" }</code> - Allow property.foo and property.bar</li>
-     * </ul>
+	 * </ul>
-     * <p>
+	 * <p>
-     * Any values specified in 
+	 * Any values specified in
-     * {@link #chainBlacklist()} will supercede (have priority over) values
+	 * {@link #chainBlacklist()} will supercede (have priority over) values
-     * here.
+	 * here.
-     * </p>
+	 * </p>
-     * <p>
+	 * <p>
-     * If the parameter annotated with this annotation is not a {@link ReferenceParam},
+	 * If the parameter annotated with this annotation is not a {@link ReferenceParam},
-     * this value must not be populated.
+	 * this value must not be populated.
-     * </p>
+	 * </p>
-     */
+	 */
-	String[] chainWhitelist() default {OptionalParam.ALLOW_CHAIN_ANY};
+	String[] chainWhitelist() default { OptionalParam.ALLOW_CHAIN_ANY };
 
 	/**
 	 * For composite parameters ({@link CompositeParam}) this parameter may be used to indicate the parameter type(s) which may be referenced by this param.

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/MethodUtil.java

@@ -407,6 +407,8 @@ public class MethodUtil {
 						parameter.setType(theContext, parameterType, innerCollectionType, outerCollectionType);
 						MethodUtil.extractDescription(parameter, annotations);
 						param = parameter;
+					} else if (nextAnnotation instanceof RawParam) {
+						param = new RawParamsParmeter(parameters);
 					} else if (nextAnnotation instanceof IncludeParam) {
 						Class<? extends Collection<Include>> instantiableCollectionType;
 						Class<?> specType;

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/RawParamsParmeter.java

@@ -0,0 +1,74 @@
+package ca.uhn.fhir.rest.method;
+
+import java.lang.reflect.Method;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.annotation.RawParam;
+import ca.uhn.fhir.rest.method.SearchMethodBinding.QualifierDetails;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+
+public class RawParamsParmeter implements IParameter {
+
+	private final List<IParameter> myAllMethodParameters;
+
+	public RawParamsParmeter(List<IParameter> theParameters) {
+		myAllMethodParameters = theParameters;
+	}
+
+	@Override
+	public void translateClientArgumentIntoQueryArgument(FhirContext theContext, Object theSourceClientArgument, Map<String, List<String>> theTargetQueryArguments, IBaseResource theTargetResource)
+			throws InternalErrorException {
+		// not supported on client for now
+	}
+
+	@Override
+	public Object translateQueryParametersIntoServerArgument(RequestDetails theRequest, BaseMethodBinding<?> theMethodBinding) throws InternalErrorException, InvalidRequestException {
+		HashMap<String, List<String>> retVal = null;
+
+		for (String nextName : theRequest.getParameters().keySet()) {
+			if (nextName.startsWith("_")) {
+				continue;
+			}
+			
+			QualifierDetails qualifiers = SearchMethodBinding.extractQualifiersFromParameterName(nextName);
+			
+			boolean alreadyCaptured = false;
+			for (IParameter nextParameter : myAllMethodParameters) {
+				if (nextParameter instanceof SearchParameter) {
+					SearchParameter nextSearchParam = (SearchParameter)nextParameter;
+					if (nextSearchParam.getName().equals(qualifiers.getParamName())) {
+						if (qualifiers.passes(nextSearchParam.getQualifierWhitelist(), nextSearchParam.getQualifierBlacklist())) {
+							alreadyCaptured = true;
+							break;
+						}
+					}
+				}
+			}
+			
+			if (!alreadyCaptured) {
+				if (retVal == null) {
+					retVal = new HashMap<String, List<String>>();
+				}
+				retVal.put(nextName, Arrays.asList(theRequest.getParameters().get(nextName)));
+			}
+			
+		}
+		
+		return retVal;
+	}
+
+	@Override
+	public void initializeTypes(Method theMethod, Class<? extends Collection<?>> theOuterCollectionType, Class<? extends Collection<?>> theInnerCollectionType, Class<?> theParameterType) {
+		Validate.isTrue(theParameterType.equals(Map.class), "Parameter with @" + RawParam.class + " must be of type Map<String, List<String>>");
+	} 
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/SearchMethodBinding.java

@@ -130,11 +130,7 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 
 	@Override
 	public ReturnTypeEnum getReturnType() {
-//		if (getContext().getVersion().getVersion() == FhirVersionEnum.DSTU1) {
 			return ReturnTypeEnum.BUNDLE;
-//		} else {
-//			return ReturnTypeEnum.RESOURCE;
-//		}
 	}
 
 	@Override
@@ -406,14 +402,27 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 			if (dotIdx < colonIdx) {
 				retVal.setDotQualifier(theParamName.substring(dotIdx, colonIdx));
 				retVal.setColonQualifier(theParamName.substring(colonIdx));
+				retVal.setParamName(theParamName.substring(0, dotIdx));
+				retVal.setWholeQualifier(theParamName.substring(dotIdx));
 			} else {
 				retVal.setColonQualifier(theParamName.substring(colonIdx, dotIdx));
 				retVal.setDotQualifier(theParamName.substring(dotIdx));
+				retVal.setParamName(theParamName.substring(0, colonIdx));
+				retVal.setWholeQualifier(theParamName.substring(colonIdx));
 			}
 		} else if (dotIdx != -1) {
 			retVal.setDotQualifier(theParamName.substring(dotIdx));
+			retVal.setParamName(theParamName.substring(0, dotIdx));
+			retVal.setWholeQualifier(theParamName.substring(dotIdx));
 		} else if (colonIdx != -1) {
 			retVal.setColonQualifier(theParamName.substring(colonIdx));
+			retVal.setParamName(theParamName.substring(0, colonIdx));
+			retVal.setWholeQualifier(theParamName.substring(colonIdx));
+		} else {
+			retVal.setParamName(theParamName);
+			retVal.setColonQualifier(null);
+			retVal.setDotQualifier(null);
+			retVal.setWholeQualifier(null);
 		}
 
 		return retVal;
@@ -423,6 +432,8 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 
 		private String myColonQualifier;
 		private String myDotQualifier;
+		private String myParamName;
+		private String myWholeQualifier;
 
 		public boolean passes(Set<String> theQualifierWhitelist, Set<String> theQualifierBlacklist) {
 			if (theQualifierWhitelist != null) {
@@ -468,6 +479,14 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 			return true;
 		}
 
+		public void setParamName(String theParamName) {
+			myParamName = theParamName;
+		}
+
+		public String getParamName() {
+			return myParamName;
+		}
+
 		public void setColonQualifier(String theColonQualifier) {
 			myColonQualifier = theColonQualifier;
 		}
@@ -476,6 +495,14 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 			myDotQualifier = theDotQualifier;
 		}
 
+		public String getWholeQualifier() {
+			return myWholeQualifier;
+		}
+
+		public void setWholeQualifier(String theWholeQualifier) {
+			myWholeQualifier = theWholeQualifier;
+		}
+
 	}
 
 	public static BaseHttpClientInvocation createSearchInvocation(FhirContext theContext, String theSearchUrl, Map<String, List<String>> theParams) {

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -43,11 +43,9 @@ ca.uhn.fhir.rest.param.ResourceParameter.noContentTypeInRequest=No Content-Type
 ca.uhn.fhir.rest.param.ResourceParameter.failedToParseRequest=Failed to parse request body as {0} resource. Error was: {1} 
 
 ca.uhn.fhir.parser.ParserState.wrongResourceTypeFound=Incorrect resource type found, expected "{0}" but found "{1}"
-
 ca.uhn.fhir.rest.server.RestfulServer.getPagesNonHttpGet=Requests for _getpages must use HTTP GET
 ca.uhn.fhir.rest.server.RestfulServer.unknownMethod=Invalid request: The FHIR endpoint on this server does not know how to handle {0} operation[{1}] with parameters [{2}]
 ca.uhn.fhir.rest.server.RestfulServer.rootRequest=This is the base URL of FHIR server. Unable to handle this request, as it does not contain a resource type or operation name.
-
 ca.uhn.fhir.validation.ValidationContext.unableToDetermineEncoding=Unable to determine encoding (e.g. XML / JSON) on validation input. Is this a valid FHIR resource body? 
 ca.uhn.fhir.validation.FhirValidator.noPhlocWarningOnStartup=Phloc-schematron library not found on classpath, will not attempt to perform schematron validation
 ca.uhn.fhir.validation.FhirValidator.noPhlocError=Phloc-schematron library not found on classpath, can not enable perform schematron validation
@@ -81,6 +79,7 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.unableToDeleteNotFound=Unable to fin
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulCreate=Successfully created resource "{0}" in {1}ms
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulUpdate=Successfully updated resource "{0}" in {1}ms
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulDeletes=Successfully deleted {0} resource(s) in {1}ms
+ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidSearchParameter=Unknown search parameter "{0}". Value search parameters for this search are: {1}
 
 ca.uhn.fhir.jpa.dao.SearchBuilder.invalidQuantityPrefix=Unable to handle quantity prefix "{0}" for value: {1}
 ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number prefix "{0}" for value: {1}

hapi-fhir-client-okhttp/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

hapi-fhir-jacoco/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

hapi-fhir-jaxrsserver-base/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

hapi-fhir-jaxrsserver-example/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu1Config.java

@@ -10,7 +10,7 @@ package ca.uhn.fhir.jpa.config;
  * 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
+ * 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,
@@ -29,7 +29,9 @@ import org.springframework.context.annotation.Lazy;
 import org.springframework.context.annotation.Primary;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.dao.SearchParamExtractorDstu1;
+import ca.uhn.fhir.jpa.dao.SearchParamRegistryDstu1;
 import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu1;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.model.api.IResource;
@@ -39,9 +41,10 @@ import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 public class BaseDstu1Config extends BaseConfig {
 	private static FhirContext ourFhirContextDstu1;
 
-	@Bean(autowire = Autowire.BY_TYPE)
+	@Bean
-	public IHapiTerminologySvc terminologyService() {
+	@Primary
-		return new HapiTerminologySvcDstu1();
+	public FhirContext defaultFhirContext() {
+		return fhirContextDstu1();
 	}
 
 	@Bean(name = "myFhirContextDstu1")
@@ -53,19 +56,22 @@ public class BaseDstu1Config extends BaseConfig {
 		return ourFhirContextDstu1;
 	}
 
-
-	@Bean
-	@Primary
-	public FhirContext defaultFhirContext() {
-		return fhirContextDstu1();
-	}
-
 	@Bean(name = "mySystemDaoDstu1", autowire = Autowire.BY_NAME)
 	public ca.uhn.fhir.jpa.dao.IFhirSystemDao<List<IResource>, MetaDt> fhirSystemDaoDstu1() {
 		ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu1 retVal = new ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu1();
 		return retVal;
 	}
 
+	@Bean(autowire = Autowire.BY_TYPE)
+	public SearchParamExtractorDstu1 searchParamExtractor() {
+		return new SearchParamExtractorDstu1();
+	}
+
+	@Bean
+	public ISearchParamRegistry searchParamRegistry() {
+		return new SearchParamRegistryDstu1();
+	}
+
 	@Bean(name = "mySystemProviderDstu1")
 	public ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1 systemDaoDstu1() {
 		ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1 retVal = new ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1();
@@ -73,9 +79,9 @@ public class BaseDstu1Config extends BaseConfig {
 		return retVal;
 	}
 
-	@Bean(autowire=Autowire.BY_TYPE)
+	@Bean(autowire = Autowire.BY_TYPE)
-	public SearchParamExtractorDstu1 searchParamExtractor() {
+	public IHapiTerminologySvc terminologyService() {
-		return new SearchParamExtractorDstu1();
+		return new HapiTerminologySvcDstu1();
 	}
-	
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java

@@ -31,7 +31,9 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
+import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.dao.SearchParamExtractorDstu2;
+import ca.uhn.fhir.jpa.dao.SearchParamRegistryDstu2;
 import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu2;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
@@ -84,6 +86,11 @@ public class BaseDstu2Config extends BaseConfig {
 		return new SearchParamExtractorDstu2();
 	}
 
+	@Bean
+	public ISearchParamRegistry searchParamRegistry() {
+		return new SearchParamRegistryDstu2();
+	}
+
 	@Bean(name = "mySystemDaoDstu2", autowire = Autowire.BY_NAME)
 	public IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDaoDstu2() {
 		ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu2 retVal = new ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu2();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java

@@ -14,7 +14,7 @@ import org.hl7.fhir.dstu3.validation.IResourceValidator.BestPracticeWarningLevel
  * 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
+ * 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,
@@ -37,7 +37,9 @@ import ca.uhn.fhir.jpa.config.BaseConfig;
 import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
+import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.dao.dstu3.SearchParamExtractorDstu3;
+import ca.uhn.fhir.jpa.dao.dstu3.SearchParamRegistryDstu3;
 import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
 import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu3;
 import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
@@ -50,25 +52,15 @@ import ca.uhn.fhir.validation.IValidatorModule;
 @EnableTransactionManagement
 public class BaseDstu3Config extends BaseConfig {
 
-	@Bean(autowire = Autowire.BY_TYPE)
-	public IHapiTerminologySvcDstu3 terminologyService() {
-		return new HapiTerminologySvcDstu3();
-	}
-	
-	@Bean(autowire = Autowire.BY_TYPE)
-	public IHapiTerminologyLoaderSvc terminologyLoaderService() {
-		return new TerminologyLoaderSvc();
-	}
-
 	@Bean
 	@Primary
 	public FhirContext fhirContextDstu3() {
 		FhirContext retVal = FhirContext.forDstu3();
-		
+
 		// Don't strip versions in some places
 		ParserOptions parserOptions = retVal.getParserOptions();
 		parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
-		
+
 		return retVal;
 	}
 
@@ -93,6 +85,16 @@ public class BaseDstu3Config extends BaseConfig {
 		return searchDao;
 	}
 
+	@Bean(autowire = Autowire.BY_TYPE)
+	public SearchParamExtractorDstu3 searchParamExtractor() {
+		return new SearchParamExtractorDstu3();
+	}
+
+	@Bean
+	public ISearchParamRegistry searchParamRegistry() {
+		return new SearchParamRegistryDstu3();
+	}
+
 	@Bean(name = "mySystemDaoDstu3", autowire = Autowire.BY_NAME)
 	public IFhirSystemDao<org.hl7.fhir.dstu3.model.Bundle, org.hl7.fhir.dstu3.model.Meta> systemDaoDstu3() {
 		ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3 retVal = new ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3();
@@ -107,23 +109,27 @@ public class BaseDstu3Config extends BaseConfig {
 		return retVal;
 	}
 
+	@Bean(autowire = Autowire.BY_TYPE)
+	public IHapiTerminologyLoaderSvc terminologyLoaderService() {
+		return new TerminologyLoaderSvc();
+	}
+
+	@Bean(autowire = Autowire.BY_TYPE)
+	public IHapiTerminologySvcDstu3 terminologyService() {
+		return new HapiTerminologySvcDstu3();
+	}
+
+	@Bean(autowire = Autowire.BY_TYPE)
+	public TerminologyUploaderProviderDstu3 terminologyUploaderProvider() {
+		TerminologyUploaderProviderDstu3 retVal = new TerminologyUploaderProviderDstu3();
+		retVal.setContext(fhirContextDstu3());
+		return retVal;
+	}
+
 	@Primary
 	@Bean(autowire = Autowire.BY_NAME, name = "myJpaValidationSupportChainDstu3")
 	public IValidationSupport validationSupportChainDstu3() {
 		return new JpaValidationSupportChainDstu3();
 	}
 
-	@Bean(autowire = Autowire.BY_TYPE)
-	public SearchParamExtractorDstu3 searchParamExtractor() {
-		return new SearchParamExtractorDstu3();
-	}
-
-	@Bean(autowire=Autowire.BY_TYPE)
-	public TerminologyUploaderProviderDstu3 terminologyUploaderProvider() {
-		TerminologyUploaderProviderDstu3 retVal = new TerminologyUploaderProviderDstu3();
-		retVal.setContext(fhirContextDstu3());
-		return retVal;
-	}
-	
-
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -130,7 +130,13 @@ import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.method.MethodUtil;
 import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
-import ca.uhn.fhir.rest.param.*;
+import ca.uhn.fhir.rest.param.DateRangeParam;
+import ca.uhn.fhir.rest.param.StringAndListParam;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.TokenAndListParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.UriAndListParam;
+import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.IBundleProvider;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -148,16 +154,17 @@ import ca.uhn.fhir.util.OperationOutcomeUtil;
 
 public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
-	private static final String PROCESSING_SUB_REQUEST = "BaseHapiFhirDao.processingSubRequest";
 	public static final long INDEX_STATUS_INDEXED = Long.valueOf(1L);
+
 	public static final long INDEX_STATUS_INDEXING_FAILED = Long.valueOf(2L);
 	public static final String NS_JPA_PROFILE = "https://github.com/jamesagnew/hapi-fhir/ns/jpa/profile";
 	public static final String OO_SEVERITY_ERROR = "error";
 	public static final String OO_SEVERITY_INFO = "information";
 	public static final String OO_SEVERITY_WARN = "warning";
-
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirDao.class);
 	private static final Map<FhirVersionEnum, FhirContext> ourRetrievalContexts = new HashMap<FhirVersionEnum, FhirContext>();
+
+	private static final String PROCESSING_SUB_REQUEST = "BaseHapiFhirDao.processingSubRequest";
 	/**
 	 * These are parameters which are supported by {@link BaseHapiFhirResourceDao#searchForIds(Map)}
 	 */
@@ -166,8 +173,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	 * These are parameters which are supported by {@link BaseHapiFhirResourceDao#searchForIds(Map)}
 	 */
 	static final Map<String, Class<? extends IQueryParameterType>> RESOURCE_META_PARAMS;
-
 	public static final String UCUM_NS = "http://unitsofmeasure.org";
+
 	static {
 		Map<String, Class<? extends IQueryParameterType>> resourceMetaParams = new HashMap<String, Class<? extends IQueryParameterType>>();
 		Map<String, Class<? extends IQueryParameterAnd<?>>> resourceMetaAndParams = new HashMap<String, Class<? extends IQueryParameterAnd<?>>>();
@@ -184,7 +191,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		RESOURCE_META_PARAMS = Collections.unmodifiableMap(resourceMetaParams);
 		RESOURCE_META_AND_PARAMS = Collections.unmodifiableMap(resourceMetaAndParams);
 	}
-
 	@Autowired(required = true)
 	private DaoConfig myConfig;
 
@@ -213,9 +219,18 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	@Autowired
 	private ISearchParamExtractor mySearchParamExtractor;
 
+	@Autowired
+	private ISearchParamRegistry mySearchParamRegistry;
+
 	@Autowired
 	private ISearchResultDao mySearchResultDao;
 
+	protected void clearRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
+		if (theRequestDetails != null) {
+			theRequestDetails.getUserData().remove(PROCESSING_SUB_REQUEST);
+		}
+	}
+
 	protected void createForcedIdIfNeeded(ResourceTable theEntity, IIdType theId) {
 		if (theId.isEmpty() == false && theId.hasIdPart()) {
 			if (isValidPid(theId)) {
@@ -530,6 +545,17 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return (IFhirResourceDao<R>) myResourceTypeToDao.get(theType);
 	}
 
+	@Override
+	public RuntimeSearchParam getSearchParamByName(RuntimeResourceDefinition theResourceDef, String theParamName) {
+		Map<String, RuntimeSearchParam> params = mySearchParamRegistry.getActiveSearchParams(theResourceDef.getName());
+		return params.get(theParamName);
+	}
+
+	@Override
+	public Collection<RuntimeSearchParam> getSearchParamsByResourceType(RuntimeResourceDefinition theResourceDef) {
+		return mySearchParamRegistry.getActiveSearchParams(theResourceDef.getName()).values();
+	}
+
 	protected TagDefinition getTag(TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) {
 		CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
 		CriteriaQuery<TagDefinition> cq = builder.createQuery(TagDefinition.class);
@@ -646,6 +672,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		theProvider.setSearchResultDao(mySearchResultDao);
 	}
 
+	protected void markRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
+		if (theRequestDetails != null) {
+			theRequestDetails.getUserData().put(PROCESSING_SUB_REQUEST, Boolean.TRUE);
+		}
+	}
+	
 	protected void notifyInterceptors(RestOperationTypeEnum theOperationType, ActionRequestDetails theRequestDetails) {
 		if (theRequestDetails.getId() != null && theRequestDetails.getId().hasResourceType() && isNotBlank(theRequestDetails.getResourceType())) {
 			if (theRequestDetails.getId().getResourceType().equals(theRequestDetails.getResourceType()) == false) {
@@ -666,18 +698,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		}
 	}
 
-	protected void markRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
-		if (theRequestDetails != null) {
-			theRequestDetails.getUserData().put(PROCESSING_SUB_REQUEST, Boolean.TRUE);
-		}
-	}
-
-	protected void clearRequestAsProcessingSubRequest(ServletRequestDetails theRequestDetails) {
-		if (theRequestDetails != null) {
-			theRequestDetails.getUserData().remove(PROCESSING_SUB_REQUEST);
-		}
-	}
-	
 	public String parseContentTextIntoWords(IBaseResource theResource) {
 		StringBuilder retVal = new StringBuilder();
 		@SuppressWarnings("rawtypes")
@@ -914,7 +934,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	}
 
 	/**
-	 * Subclasses may override to provide behaviour. Called when a resource has been inserved into the database for the first time.
+	 * Subclasses may override to provide behaviour. Called when a resource has been inserted into the database for the first time.
 	 * 
 	 * @param theEntity
 	 *           The entity being updated (Do not modify the entity! Undefined behaviour will occur!)
@@ -928,7 +948,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	}
 
 	/**
-	 * Subclasses may override to provide behaviour. Called when a resource has been inserved into the database for the first time.
+	 * Subclasses may override to provide behaviour. Called when a pre-existing resource has been updated in the database
 	 * 
 	 * @param theEntity
 	 *           The resource
@@ -943,7 +963,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	public <R extends IBaseResource> Set<Long> processMatchUrl(String theMatchUrl, Class<R> theResourceType) {
 		RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(theResourceType);
 
-		SearchParameterMap paramMap = translateMatchUrl(myContext, theMatchUrl, resourceDef);
+		SearchParameterMap paramMap = translateMatchUrl(this, myContext, theMatchUrl, resourceDef);
 		paramMap.setPersistResults(false);
 
 		if (paramMap.isEmpty() && paramMap.getLastUpdated() == null) {
@@ -962,24 +982,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		throw new NotImplementedException("");
 	}
 
-	// protected MetaDt toMetaDt(Collection<TagDefinition> tagDefinitions) {
-	// MetaDt retVal = new MetaDt();
-	// for (TagDefinition next : tagDefinitions) {
-	// switch (next.getTagType()) {
-	// case PROFILE:
-	// retVal.addProfile(next.getCode());
-	// break;
-	// case SECURITY_LABEL:
-	// retVal.addSecurity().setSystem(next.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
-	// break;
-	// case TAG:
-	// retVal.addTag().setSystem(next.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
-	// break;
-	// }
-	// }
-	// return retVal;
-	// }
-
 	public void setConfig(DaoConfig theConfig) {
 		myConfig = theConfig;
 	}
@@ -1698,27 +1700,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		}
 	}
 
-	protected static List<NameValuePair> translateMatchUrl(String theMatchUrl) {
+	public static SearchParameterMap translateMatchUrl(IDao theCallingDao, FhirContext theContext, String theMatchUrl, RuntimeResourceDefinition resourceDef) {
-		List<NameValuePair> parameters;
-		String matchUrl = theMatchUrl;
-		int questionMarkIndex = matchUrl.indexOf('?');
-		if (questionMarkIndex != -1) {
-			matchUrl = matchUrl.substring(questionMarkIndex + 1);
-		}
-		matchUrl = matchUrl.replace("|", "%7C");
-		matchUrl = matchUrl.replace("=>=", "=%3E%3D");
-		matchUrl = matchUrl.replace("=<=", "=%3C%3D");
-		matchUrl = matchUrl.replace("=>", "=%3E");
-		matchUrl = matchUrl.replace("=<", "=%3C");
-		if (matchUrl.contains(" ")) {
-			throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - URL is invalid (must not contain spaces)");
-		}
-
-		parameters = URLEncodedUtils.parse((matchUrl), Constants.CHARSET_UTF8, '&');
-		return parameters;
-	}
-
-	public static SearchParameterMap translateMatchUrl(FhirContext theContext, String theMatchUrl, RuntimeResourceDefinition resourceDef) {
 		SearchParameterMap paramMap = new SearchParameterMap();
 		List<NameValuePair> parameters = translateMatchUrl(theMatchUrl);
 
@@ -1788,7 +1770,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			} else if (nextParamName.startsWith("_")) {
 				// ignore these since they aren't search params (e.g. _sort)
 			} else {
-				RuntimeSearchParam paramDef = resourceDef.getSearchParam(nextParamName);
+				RuntimeSearchParam paramDef = theCallingDao.getSearchParamByName(resourceDef, nextParamName);
 				if (paramDef == null) {
 					throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Resource type " + resourceDef.getName() + " does not have a parameter with name: " + nextParamName);
 				}
@@ -1800,6 +1782,26 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return paramMap;
 	}
 
+	protected static List<NameValuePair> translateMatchUrl(String theMatchUrl) {
+		List<NameValuePair> parameters;
+		String matchUrl = theMatchUrl;
+		int questionMarkIndex = matchUrl.indexOf('?');
+		if (questionMarkIndex != -1) {
+			matchUrl = matchUrl.substring(questionMarkIndex + 1);
+		}
+		matchUrl = matchUrl.replace("|", "%7C");
+		matchUrl = matchUrl.replace("=>=", "=%3E%3D");
+		matchUrl = matchUrl.replace("=<=", "=%3C%3D");
+		matchUrl = matchUrl.replace("=>", "=%3E");
+		matchUrl = matchUrl.replace("=<", "=%3C");
+		if (matchUrl.contains(" ")) {
+			throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - URL is invalid (must not contain spaces)");
+		}
+
+		parameters = URLEncodedUtils.parse((matchUrl), Constants.CHARSET_UTF8, '&');
+		return parameters;
+	}
+
 	public static void validateResourceType(BaseHasResource theEntity, String theResourceName) {
 		if (!theResourceName.equals(theEntity.getResourceType())) {
 			throw new ResourceNotFoundException(

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java

@@ -22,15 +22,29 @@ package ca.uhn.fhir.jpa.dao;
 
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
 import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeSet;
 
 import javax.annotation.PostConstruct;
 import javax.persistence.NoResultException;
 import javax.persistence.TypedQuery;
 
 import org.hl7.fhir.dstu3.model.IdType;
-import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseCoding;
+import org.hl7.fhir.instance.model.api.IBaseMetaType;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Required;
 import org.springframework.transaction.PlatformTransactionManager;
@@ -43,22 +57,44 @@ import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
 import ca.uhn.fhir.jpa.dao.data.IResourceIndexedSearchParamUriDao;
+import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.dao.data.ISearchResultDao;
-import ca.uhn.fhir.jpa.entity.*;
+import ca.uhn.fhir.jpa.entity.BaseHasResource;
+import ca.uhn.fhir.jpa.entity.BaseTag;
+import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
+import ca.uhn.fhir.jpa.entity.ResourceLink;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.jpa.entity.TagDefinition;
+import ca.uhn.fhir.jpa.entity.TagTypeEnum;
 import ca.uhn.fhir.jpa.interceptor.IJpaServerInterceptor;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
 import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
-import ca.uhn.fhir.model.api.*;
+import ca.uhn.fhir.model.api.IQueryParameterAnd;
+import ca.uhn.fhir.model.api.IQueryParameterType;
+import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
+import ca.uhn.fhir.rest.method.MethodUtil;
+import ca.uhn.fhir.rest.method.QualifiedParamList;
 import ca.uhn.fhir.rest.method.RequestDetails;
 import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
+import ca.uhn.fhir.rest.method.SearchMethodBinding;
+import ca.uhn.fhir.rest.method.SearchMethodBinding.QualifierDetails;
 import ca.uhn.fhir.rest.server.IBundleProvider;
-import ca.uhn.fhir.rest.server.exceptions.*;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
 import ca.uhn.fhir.util.FhirTerser;
@@ -74,6 +110,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Autowired
 	private DaoConfig myDaoConfig;
 	@Autowired
+	protected IResourceTableDao myResourceTableDao;
+	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
 	@Autowired
 	private IResourceHistoryTableDao myResourceHistoryTableDao;
@@ -86,6 +124,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Autowired()
 	protected ISearchResultDao mySearchResultDao;
 	private String mySecondaryPrimaryKeyParamName;
+	@Autowired
+	private ISearchParamRegistry mySerarchParamRegistry;
 	@Autowired()
 	protected IHapiTerminologySvc myTerminologySvc;
 
@@ -662,13 +702,37 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return retVal;
 	}
 
+	@Override
+	public DaoMethodOutcome patch(IIdType theId, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails) {
+		ResourceTable entityToUpdate = readEntityLatestVersion(theId);
+		if (theId.hasVersionIdPart()) {
+			if (theId.getVersionIdPartAsLong() != entityToUpdate.getVersion()) {
+				throw new ResourceVersionConflictException("Version " + theId.getVersionIdPart() + " is not the most recent version of this resource, unable to apply patch");
+			}
+		}
+		
+		validateResourceType(entityToUpdate);
+		
+		IBaseResource resourceToUpdate = toResource(entityToUpdate, false);
+		IBaseResource destination;
+		if (thePatchType == PatchTypeEnum.JSON_PATCH) {
+			destination = JsonPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
+		} else {
+			destination = XmlPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
+		}
+		
+		@SuppressWarnings("unchecked")
+		T destinationCasted = (T) destination;
+		return update(destinationCasted, null, true, theRequestDetails);
+	}
+
 	@PostConstruct
 	public void postConstruct() {
 		RuntimeResourceDefinition def = getContext().getResourceDefinition(myResourceType);
 		myResourceName = def.getName();
 
 		if (mySecondaryPrimaryKeyParamName != null) {
-			RuntimeSearchParam sp = def.getSearchParam(mySecondaryPrimaryKeyParamName);
+			RuntimeSearchParam sp = getSearchParamByName(def, mySecondaryPrimaryKeyParamName);
 			if (sp == null) {
 				throw new ConfigurationException("Unknown search param on resource[" + myResourceName + "] for secondary key[" + mySecondaryPrimaryKeyParamName + "]");
 			}
@@ -870,7 +934,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		notifyInterceptors(RestOperationTypeEnum.SEARCH_TYPE, requestDetails);
 
 		SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this, myResourceIndexedSearchParamUriDao, myForcedIdDao,
-				myTerminologySvc);
+				myTerminologySvc, mySerarchParamRegistry);
 		builder.setType(getResourceType(), getResourceName());
 		return builder.search(theParams);
 	}
@@ -899,7 +963,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		theParams.setPersistResults(false);
 
 		SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this, myResourceIndexedSearchParamUriDao, myForcedIdDao,
-				myTerminologySvc);
+				myTerminologySvc, mySerarchParamRegistry);
 		builder.setType(getResourceType(), getResourceName());
 		builder.search(theParams);
 		return builder.doGetPids();
@@ -985,6 +1049,39 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return retVal;
 	}
 
+	@Override
+	public void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget) {
+		if (theSource == null || theSource.isEmpty()) {
+			return;
+		}
+		
+		Map<String, RuntimeSearchParam> searchParams = mySerarchParamRegistry.getActiveSearchParams(getResourceName());
+		
+		Set<String> paramNames = theSource.keySet();
+		for (String nextParamName : paramNames) {
+			QualifierDetails qualifiedParamName = SearchMethodBinding.extractQualifiersFromParameterName(nextParamName);
+			RuntimeSearchParam param = searchParams.get(qualifiedParamName.getParamName());
+			if (param == null) {
+				String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidSearchParameter", qualifiedParamName.getParamName(), new TreeSet<String>(searchParams.keySet()));
+				throw new InvalidRequestException(msg);
+			}
+
+			// Should not be null since the check above would have caught it
+			RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(myResourceName);
+			RuntimeSearchParam paramDef = getSearchParamByName(resourceDef, qualifiedParamName.getParamName());
+
+			for (String nextValue : theSource.get(nextParamName)) {
+				if (isNotBlank(nextValue)) {
+					QualifiedParamList qualifiedParam = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifiedParamName.getWholeQualifier(), nextValue);
+					List<QualifiedParamList> paramList = Collections.singletonList(qualifiedParam);
+					IQueryParameterAnd<?> parsedParam = MethodUtil.parseQueryParams(getContext(), paramDef, nextParamName, paramList);
+					theTarget.add(qualifiedParamName.getParamName(), parsedParam);
+				}
+			}
+			
+		}
+	}
+
 	@Override
 	public DaoMethodOutcome update(T theResource) {
 		return update(theResource, null, null);
@@ -1075,30 +1172,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		ourLog.info(msg);
 		return outcome;
 	}
-
-	@Override
-	public DaoMethodOutcome patch(IIdType theId, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails) {
-		ResourceTable entityToUpdate = readEntityLatestVersion(theId);
-		if (theId.hasVersionIdPart()) {
-			if (theId.getVersionIdPartAsLong() != entityToUpdate.getVersion()) {
-				throw new ResourceVersionConflictException("Version " + theId.getVersionIdPart() + " is not the most recent version of this resource, unable to apply patch");
-			}
-		}
-		
-		validateResourceType(entityToUpdate);
-		
-		IBaseResource resourceToUpdate = toResource(entityToUpdate, false);
-		IBaseResource destination;
-		if (thePatchType == PatchTypeEnum.JSON_PATCH) {
-			destination = JsonPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
-		} else {
-			destination = XmlPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
-		}
-		
-		@SuppressWarnings("unchecked")
-		T destinationCasted = (T) destination;
-		return update(destinationCasted, null, true, theRequestDetails);
-	}
 	
 	
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseSearchParamExtractor.java

@@ -21,9 +21,12 @@ package ca.uhn.fhir.jpa.dao;
  */
 
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
 import java.util.regex.Pattern;
 
+import org.apache.commons.lang3.ObjectUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -37,17 +40,37 @@ import ca.uhn.fhir.util.FhirTerser;
 public abstract class BaseSearchParamExtractor implements ISearchParamExtractor {
 	
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseSearchParamExtractor.class);
-	protected static final Pattern SPLIT = Pattern.compile("\\||( or )");
+	public static final Pattern SPLIT = Pattern.compile("\\||( or )");
 
 	@Autowired
 	private FhirContext myContext;
 	
+	@Autowired
+	private ISearchParamRegistry mySearchParamRegistry;
+	
 	public BaseSearchParamExtractor() {
 		super();
 	}
-	
+
-	public BaseSearchParamExtractor(FhirContext theCtx) {
+	public BaseSearchParamExtractor(FhirContext theCtx, ISearchParamRegistry theSearchParamRegistry) {
 		myContext = theCtx;
+		mySearchParamRegistry = theSearchParamRegistry;
+	}
+	
+	@Override
+	public List<PathAndRef> extractResourceLinks(IBaseResource theResource, RuntimeSearchParam theNextSpDef) {
+		List<PathAndRef> refs = new ArrayList<PathAndRef>();
+		String[] nextPathsSplit = theNextSpDef.getPath().split("\\|");
+		for (String nextPath : nextPathsSplit) {
+			nextPath = nextPath.trim();
+			for (Object nextObject : extractValues(nextPath, theResource)) {
+				if (nextObject == null) {
+					continue;
+				}
+				refs.add(new PathAndRef(nextPath, nextObject));
+			}
+		}
+		return refs;
 	}
 
 	protected List<Object> extractValues(String thePaths, IBaseResource theResource) {
@@ -70,26 +93,18 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
 		return myContext;
 	}
 
+	protected Collection<RuntimeSearchParam> getSearchParams(IBaseResource theResource) {
+		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> retVal = mySearchParamRegistry.getActiveSearchParams(def.getName()).values();
+		List<RuntimeSearchParam> defaultList= Collections.emptyList();
+		retVal = ObjectUtils.defaultIfNull(retVal, defaultList);
+		return retVal;
+	}
+
 	@VisibleForTesting
 	void setContextForUnitTest(FhirContext theContext) {
 		myContext = theContext;
 	}
 
-	@Override
-	public List<PathAndRef> extractResourceLinks(IBaseResource theResource, RuntimeSearchParam theNextSpDef) {
-		List<PathAndRef> refs = new ArrayList<PathAndRef>();
-		String[] nextPathsSplit = theNextSpDef.getPath().split("\\|");
-		for (String nextPath : nextPathsSplit) {
-			nextPath = nextPath.trim();
-			for (Object nextObject : extractValues(nextPath, theResource)) {
-				if (nextObject == null) {
-					continue;
-				}
-				refs.add(new PathAndRef(nextPath, nextObject));
-			}
-		}
-		return refs;
-	}
-
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseSearchParamRegistry.java

@@ -0,0 +1,77 @@
+package ca.uhn.fhir.jpa.dao;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.annotation.PostConstruct;
+
+import org.apache.commons.lang3.ObjectUtils;
+import org.apache.commons.lang3.Validate;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
+
+public abstract class BaseSearchParamRegistry implements ISearchParamRegistry {
+
+	private static final Map<String, RuntimeSearchParam> EMPTY_SP_MAP = Collections.emptyMap();
+
+	private Map<String, Map<String, RuntimeSearchParam>> myBuiltInSearchParams;
+
+	@Autowired
+	private FhirContext myCtx;
+
+	@Autowired
+	private Collection<IFhirResourceDao<?>> myDaos;
+
+	public BaseSearchParamRegistry() {
+		super();
+	}
+
+	@Override
+	public void forceRefresh() {
+		// nothing by default
+	}
+
+	public Map<String, Map<String, RuntimeSearchParam>> getBuiltInSearchParams() {
+		return myBuiltInSearchParams;
+	}
+
+	@Override
+	public Map<String,RuntimeSearchParam> getActiveSearchParams(String theResourceName) {
+		Validate.notBlank(theResourceName, "theResourceName must not be blank or null");
+
+		return myBuiltInSearchParams.get(theResourceName);
+	}
+
+	@PostConstruct
+	public void postConstruct() {
+		Map<String, Map<String, RuntimeSearchParam>> resourceNameToSearchParams = new HashMap<String, Map<String,RuntimeSearchParam>>();
+
+		for (IFhirResourceDao<?> nextDao : myDaos) {
+			RuntimeResourceDefinition nextResDef = myCtx.getResourceDefinition(nextDao.getResourceType());
+			String nextResourceName = nextResDef.getName();
+			HashMap<String, RuntimeSearchParam> nameToParam = new HashMap<String, RuntimeSearchParam>();
+			resourceNameToSearchParams.put(nextResourceName, nameToParam);
+			
+			for (RuntimeSearchParam nextSp : nextResDef.getSearchParams()) {
+				nameToParam.put(nextSp.getName(), nextSp);
+			}
+		}
+
+		myBuiltInSearchParams = Collections.unmodifiableMap(resourceNameToSearchParams);
+	}
+
+	@Override
+	public Collection<RuntimeSearchParam> getAllSearchParams(String theResourceName) {
+		Validate.notBlank(theResourceName, "theResourceName must not be null or blank");
+		
+		Map<String, RuntimeSearchParam> map = myBuiltInSearchParams.get(theResourceName);
+		map = ObjectUtils.defaultIfNull(map, EMPTY_SP_MAP);
+		return Collections.unmodifiableCollection(map.values());
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java

@@ -16,7 +16,7 @@ import org.apache.commons.lang3.time.DateUtils;
  * 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
+ * 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,
@@ -35,26 +35,28 @@ public class DaoConfig {
 	// ***
 	// update setter javadoc if default changes
 	// ***
-	private boolean myAllowExternalReferences = false; 
+	private boolean myAllowExternalReferences = false;
 
 	// ***
 	// update setter javadoc if default changes
 	// ***
-	private boolean myAllowInlineMatchUrlReferences = false; 
+	private boolean myAllowInlineMatchUrlReferences = false;
 
 	private boolean myAllowMultipleDelete;
+	private boolean myDefaultSearchParamsCanBeOverridden = false;
 	// ***
 	// update setter javadoc if default changes
 	// ***
 	private int myDeferIndexingForCodesystemsOfSize = 2000;
 	private boolean myDeleteStaleSearches = true;
+
 	// ***
 	// update setter javadoc if default changes
 	// ***
 	private long myExpireSearchResultsAfterMillis = DateUtils.MILLIS_PER_HOUR;
-	
+
 	private int myHardTagListLimit = 1000;
-	
+
 	private int myIncludeLimit = 2000;
 
 	// ***
@@ -63,19 +65,19 @@ public class DaoConfig {
 	private boolean myIndexContainedResources = true;
 
 	private List<IServerInterceptor> myInterceptors;
-	
 	// ***
 	// update setter javadoc if default changes
 	// ***
 	private int myMaximumExpansionSize = 5000;
+
 	private ResourceEncodingEnum myResourceEncoding = ResourceEncodingEnum.JSONC;
 
 	private boolean mySchedulingDisabled;
 
 	private boolean mySubscriptionEnabled;
-	
+
 	private long mySubscriptionPollDelay = 1000;
-	
+
 	private Long mySubscriptionPurgeInactiveAfterMillis;
 
 	private Set<String> myTreatBaseUrlsAsLocal = new HashSet<String>();
@@ -91,42 +93,44 @@ public class DaoConfig {
 	public int getDeferIndexingForCodesystemsOfSize() {
 		return myDeferIndexingForCodesystemsOfSize;
 	}
+
 	/**
-	 * Sets the number of milliseconds that search results for a given client search 
+	 * Sets the number of milliseconds that search results for a given client search
 	 * should be preserved before being purged from the database.
 	 * <p>
-	 * Search results are stored in the database so that they can be paged over multiple 
+	 * Search results are stored in the database so that they can be paged over multiple
 	 * requests. After this
 	 * number of milliseconds, they will be deleted from the database, and any paging links
-	 * (next/prev links in search response bundles) will become invalid. Defaults to 1 hour. 
+	 * (next/prev links in search response bundles) will become invalid. Defaults to 1 hour.
 	 * </p>
 	 * <p>
+	 * 
 	 * @see To disable this feature entirely, see {@link #setExpireSearchResults(boolean)}
-	 * </p>
+	 *      </p>
 	 * 
 	 * @since 1.5
 	 */
 	public long getExpireSearchResultsAfterMillis() {
 		return myExpireSearchResultsAfterMillis;
 	}
-	
+
 	/**
 	 * Gets the maximum number of results to return in a GetTags query (DSTU1 only)
 	 */
 	public int getHardTagListLimit() {
 		return myHardTagListLimit;
 	}
-	
+
 	public int getIncludeLimit() {
 		return myIncludeLimit;
 	}
-	
+
 	/**
 	 * Returns the interceptors which will be notified of operations.
 	 * 
 	 * @see #setInterceptors(List)
 	 * @deprecated As of 2.2 this method is deprecated. There is no good reason to register an interceptor
-	 * with the DaoConfig and not with the server via {@link RestfulServer#registerInterceptor(IServerInterceptor)}
+	 *             with the DaoConfig and not with the server via {@link RestfulServer#registerInterceptor(IServerInterceptor)}
 	 */
 	@Deprecated
 	public List<IServerInterceptor> getInterceptors() {
@@ -135,22 +139,26 @@ public class DaoConfig {
 		}
 		return myInterceptors;
 	}
-	
+
 	/**
 	 * See {@link #setMaximumExpansionSize(int)}
 	 */
 	public int getMaximumExpansionSize() {
 		return myMaximumExpansionSize;
 	}
+
 	public ResourceEncodingEnum getResourceEncoding() {
 		return myResourceEncoding;
 	}
+
 	public long getSubscriptionPollDelay() {
 		return mySubscriptionPollDelay;
 	}
+
 	public Long getSubscriptionPurgeInactiveAfterMillis() {
 		return mySubscriptionPurgeInactiveAfterMillis;
 	}
+
 	/**
 	 * This setting may be used to advise the server that any references found in
 	 * resources that have any of the base URLs given here will be replaced with
@@ -165,6 +173,7 @@ public class DaoConfig {
 	public Set<String> getTreatBaseUrlsAsLocal() {
 		return myTreatBaseUrlsAsLocal;
 	}
+
 	/**
 	 * If set to <code>true</code> (default is <code>false</code>) the server will allow
 	 * resources to have references to external servers. For example if this server is
@@ -179,7 +188,7 @@ public class DaoConfig {
 	 * <p>
 	 * Note that external references will be indexed by the server and may be searched
 	 * (e.g. <code>Patient:organization</code>), but
-	 * chained searches (e.g. <code>Patient:organization.name</code>) will not work across 
+	 * chained searches (e.g. <code>Patient:organization.name</code>) will not work across
 	 * these references.
 	 * </p>
 	 * <p>
@@ -193,19 +202,37 @@ public class DaoConfig {
 	public boolean isAllowExternalReferences() {
 		return myAllowExternalReferences;
 	}
+
 	/**
 	 * @see #setAllowInlineMatchUrlReferences(boolean)
 	 */
 	public boolean isAllowInlineMatchUrlReferences() {
 		return myAllowInlineMatchUrlReferences;
 	}
+
 	public boolean isAllowMultipleDelete() {
 		return myAllowMultipleDelete;
 	}
 
 	/**
-	 * If this is set to <code>false</code> (default is <code>true</code>) the stale search deletion 
+	 * If set to {@code true} the default search params (i.e. the search parameters that are
-	 * task will be disabled (meaning that search results will be retained in the database indefinitely). USE WITH CAUTION. 
+	 * defined by the FHIR specification itself) may be overridden by uploading search
+	 * parameters to the server with the same code as the built-in search parameter.
+	 * <p>
+	 * This can be useful if you want to be able to disable or alter
+	 * the behaviour of the default search parameters.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code false}
+	 * </p>
+	 */
+	public boolean isDefaultSearchParamsCanBeOverridden() {
+		return myDefaultSearchParamsCanBeOverridden;
+	}
+
+	/**
+	 * If this is set to <code>false</code> (default is <code>true</code>) the stale search deletion
+	 * task will be disabled (meaning that search results will be retained in the database indefinitely). USE WITH CAUTION.
 	 * <p>
 	 * This feature is useful if you want to define your own process for deleting these (e.g. because
 	 * you are running in a cluster)
@@ -217,7 +244,7 @@ public class DaoConfig {
 
 	/**
 	 * Should contained IDs be indexed the same way that non-contained IDs are (default is
-	 * <code>true</code>) 
+	 * <code>true</code>)
 	 */
 	public boolean isIndexContainedResources() {
 		return myIndexContainedResources;
@@ -248,7 +275,7 @@ public class DaoConfig {
 	 * <p>
 	 * Note that external references will be indexed by the server and may be searched
 	 * (e.g. <code>Patient:organization</code>), but
-	 * chained searches (e.g. <code>Patient:organization.name</code>) will not work across 
+	 * chained searches (e.g. <code>Patient:organization.name</code>) will not work across
 	 * these references.
 	 * </p>
 	 * <p>
@@ -271,6 +298,7 @@ public class DaoConfig {
 	 * <p>
 	 * Default is false for now, as this is an experimental feature.
 	 * </p>
+	 * 
 	 * @since 1.5
 	 */
 	public void setAllowInlineMatchUrlReferences(boolean theAllowInlineMatchUrlReferences) {
@@ -281,6 +309,22 @@ public class DaoConfig {
 		myAllowMultipleDelete = theAllowMultipleDelete;
 	}
 
+	/**
+	 * If set to {@code true} the default search params (i.e. the search parameters that are
+	 * defined by the FHIR specification itself) may be overridden by uploading search
+	 * parameters to the server with the same code as the built-in search parameter.
+	 * <p>
+	 * This can be useful if you want to be able to disable or alter
+	 * the behaviour of the default search parameters.
+	 * </p>
+	 * <p>
+	 * The default value for this setting is {@code false}
+	 * </p>
+	 */
+	public void setDefaultSearchParamsCanBeOverridden(boolean theDefaultSearchParamsCanBeOverridden) {
+		myDefaultSearchParamsCanBeOverridden = theDefaultSearchParamsCanBeOverridden;
+	}
+
 	/**
 	 * When a code system is added that contains more than this number of codes,
 	 * the code system will be indexed later in an incremental process in order to
@@ -294,8 +338,8 @@ public class DaoConfig {
 	}
 
 	/**
-	 * If this is set to <code>false</code> (default is <code>true</code>) the stale search deletion 
+	 * If this is set to <code>false</code> (default is <code>true</code>) the stale search deletion
-	 * task will be disabled (meaning that search results will be retained in the database indefinitely). USE WITH CAUTION. 
+	 * task will be disabled (meaning that search results will be retained in the database indefinitely). USE WITH CAUTION.
 	 * <p>
 	 * This feature is useful if you want to define your own process for deleting these (e.g. because
 	 * you are running in a cluster)
@@ -306,17 +350,18 @@ public class DaoConfig {
 	}
 
 	/**
-	 * Sets the number of milliseconds that search results for a given client search 
+	 * Sets the number of milliseconds that search results for a given client search
 	 * should be preserved before being purged from the database.
 	 * <p>
-	 * Search results are stored in the database so that they can be paged over multiple 
+	 * Search results are stored in the database so that they can be paged over multiple
 	 * requests. After this
 	 * number of milliseconds, they will be deleted from the database, and any paging links
-	 * (next/prev links in search response bundles) will become invalid. Defaults to 1 hour. 
+	 * (next/prev links in search response bundles) will become invalid. Defaults to 1 hour.
 	 * </p>
 	 * <p>
+	 * 
 	 * @see To disable this feature entirely, see {@link #setExpireSearchResults(boolean)}
-	 * </p>
+	 *      </p>
 	 * @since 1.5
 	 */
 	public void setExpireSearchResultsAfterMillis(long theExpireSearchResultsAfterMillis) {
@@ -329,7 +374,7 @@ public class DaoConfig {
 	 * paging provider instead.
 	 * 
 	 * @deprecated This method does not do anything. Configure the page size on your
-	 * paging provider instead. Deprecated in HAPI FHIR 2.3 (Jan 2017) 
+	 *             paging provider instead. Deprecated in HAPI FHIR 2.3 (Jan 2017)
 	 */
 	@Deprecated
 	public void setHardSearchLimit(@SuppressWarnings("unused") int theHardSearchLimit) {
@@ -354,7 +399,7 @@ public class DaoConfig {
 
 	/**
 	 * Should contained IDs be indexed the same way that non-contained IDs are (default is
-	 * <code>true</code>) 
+	 * <code>true</code>)
 	 */
 	public void setIndexContainedResources(boolean theIndexContainedResources) {
 		myIndexContainedResources = theIndexContainedResources;
@@ -362,8 +407,9 @@ public class DaoConfig {
 
 	/**
 	 * This may be used to optionally register server interceptors directly against the DAOs.
+	 * 
 	 * @deprecated As of 2.2 this method is deprecated. There is no good reason to register an interceptor
-	 * with the DaoConfig and not with the server via {@link RestfulServer#registerInterceptor(IServerInterceptor)}
+	 *             with the DaoConfig and not with the server via {@link RestfulServer#registerInterceptor(IServerInterceptor)}
 	 */
 	@Deprecated
 	public void setInterceptors(IServerInterceptor... theInterceptor) {
@@ -375,8 +421,9 @@ public class DaoConfig {
 
 	/**
 	 * This may be used to optionally register server interceptors directly against the DAOs.
+	 * 
 	 * @deprecated As of 2.2 this method is deprecated. There is no good reason to register an interceptor
-	 * with the DaoConfig and not with the server via {@link RestfulServer#registerInterceptor(IServerInterceptor)}
+	 *             with the DaoConfig and not with the server via {@link RestfulServer#registerInterceptor(IServerInterceptor)}
 	 */
 	@Deprecated
 	public void setInterceptors(List<IServerInterceptor> theInterceptors) {
@@ -419,11 +466,11 @@ public class DaoConfig {
 		}
 		mySubscriptionPurgeInactiveAfterMillis = theMillis;
 	}
-	
+
 	public void setSubscriptionPurgeInactiveAfterSeconds(int theSeconds) {
 		setSubscriptionPurgeInactiveAfterMillis(theSeconds * DateUtils.MILLIS_PER_SECOND);
 	}
-	
+
 	/**
 	 * This setting may be used to advise the server that any references found in
 	 * resources that have any of the base URLs given here will be replaced with
@@ -435,8 +482,9 @@ public class DaoConfig {
 	 * convert this reference to <code>Patient/1</code>
 	 * </p>
 	 * 
-	 * @param theTreatBaseUrlsAsLocal The set of base URLs. May be <code>null</code>, which
+	 * @param theTreatBaseUrlsAsLocal
-	 * means no references will be treated as external
+	 *           The set of base URLs. May be <code>null</code>, which
+	 *           means no references will be treated as external
 	 */
 	public void setTreatBaseUrlsAsLocal(Set<String> theTreatBaseUrlsAsLocal) {
 		HashSet<String> treatBaseUrlsAsLocal = new HashSet<String>();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2.java

@@ -79,7 +79,8 @@ public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResou
 			values.addAll(theTerser.getAllPopulatedChildElementsOfType(theResource, BaseResourceReferenceDt.class));
 		} else if (theInclude.getValue().startsWith(theResourceDef.getName() + ":")) {
 			values = new ArrayList<Object>();
-			RuntimeSearchParam sp = theResourceDef.getSearchParam(theInclude.getValue().substring(theInclude.getValue().indexOf(':') + 1));
+			String paramName = theInclude.getValue().substring(theInclude.getValue().indexOf(':') + 1);
+			RuntimeSearchParam sp = getSearchParamByName(theResourceDef, paramName);
 			for (String nextPath : sp.getPathsSplit()) {
 				values.addAll(theTerser.getValues(theResource, nextPath));
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoPatientDstu2.java

@@ -26,6 +26,7 @@ import javax.servlet.http.HttpServletRequest;
 
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.springframework.beans.factory.annotation.Autowired;
 
 import ca.uhn.fhir.jpa.dao.SearchParameterMap.EverythingModeEnum;
 import ca.uhn.fhir.model.api.IResource;
@@ -46,6 +47,9 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
 		super();
 	}
 	
+	@Autowired
+	private ISearchParamRegistry mySerarchParamRegistry;
+
 	private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative) {
 		SearchParameterMap paramMap = new SearchParameterMap();
 		if (theCount != null) {
@@ -65,7 +69,7 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
 			paramMap.add("_id", new StringParam(theId.getIdPart()));
 		}
 		
-		SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this, myResourceIndexedSearchParamUriDao, myForcedIdDao, myTerminologySvc);
+		SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this, myResourceIndexedSearchParamUriDao, myForcedIdDao, myTerminologySvc, mySerarchParamRegistry);
 		builder.setType(getResourceType(), getResourceName());
 		return builder.search(paramMap);
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java

@@ -152,7 +152,7 @@ public class FhirResourceDaoSubscriptionDstu2 extends FhirResourceDaoDstu2<Subsc
 	private int pollForNewUndeliveredResources(SubscriptionTable theSubscriptionTable) {
 		Subscription subscription = toResource(Subscription.class, theSubscriptionTable.getSubscriptionResource(), false);
 		RuntimeResourceDefinition resourceDef = validateCriteriaAndReturnResourceDefinition(subscription);
-		SearchParameterMap criteriaUrl = translateMatchUrl(getContext(), subscription.getCriteria(), resourceDef);
+		SearchParameterMap criteriaUrl = translateMatchUrl(this, getContext(), subscription.getCriteria(), resourceDef);
 
 		criteriaUrl = new SearchParameterMap();
 		long start = theSubscriptionTable.getMostRecentMatch().getTime();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IDao.java

@@ -1,11 +1,14 @@
 package ca.uhn.fhir.jpa.dao;
 
+import java.util.Collection;
 import java.util.Set;
 
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.entity.BaseHasResource;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
@@ -73,4 +76,9 @@ public interface IDao {
 	<R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation);
 
 	void populateFullTextFields(IBaseResource theResource, ResourceTable theEntity);
+
+	RuntimeSearchParam getSearchParamByName(RuntimeResourceDefinition theResourceDef, String theParamName);
+
+	Collection<RuntimeSearchParam> getSearchParamsByResourceType(RuntimeResourceDefinition theResourceDef);
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDao.java

@@ -39,8 +39,10 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
 import ca.uhn.fhir.rest.method.RequestDetails;
+import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.EncodingEnum;
 import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 
 public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
@@ -134,6 +136,8 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 */
 	<MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, RequestDetails theRequestDetails);
 
+	DaoMethodOutcome patch(IIdType theId, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails);
+
 	Set<Long> processMatchUrl(String theMatchUrl);
 
 	/**
@@ -181,6 +185,15 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 
 	Set<Long> searchForIdsWithAndOr(SearchParameterMap theParams);
 
+	/**
+	 * Takes a map of incoming raw search parameters and translates/parses them into 
+	 * appropriate {@link IQueryParameterType} instances of the appropriate type
+	 * for the given param
+	 * 
+	 * @throws InvalidRequestException If any of the parameters are not known
+	 */
+	void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget);
+
 	/**
 	 * Update a resource - Note that this variant of the method does not take in a {@link RequestDetails} and 
 	 * therefore can not fire any interceptors. Use only for internal system calls 
@@ -211,8 +224,6 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 */
 	MethodOutcome validate(T theResource, IIdType theId, String theRawResource, EncodingEnum theEncoding, ValidationModeEnum theMode, String theProfile, RequestDetails theRequestDetails);
 
-	DaoMethodOutcome patch(IIdType theId, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails);
-
 //	/**
 //	 * Invoke the everything operation
 //	 */

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/ISearchParamRegistry.java

@@ -0,0 +1,16 @@
+package ca.uhn.fhir.jpa.dao;
+
+import java.util.Collection;
+import java.util.Map;
+
+import ca.uhn.fhir.context.RuntimeSearchParam;
+
+public interface ISearchParamRegistry {
+
+	Map<String,RuntimeSearchParam> getActiveSearchParams(String theResourceName);
+
+	Collection<RuntimeSearchParam> getAllSearchParams(String theResourceName);
+
+	void forceRefresh();
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java

@@ -41,6 +41,7 @@ import org.apache.commons.lang3.tuple.Pair;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallback;
@@ -95,10 +96,12 @@ public class SearchBuilder {
 	private IFulltextSearchSvc mySearchDao;
 	private Search mySearchEntity;
 	private ISearchResultDao mySearchResultDao;
+	private ISearchParamRegistry mySerarchParamRegistry;
+
 	private IHapiTerminologySvc myTerminologySvc;
 
 	public SearchBuilder(FhirContext theFhirContext, EntityManager theEntityManager, PlatformTransactionManager thePlatformTransactionManager, IFulltextSearchSvc theSearchDao, ISearchResultDao theSearchResultDao, BaseHapiFhirDao<?> theDao,
-			IResourceIndexedSearchParamUriDao theResourceIndexedSearchParamUriDao, IForcedIdDao theForcedIdDao, IHapiTerminologySvc theTerminologySvc) {
+			IResourceIndexedSearchParamUriDao theResourceIndexedSearchParamUriDao, IForcedIdDao theForcedIdDao, IHapiTerminologySvc theTerminologySvc, ISearchParamRegistry theSearchParamRegistry) {
 		myContext = theFhirContext;
 		myEntityManager = theEntityManager;
 		myPlatformTransactionManager = thePlatformTransactionManager;
@@ -108,6 +111,7 @@ public class SearchBuilder {
 		myResourceIndexedSearchParamUriDao = theResourceIndexedSearchParamUriDao;
 		myForcedIdDao = theForcedIdDao;
 		myTerminologySvc = theTerminologySvc;
+		mySerarchParamRegistry = theSearchParamRegistry;
 	}
 
 	private void addPredicateComposite(RuntimeSearchParam theParamDef, List<? extends IQueryParameterType> theNextAnd) {
@@ -212,12 +216,13 @@ public class SearchBuilder {
 				throw new InvalidRequestException("Invalid resource type: " + targetResourceType);
 			}
 
-			RuntimeSearchParam owningParameterDef = targetResourceDefinition.getSearchParam(parameterName.replaceAll("\\..*", ""));
+			String paramName = parameterName.replaceAll("\\..*", "");
+			RuntimeSearchParam owningParameterDef = myCallingDao.getSearchParamByName(targetResourceDefinition, paramName);
 			if (owningParameterDef == null) {
 				throw new InvalidRequestException("Unknown parameter name: " + targetResourceType + ':' + parameterName);
 			}
 
-			owningParameterDef = targetResourceDefinition.getSearchParam(owningParameter);
+			owningParameterDef = myCallingDao.getSearchParamByName(targetResourceDefinition, owningParameter);
 			if (owningParameterDef == null) {
 				throw new InvalidRequestException("Unknown parameter name: " + targetResourceType + ':' + owningParameter);
 			}
@@ -237,7 +242,7 @@ public class SearchBuilder {
 			List<Predicate> predicates = new ArrayList<Predicate>();
 			predicates.add(builder.equal(from.get("mySourceResourceType"), targetResourceType));
 			predicates.add(from.get("mySourceResourcePid").in(match));
-			predicates.add(createResourceLinkPathPredicate(myContext, owningParameter, from, resourceType));
+			predicates.add(createResourceLinkPathPredicate(myCallingDao, myContext, owningParameter, from, resourceType));
 			predicates.add(builder.equal(from.get("myTargetResourceType"), myResourceName));
 			createPredicateResourceId(builder, cq, predicates, from.get("myId").as(Long.class));
 			createPredicateLastUpdatedForResourceLink(builder, from, predicates);
@@ -548,7 +553,8 @@ public class SearchBuilder {
 					String resourceId;
 					if (!ref.getValue().matches("[a-zA-Z]+\\/.*")) {
 						
-						String paramPath = myContext.getResourceDefinition(myResourceType).getSearchParam(theParamName).getPath();
+						RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(myResourceType);
+						String paramPath = myCallingDao.getSearchParamByName(resourceDef, theParamName).getPath();
 						if (paramPath.endsWith(".as(Reference)")) {
 							paramPath = paramPath.substring(0, paramPath.length() - ".as(Reference)".length()) + "Reference";
 						}
@@ -602,7 +608,7 @@ public class SearchBuilder {
 						boolean isMeta = BaseHapiFhirDao.RESOURCE_META_PARAMS.containsKey(chain);
 						RuntimeSearchParam param = null;
 						if (!isMeta) {
-							param = typeDef.getSearchParam(chain);
+							param = myCallingDao.getSearchParamByName(typeDef, chain);
 							if (param == null) {
 								ourLog.debug("Type {} doesn't have search param {}", nextType.getSimpleName(), param);
 								continue;
@@ -1380,43 +1386,8 @@ public class SearchBuilder {
 		return singleCode;
 	}
 
-	private String determineSystemIfMissing(String theParamName, String code, String system) {
-		if (system == null) {
-			RuntimeSearchParam param = getSearchParam(theParamName);
-			if (param != null) {
-				Set<String> valueSetUris = Sets.newHashSet();
-				for (String nextPath : param.getPathsSplit()) {
-					BaseRuntimeChildDefinition def = myContext.newTerser().getDefinition(myResourceType, nextPath);
-					if (def instanceof BaseRuntimeDeclaredChildDefinition) {
-						String valueSet = ((BaseRuntimeDeclaredChildDefinition) def).getBindingValueSet();
-						if (isNotBlank(valueSet)) {
-							valueSetUris.add(valueSet);
-						}
-					}
-				}
-				if (valueSetUris.size() == 1) {
-					List<VersionIndependentConcept> candidateCodes = myTerminologySvc.expandValueSet(valueSetUris.iterator().next());
-					for (VersionIndependentConcept nextCandidate : candidateCodes) {
-						if (nextCandidate.getCode().equals(code)) {
-							system = nextCandidate.getSystem();
-							break;
-						}
-					}
-				}
-			}
-		}
-		return system;
-	}
-
 	private Predicate createResourceLinkPathPredicate(String theParamName, Root<? extends ResourceLink> from) {
-		return createResourceLinkPathPredicate(myContext, theParamName, from, myResourceType);
+		return createResourceLinkPathPredicate(myCallingDao, myContext, theParamName, from, myResourceType);
-	}
-
-	private static Predicate createResourceLinkPathPredicate(FhirContext theContext, String theParamName, Root<? extends ResourceLink> from, Class<? extends IBaseResource> resourceType) {
-		RuntimeSearchParam param = theContext.getResourceDefinition(resourceType).getSearchParam(theParamName);
-		List<String> path = param.getPathsSplit();
-		Predicate type = from.get("mySourcePath").in(path);
-		return type;
 	}
 
 	private TypedQuery<Long> createSearchAllByTypeQuery(DateRangeParam theLastUpdated) {
@@ -1468,7 +1439,8 @@ public class SearchBuilder {
 			return;
 		}
 
-		RuntimeSearchParam param = getSearchParam(theSort.getParamName());
+		RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(myResourceName);
+		RuntimeSearchParam param = myCallingDao.getSearchParamByName(resourceDef, theSort.getParamName());
 		if (param == null) {
 			throw new InvalidRequestException("Unknown sort parameter '" + theSort.getParamName() + "'");
 		}
@@ -1532,10 +1504,33 @@ public class SearchBuilder {
 		createSort(theBuilder, theFrom, theSort.getChain(), theOrders, thePredicates);
 	}
 
-	private RuntimeSearchParam getSearchParam(String theParamName) {
+	private String determineSystemIfMissing(String theParamName, String code, String system) {
-		RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(myResourceType);
+		if (system == null) {
-		RuntimeSearchParam param = resourceDef.getSearchParam(theParamName);
+			RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(myResourceName);
-		return param;
+			RuntimeSearchParam param = myCallingDao.getSearchParamByName(resourceDef, theParamName);
+			if (param != null) {
+				Set<String> valueSetUris = Sets.newHashSet();
+				for (String nextPath : param.getPathsSplit()) {
+					BaseRuntimeChildDefinition def = myContext.newTerser().getDefinition(myResourceType, nextPath);
+					if (def instanceof BaseRuntimeDeclaredChildDefinition) {
+						String valueSet = ((BaseRuntimeDeclaredChildDefinition) def).getBindingValueSet();
+						if (isNotBlank(valueSet)) {
+							valueSetUris.add(valueSet);
+						}
+					}
+				}
+				if (valueSetUris.size() == 1) {
+					List<VersionIndependentConcept> candidateCodes = myTerminologySvc.expandValueSet(valueSetUris.iterator().next());
+					for (VersionIndependentConcept nextCandidate : candidateCodes) {
+						if (nextCandidate.getCode().equals(code)) {
+							system = nextCandidate.getSystem();
+							break;
+						}
+					}
+				}
+			}
+		}
+		return system;
 	}
 
 	public Set<Long> doGetPids() {
@@ -1820,7 +1815,8 @@ public class SearchBuilder {
 
 		doInitializeSearch();
 
-		RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(myResourceType);
+//		RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(myResourceType);
+		Map<String, RuntimeSearchParam> searchParams = mySerarchParamRegistry.getActiveSearchParams(myResourceName);
 
 		for (Entry<String, List<List<? extends IQueryParameterType>>> nextParamEntry : params.entrySet()) {
 			String nextParamName = nextParamEntry.getKey();
@@ -1875,7 +1871,7 @@ public class SearchBuilder {
 
 			} else {
 
-				RuntimeSearchParam nextParamDef = resourceDef.getSearchParam(nextParamName);
+				RuntimeSearchParam nextParamDef = searchParams.get(nextParamName);
 				if (nextParamDef != null) {
 					switch (nextParamDef.getParamType()) {
 					case DATE:
@@ -1953,7 +1949,7 @@ public class SearchBuilder {
 		}
 
 	}
-
+	
 	public void setType(Class<? extends IBaseResource> theResourceType, String theResourceName) {
 		myResourceType = theResourceType;
 		myResourceName = theResourceName;
@@ -2044,6 +2040,14 @@ public class SearchBuilder {
 		return likeExpression.replace("%", "[%]") + "%";
 	}
 
+	private static Predicate createResourceLinkPathPredicate(IDao theCallingDao, FhirContext theContext, String theParamName, Root<? extends ResourceLink> from, Class<? extends IBaseResource> resourceType) {
+		RuntimeResourceDefinition resourceDef = theContext.getResourceDefinition(resourceType);
+		RuntimeSearchParam param = theCallingDao.getSearchParamByName(resourceDef, theParamName);
+		List<String> path = param.getPathsSplit();
+		Predicate type = from.get("mySourcePath").in(path);
+		return type;
+	}
+
 	private static List<Long> filterResourceIdsByLastUpdated(EntityManager theEntityManager, final DateRangeParam theLastUpdated, Collection<Long> thePids) {
 		CriteriaBuilder builder = theEntityManager.getCriteriaBuilder();
 		CriteriaQuery<Long> cq = builder.createQuery(Long.class);
@@ -2109,7 +2113,7 @@ public class SearchBuilder {
 	 * 
 	 * @param theLastUpdated
 	 */
-	public static HashSet<Long> loadReverseIncludes(FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode, DateRangeParam theLastUpdated) {
+	public static HashSet<Long> loadReverseIncludes(IDao theCallingDao, FhirContext theContext, EntityManager theEntityManager, Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode, DateRangeParam theLastUpdated) {
 		if (theMatches.size() == 0) {
 			return new HashSet<Long>();
 		}
@@ -2177,7 +2181,11 @@ public class SearchBuilder {
 						}
 
 						String paramName = nextInclude.getParamName();
-						param = isNotBlank(paramName) ? def.getSearchParam(paramName) : null;
+						if (isNotBlank(paramName)) {
+							param = theCallingDao.getSearchParamByName(def, paramName);
+						} else {
+							param = null;
+						}
 						if (param == null) {
 							ourLog.warn("Unknown param name in include/revinclude=" + nextInclude.getValue());
 							continue;
@@ -2278,9 +2286,9 @@ public class SearchBuilder {
 
 					Set<Long> revIncludedPids = new HashSet<Long>();
 					if (myParams.getEverythingMode() == null) {
-						revIncludedPids.addAll(loadReverseIncludes(myContext, myEntityManager, pidsSubList, myParams.getRevIncludes(), true, myParams.getLastUpdated()));
+						revIncludedPids.addAll(loadReverseIncludes(myCallingDao, myContext, myEntityManager, pidsSubList, myParams.getRevIncludes(), true, myParams.getLastUpdated()));
 					}
-					revIncludedPids.addAll(loadReverseIncludes(myContext, myEntityManager, pidsSubList, myParams.getIncludes(), false, myParams.getLastUpdated()));
+					revIncludedPids.addAll(loadReverseIncludes(myCallingDao, myContext, myEntityManager, pidsSubList, myParams.getIncludes(), false, myParams.getLastUpdated()));
 
 					// Execute the query and make sure we return distinct results
 					List<IBaseResource> resources = new ArrayList<IBaseResource>();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamExtractorDstu1.java

@@ -25,6 +25,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.math.BigDecimal;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -38,8 +39,6 @@ import org.apache.commons.lang3.tuple.Pair;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 
 import ca.uhn.fhir.context.ConfigurationException;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
@@ -79,8 +78,8 @@ public class SearchParamExtractorDstu1 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamDate> retVal = new HashSet<ResourceIndexedSearchParamDate>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.DATE) {
 				continue;
 			}
@@ -130,12 +129,13 @@ public class SearchParamExtractorDstu1 extends BaseSearchParamExtractor implemen
 		return retVal;
 	}
 
+
 	@Override
 	public HashSet<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamNumber> retVal = new HashSet<ResourceIndexedSearchParamNumber>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.NUMBER) {
 				continue;
 			}
@@ -229,8 +229,8 @@ public class SearchParamExtractorDstu1 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamQuantity> retVal = new HashSet<ResourceIndexedSearchParamQuantity>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.QUANTITY) {
 				continue;
 			}
@@ -277,8 +277,8 @@ public class SearchParamExtractorDstu1 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamString> retVal = new HashSet<ResourceIndexedSearchParamString>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.STRING) {
 				continue;
 			}
@@ -363,8 +363,8 @@ public class SearchParamExtractorDstu1 extends BaseSearchParamExtractor implemen
 	public Set<BaseResourceIndexedSearchParam> extractSearchParamTokens(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<BaseResourceIndexedSearchParam> retVal = new HashSet<BaseResourceIndexedSearchParam>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.TOKEN) {
 				continue;
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamExtractorDstu2.java

@@ -24,6 +24,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.math.BigDecimal;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -120,8 +121,8 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamDate> retVal = new HashSet<ResourceIndexedSearchParamDate>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.DATE) {
 				continue;
 			}
@@ -181,8 +182,8 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 	public HashSet<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamNumber> retVal = new HashSet<ResourceIndexedSearchParamNumber>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.NUMBER) {
 				continue;
 			}
@@ -281,8 +282,8 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamQuantity> retVal = new HashSet<ResourceIndexedSearchParamQuantity>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.QUANTITY) {
 				continue;
 			}
@@ -335,23 +336,25 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamString> retVal = new HashSet<ResourceIndexedSearchParamString>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		String resourceName = getContext().getResourceDefinition(theResource).getName();
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.STRING) {
 				continue;
 			}
 
 			String nextPath = nextSpDef.getPath();
-			String resourceName = nextSpDef.getName();
+			String nextSpName = nextSpDef.getName();
 
 			if (isBlank(nextPath)) {
 
 				// TODO: implement phonetic, and any others that have no path
 
-				if ("Questionnaire".equals(def.getName()) && nextSpDef.getName().equals("title")) {
+				if ("Questionnaire".equals(resourceName) && nextSpDef.getName().equals("title")) {
 					Questionnaire q = (Questionnaire) theResource;
 					String title = q.getGroup().getTitle();
-					addSearchTerm(theEntity, retVal, resourceName, title);
+					addSearchTerm(theEntity, retVal, nextSpName, title);
 				}
 				continue;
 			}
@@ -369,7 +372,7 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 				if (nextObject instanceof IPrimitiveDatatype<?>) {
 					IPrimitiveDatatype<?> nextValue = (IPrimitiveDatatype<?>) nextObject;
 					String searchTerm = nextValue.getValueAsString();
-					addSearchTerm(theEntity, retVal, resourceName, searchTerm);
+					addSearchTerm(theEntity, retVal, nextSpName, searchTerm);
 				} else {
 					if (nextObject instanceof BaseHumanNameDt) {
 						ArrayList<StringDt> allNames = new ArrayList<StringDt>();
@@ -377,7 +380,7 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 						allNames.addAll(nextHumanName.getFamily());
 						allNames.addAll(nextHumanName.getGiven());
 						for (StringDt nextName : allNames) {
-							addSearchTerm(theEntity, retVal, resourceName, nextName.getValue());
+							addSearchTerm(theEntity, retVal, nextSpName, nextName.getValue());
 						}
 					} else if (nextObject instanceof AddressDt) {
 						ArrayList<StringDt> allNames = new ArrayList<StringDt>();
@@ -388,16 +391,16 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 						allNames.add(nextAddress.getCountryElement());
 						allNames.add(nextAddress.getPostalCodeElement());
 						for (StringDt nextName : allNames) {
-							addSearchTerm(theEntity, retVal, resourceName, nextName.getValue());
+							addSearchTerm(theEntity, retVal, nextSpName, nextName.getValue());
 						}
 					} else if (nextObject instanceof ContactPointDt) {
 						ContactPointDt nextContact = (ContactPointDt) nextObject;
 						if (nextContact.getValueElement().isEmpty() == false) {
-							addSearchTerm(theEntity, retVal, resourceName, nextContact.getValue());
+							addSearchTerm(theEntity, retVal, nextSpName, nextContact.getValue());
 						}
 					} else {
 						if (!multiType) {
-							throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass());
+							throw new ConfigurationException("Search param " + nextSpName + " is of unexpected datatype: " + nextObject.getClass());
 						}
 					}
 				}
@@ -423,8 +426,8 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 			useSystem = vs.getCodeSystem().getSystem();
 		}
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.TOKEN) {
 				continue;
 			}
@@ -575,8 +578,8 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamUri> extractSearchParamUri(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamUri> retVal = new HashSet<ResourceIndexedSearchParamUri>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.URI) {
 				continue;
 			}
@@ -622,6 +625,7 @@ public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implemen
 		return retVal;
 	}
 
+
 	private void extractTokensFromCodeableConcept(List<String> theSystems, List<String> theCodes, CodeableConceptDt theCodeableConcept, ResourceTable theEntity, Set<BaseResourceIndexedSearchParam> theListToPopulate, RuntimeSearchParam theParameterDef) {
 		for (CodingDt nextCoding : theCodeableConcept.getCoding()) {
 			extractTokensFromCoding(theSystems, theCodes, theEntity, theListToPopulate, theParameterDef, nextCoding);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamRegistryDstu1.java

@@ -0,0 +1,6 @@
+package ca.uhn.fhir.jpa.dao;
+
+public class SearchParamRegistryDstu1 extends BaseSearchParamRegistry {
+	// nothing yet
+	
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchParamRegistryDstu2.java

@@ -0,0 +1,6 @@
+package ca.uhn.fhir.jpa.dao;
+
+public class SearchParamRegistryDstu2 extends BaseSearchParamRegistry {
+	// nothing yet
+	
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IResourceTableDao.java

@@ -10,7 +10,7 @@ package ca.uhn.fhir.jpa.dao.data;
  * 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
+ * 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,
@@ -21,9 +21,16 @@ package ca.uhn.fhir.jpa.dao.data;
  */
 
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 
 public interface IResourceTableDao extends JpaRepository<ResourceTable, Long> {
-	// nothing yet
+
+	@Modifying
+	@Query("UPDATE ResourceTable r SET r.myIndexStatus = null WHERE r.myResourceType = :restype")
+	int markResourcesOfTypeAsRequiringReindexing(@Param("restype") String theResourceType);
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3.java

@@ -92,7 +92,8 @@ public class FhirResourceDaoDstu3<T extends IAnyResource> extends BaseHapiFhirRe
 			values.addAll(theTerser.getAllPopulatedChildElementsOfType(theResource, BaseResourceReferenceDt.class));
 		} else if (theInclude.getValue().startsWith(theResourceDef.getName() + ":")) {
 			values = new ArrayList<Object>();
-			RuntimeSearchParam sp = theResourceDef.getSearchParam(theInclude.getValue().substring(theInclude.getValue().indexOf(':') + 1));
+			String paramName = theInclude.getValue().substring(theInclude.getValue().indexOf(':') + 1);
+			RuntimeSearchParam sp = getSearchParamByName(theResourceDef, paramName);
 			for (String nextPath : sp.getPathsSplit()) {
 				values.addAll(theTerser.getValues(theResource, nextPath));
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoPatientDstu3.java

@@ -27,8 +27,10 @@ import javax.servlet.http.HttpServletRequest;
 import org.hl7.fhir.dstu3.model.Patient;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.instance.model.api.IPrimitiveType;
+import org.springframework.beans.factory.annotation.Autowired;
 
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoPatient;
+import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.dao.SearchBuilder;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap.EverythingModeEnum;
@@ -45,6 +47,9 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetai
 
 public class FhirResourceDaoPatientDstu3 extends FhirResourceDaoDstu3<Patient>implements IFhirResourceDaoPatient<Patient> {
 
+	@Autowired
+	private ISearchParamRegistry mySerarchParamRegistry;
+
 	private IBundleProvider doEverythingOperation(IIdType theId, IPrimitiveType<Integer> theCount, DateRangeParam theLastUpdated, SortSpec theSort, StringAndListParam theContent, StringAndListParam theNarrative) {
 		SearchParameterMap paramMap = new SearchParameterMap();
 		if (theCount != null) {
@@ -64,7 +69,7 @@ public class FhirResourceDaoPatientDstu3 extends FhirResourceDaoDstu3<Patient>im
 			paramMap.add("_id", new StringParam(theId.getIdPart()));
 		}
 		
-		SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this, myResourceIndexedSearchParamUriDao, myForcedIdDao, myTerminologySvc);
+		SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this, myResourceIndexedSearchParamUriDao, myForcedIdDao, myTerminologySvc, mySerarchParamRegistry);
 		builder.setType(getResourceType(), getResourceName());
 		return builder.search(paramMap);
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -10,7 +12,7 @@ package ca.uhn.fhir.jpa.dao.dstu3;
  * 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
+ * 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,
@@ -27,22 +29,37 @@ import org.hl7.fhir.dstu3.model.SearchParameter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.scheduling.annotation.Scheduled;
 
+import ca.uhn.fhir.jpa.dao.BaseSearchParamExtractor;
 import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSearchParameter;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 
-public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<SearchParameter>implements IFhirResourceDaoSearchParameter<SearchParameter> {
+public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<SearchParameter> implements IFhirResourceDaoSearchParameter<SearchParameter> {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoSearchParameterDstu3.class);
 
 	@Autowired
 	private IFhirSystemDao<Bundle, Meta> mySystemDao;
-	
+
+	private void markAffectedResources(SearchParameter theResource) {
+		String xpath = theResource.getXpath();
+		String resourceType = xpath.substring(0, xpath.indexOf('.'));
+		ourLog.info("Marking all resources of type {} for reindexing due to updated search parameter with path: {}", xpath);
+		int updatedCount = myResourceTableDao.markResourcesOfTypeAsRequiringReindexing(resourceType);
+		ourLog.info("Marked {} resources for reindexing", updatedCount);
+	}
+
 	/**
 	 * This method is called once per minute to perform any required re-indexing. During most passes this will
 	 * just check and find that there are no resources requiring re-indexing. In that case the method just returns
-	 * immediately. If the search finds that some resources require reindexing, the system will do a bunch of
+	 * immediately. If the search finds that some resources require reindexing, the system will do multiple
-	 * reindexing and then return.
+	 * reindexing passes and then return.
 	 */
 	@Override
-	@Scheduled(fixedDelay=DateUtils.MILLIS_PER_MINUTE)
+	@Scheduled(fixedDelay = DateUtils.MILLIS_PER_MINUTE)
 	public void performReindexingPass() {
 		if (getConfig().isSchedulingDisabled()) {
 			return;
@@ -57,7 +74,57 @@ public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<Se
 				break;
 			}
 		}
-		
+
 	}
-	
+
+	@Override
+	protected void postPersist(ResourceTable theEntity, SearchParameter theResource) {
+		markAffectedResources(theResource);
+	}
+
+	@Override
+	protected void postUpdate(ResourceTable theEntity, SearchParameter theResource) {
+		markAffectedResources(theResource);
+	}
+
+	@Override
+	protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
+		super.validateResourceForStorage(theResource, theEntityToSave);
+
+		if (theResource.getStatus() == null) {
+			throw new UnprocessableEntityException("Resource.status is missing or invalid: " + theResource.getStatusElement().getValueAsString());
+		}
+		
+		String xpath = theResource.getXpath();
+		if (isBlank(xpath)) {
+			throw new UnprocessableEntityException("Resource.xpath is missing");
+		}
+			
+		String[] xpathSplit = BaseSearchParamExtractor.SPLIT.split(xpath);
+		String allResourceName = null;
+		for (String nextPath : xpathSplit) {
+			int dotIdx = nextPath.indexOf('.');
+			if (dotIdx == -1) {
+				throw new UnprocessableEntityException("Invalid path value \"" + nextPath + "\". Must start with a resource name");
+			}
+			
+			String resourceName = nextPath.substring(0, dotIdx);
+			try {
+				getContext().getResourceDefinition(resourceName);
+			} catch (DataFormatException e) {
+				throw new UnprocessableEntityException("Invalid path value \"" + nextPath + "\": " + e.getMessage());
+			}
+			
+			if (allResourceName == null) {
+				allResourceName = resourceName;
+			} else {
+				if (!allResourceName.equals(resourceName)) {
+					throw new UnprocessableEntityException("Invalid path value \"" + nextPath + "\". All paths in a single SearchParameter must match the same resource type");
+				}
+			}
+			
+		}
+
+	}
+
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSubscriptionDstu3.java

@@ -157,7 +157,7 @@ public class FhirResourceDaoSubscriptionDstu3 extends FhirResourceDaoDstu3<Subsc
 	private int pollForNewUndeliveredResources(SubscriptionTable theSubscriptionTable) {
 		Subscription subscription = toResource(Subscription.class, theSubscriptionTable.getSubscriptionResource(), false);
 		RuntimeResourceDefinition resourceDef = validateCriteriaAndReturnResourceDefinition(subscription);
-		SearchParameterMap criteriaUrl = translateMatchUrl(getContext(), subscription.getCriteria(), resourceDef);
+		SearchParameterMap criteriaUrl = translateMatchUrl(this, getContext(), subscription.getCriteria(), resourceDef);
 
 		criteriaUrl = new SearchParameterMap();
 		long start = theSubscriptionTable.getMostRecentMatch().getTime();

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamExtractorDstu3.java

@@ -24,6 +24,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.math.BigDecimal;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
 import java.util.HashSet;
@@ -56,7 +57,6 @@ import org.hl7.fhir.dstu3.model.Location.LocationPositionComponent;
 import org.hl7.fhir.dstu3.model.Patient.PatientCommunicationComponent;
 import org.hl7.fhir.dstu3.model.Period;
 import org.hl7.fhir.dstu3.model.Quantity;
-import org.hl7.fhir.dstu3.model.Questionnaire;
 import org.hl7.fhir.dstu3.model.Range;
 import org.hl7.fhir.dstu3.model.SimpleQuantity;
 import org.hl7.fhir.dstu3.model.StringType;
@@ -73,11 +73,11 @@ import com.google.common.annotations.VisibleForTesting;
 
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.BaseSearchParamExtractor;
 import ca.uhn.fhir.jpa.dao.ISearchParamExtractor;
+import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.dao.PathAndRef;
 import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
@@ -97,7 +97,7 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 
 	@Autowired
 	private org.hl7.fhir.dstu3.hapi.validation.IValidationSupport myValidationSupport;
-
+	
 	/**
 	 * Constructor
 	 */
@@ -105,8 +105,8 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 		super();
 	}
 
-	public SearchParamExtractorDstu3(FhirContext theCtx, IValidationSupport theValidationSupport) {
+	public SearchParamExtractorDstu3(FhirContext theCtx, IValidationSupport theValidationSupport, ISearchParamRegistry theSearchParamRegistry) {
-		super(theCtx);
+		super(theCtx, theSearchParamRegistry);
 		myValidationSupport = theValidationSupport;
 	}
 
@@ -147,8 +147,8 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamDate> retVal = new HashSet<ResourceIndexedSearchParamDate>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.DATE) {
 				continue;
 			}
@@ -226,8 +226,8 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 	public HashSet<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamNumber> retVal = new HashSet<ResourceIndexedSearchParamNumber>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.NUMBER) {
 				continue;
 			}
@@ -320,8 +320,8 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamQuantity> retVal = new HashSet<ResourceIndexedSearchParamQuantity>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.QUANTITY) {
 				continue;
 			}
@@ -384,24 +384,28 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamString> retVal = new HashSet<ResourceIndexedSearchParamString>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		String resourceName = getContext().getResourceDefinition(theResource).getName();
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.STRING) {
 				continue;
 			}
 
 			String nextPath = nextSpDef.getPath();
-			String resourceName = nextSpDef.getName();
+			String nextSpName = nextSpDef.getName();
 
 			if (isBlank(nextPath)) {
 
-				// TODO: implement phonetic, and any others that have no path
+//				// TODO: implement phonetic, and any others that have no path
-
+//
-				if ("Questionnaire".equals(def.getName()) && nextSpDef.getName().equals("title")) {
+//				// TODO: do we still need this check?
-					Questionnaire q = (Questionnaire) theResource;
+//				if ("Questionnaire".equals(nextSpName) && nextSpDef.getName().equals("title")) {
-					String title = "";// q.getGroup().getTitle();
+//					Questionnaire q = (Questionnaire) theResource;
-					addSearchTerm(theEntity, retVal, resourceName, title);
+//					String title = "";// q.getGroup().getTitle();
-				}
+//					addSearchTerm(theEntity, retVal, nextSpName, title);
+//				}
+				
 				continue;
 			}
 
@@ -418,7 +422,7 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 				if (nextObject instanceof IPrimitiveType<?>) {
 					IPrimitiveType<?> nextValue = (IPrimitiveType<?>) nextObject;
 					String searchTerm = nextValue.getValueAsString();
-					addSearchTerm(theEntity, retVal, resourceName, searchTerm);
+					addSearchTerm(theEntity, retVal, nextSpName, searchTerm);
 				} else {
 					if (nextObject instanceof HumanName) {
 						ArrayList<StringType> allNames = new ArrayList<StringType>();
@@ -428,7 +432,7 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 						}
 						allNames.addAll(nextHumanName.getGiven());
 						for (StringType nextName : allNames) {
-							addSearchTerm(theEntity, retVal, resourceName, nextName.getValue());
+							addSearchTerm(theEntity, retVal, nextSpName, nextName.getValue());
 						}
 					} else if (nextObject instanceof Address) {
 						ArrayList<StringType> allNames = new ArrayList<StringType>();
@@ -439,29 +443,29 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 						allNames.add(nextAddress.getCountryElement());
 						allNames.add(nextAddress.getPostalCodeElement());
 						for (StringType nextName : allNames) {
-							addSearchTerm(theEntity, retVal, resourceName, nextName.getValue());
+							addSearchTerm(theEntity, retVal, nextSpName, nextName.getValue());
 						}
 					} else if (nextObject instanceof ContactPoint) {
 						ContactPoint nextContact = (ContactPoint) nextObject;
 						if (nextContact.getValueElement().isEmpty() == false) {
-							addSearchTerm(theEntity, retVal, resourceName, nextContact.getValue());
+							addSearchTerm(theEntity, retVal, nextSpName, nextContact.getValue());
 						}
 					} else if (nextObject instanceof Quantity) {
 						BigDecimal value = ((Quantity) nextObject).getValue();
 						if (value != null) {
-							addSearchTerm(theEntity, retVal, resourceName, value.toPlainString());
+							addSearchTerm(theEntity, retVal, nextSpName, value.toPlainString());
 						}
 					} else if (nextObject instanceof Range) {
 						SimpleQuantity low = ((Range) nextObject).getLow();
 						if (low != null) {
 							BigDecimal value = low.getValue();
 							if (value != null) {
-								addSearchTerm(theEntity, retVal, resourceName, value.toPlainString());
+								addSearchTerm(theEntity, retVal, nextSpName, value.toPlainString());
 							}
 						}
 					} else {
 						if (!multiType) {
-							throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass());
+							throw new ConfigurationException("Search param " + nextSpName + " is of unexpected datatype: " + nextObject.getClass());
 						}
 					}
 				}
@@ -486,8 +490,8 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 			useSystem = cs.getUrl();
 		}
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.TOKEN) {
 				continue;
 			}
@@ -633,8 +637,8 @@ public class SearchParamExtractorDstu3 extends BaseSearchParamExtractor implemen
 	public Set<ResourceIndexedSearchParamUri> extractSearchParamUri(ResourceTable theEntity, IBaseResource theResource) {
 		HashSet<ResourceIndexedSearchParamUri> retVal = new HashSet<ResourceIndexedSearchParamUri>();
 
-		RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
+		Collection<RuntimeSearchParam> searchParams = getSearchParams(theResource);
-		for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
+		for (RuntimeSearchParam nextSpDef : searchParams) {
 			if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.URI) {
 				continue;
 			}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamRegistryDstu3.java

@@ -0,0 +1,205 @@
+package ca.uhn.fhir.jpa.dao.dstu3;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import org.apache.commons.lang3.time.DateUtils;
+import org.hl7.fhir.dstu3.model.CodeType;
+import org.hl7.fhir.dstu3.model.SearchParameter;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.context.RuntimeSearchParam.RuntimeSearchParamStatusEnum;
+import ca.uhn.fhir.jpa.dao.BaseSearchParamRegistry;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import ca.uhn.fhir.jpa.util.StopWatch;
+import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+
+public class SearchParamRegistryDstu3 extends BaseSearchParamRegistry {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchParamRegistryDstu3.class);
+
+	@Autowired
+	private IFhirResourceDao<SearchParameter> mySpDao;
+
+	private long myLastRefresh;
+
+	private volatile Map<String, Map<String, RuntimeSearchParam>> myActiveSearchParams;
+
+	@Autowired
+	private DaoConfig myDaoConfig;
+
+	@Override
+	public Map<String, RuntimeSearchParam> getActiveSearchParams(String theResourceName) {
+
+		long refreshInterval = 60 * DateUtils.MILLIS_PER_MINUTE;
+		if (System.currentTimeMillis() - refreshInterval > myLastRefresh) {
+			StopWatch sw = new StopWatch();
+
+			Map<String, Map<String, RuntimeSearchParam>> searchParams = new HashMap<String, Map<String, RuntimeSearchParam>>();
+			for (Entry<String, Map<String, RuntimeSearchParam>> nextBuiltInEntry : getBuiltInSearchParams().entrySet()) {
+				for (RuntimeSearchParam nextParam : nextBuiltInEntry.getValue().values()) {
+					String nextResourceName = nextBuiltInEntry.getKey();
+					getSearchParamMap(searchParams, nextResourceName).put(nextParam.getName(), nextParam);
+				}
+			}
+
+			IBundleProvider allSearchParamsBp = mySpDao.search(new SearchParameterMap());
+			int size = allSearchParamsBp.size();
+
+			// Just in case..
+			if (size > 10000) {
+				ourLog.warn("Unable to support >10000 search params!");
+				size = 10000;
+			}
+
+			List<IBaseResource> allSearchParams = allSearchParamsBp.getResources(0, size);
+			for (IBaseResource nextResource : allSearchParams) {
+				SearchParameter nextSp = (SearchParameter) nextResource;
+				RuntimeSearchParam runtimeSp = toRuntimeSp(nextSp);
+				if (runtimeSp == null) {
+					continue;
+				}
+				
+				int dotIdx = runtimeSp.getPath().indexOf('.');
+				if (dotIdx == -1) {
+					ourLog.warn("Can not determine resource type of {}", runtimeSp.getPath());
+					continue;
+				}
+				String resourceType = runtimeSp.getPath().substring(0, dotIdx);
+
+				Map<String, RuntimeSearchParam> searchParamMap = getSearchParamMap(searchParams, resourceType);
+				String name = runtimeSp.getName();
+				if (myDaoConfig.isDefaultSearchParamsCanBeOverridden() || !searchParamMap.containsKey(name)) {
+					searchParamMap.put(name, runtimeSp);
+				}
+			}
+
+			Map<String, Map<String, RuntimeSearchParam>> activeSearchParams = new HashMap<String, Map<String, RuntimeSearchParam>>();
+			for (Entry<String, Map<String, RuntimeSearchParam>> nextEntry : searchParams.entrySet()) {
+				for (RuntimeSearchParam nextSp : nextEntry.getValue().values()) {
+					String nextName = nextSp.getName();
+					if (nextSp.getStatus() != RuntimeSearchParamStatusEnum.ACTIVE) {
+						nextSp = null;
+					}
+					
+					if (!activeSearchParams.containsKey(nextEntry.getKey())) {
+						activeSearchParams.put(nextEntry.getKey(), new HashMap<String, RuntimeSearchParam>());
+					}
+					if (activeSearchParams.containsKey(nextEntry.getKey())) {
+						ourLog.info("Replacing existing/built in search param {}:{} with new one", nextEntry.getKey(), nextName);
+					}
+					
+					if (nextSp != null) {
+						activeSearchParams.get(nextEntry.getKey()).put(nextName, nextSp);
+					} else {
+						activeSearchParams.get(nextEntry.getKey()).remove(nextName);
+					}
+				}
+			}
+
+			myActiveSearchParams = activeSearchParams;
+
+			myLastRefresh = System.currentTimeMillis();
+			ourLog.info("Refreshed search parameter cache in {}ms", sw.getMillis());
+		}
+
+		return myActiveSearchParams.get(theResourceName);
+	}
+
+	@Override
+	public void forceRefresh() {
+		myLastRefresh = 0;
+	}
+
+	private Map<String, RuntimeSearchParam> getSearchParamMap(Map<String, Map<String, RuntimeSearchParam>> searchParams, String theResourceName) {
+		Map<String, RuntimeSearchParam> retVal = searchParams.get(theResourceName);
+		if (retVal == null) {
+			retVal = new HashMap<String, RuntimeSearchParam>();
+			searchParams.put(theResourceName, retVal);
+		}
+		return retVal;
+	}
+
+	private RuntimeSearchParam toRuntimeSp(SearchParameter theNextSp) {
+		String name = theNextSp.getCode();
+		String description = theNextSp.getDescription();
+		String path = theNextSp.getXpath();
+		RestSearchParameterTypeEnum paramType = null;
+		RuntimeSearchParamStatusEnum status = null;
+		switch (theNextSp.getType()) {
+		case COMPOSITE:
+			paramType = RestSearchParameterTypeEnum.COMPOSITE;
+			break;
+		case DATE:
+			paramType = RestSearchParameterTypeEnum.DATE;
+			break;
+		case NUMBER:
+			paramType = RestSearchParameterTypeEnum.NUMBER;
+			break;
+		case QUANTITY:
+			paramType = RestSearchParameterTypeEnum.QUANTITY;
+			break;
+		case REFERENCE:
+			paramType = RestSearchParameterTypeEnum.REFERENCE;
+			break;
+		case STRING:
+			paramType = RestSearchParameterTypeEnum.STRING;
+			break;
+		case TOKEN:
+			paramType = RestSearchParameterTypeEnum.TOKEN;
+			break;
+		case URI:
+			paramType = RestSearchParameterTypeEnum.URI;
+			break;
+		case NULL:
+			break;
+		}
+		if (theNextSp.getStatus() != null) {
+			switch (theNextSp.getStatus()) {
+			case ACTIVE:
+				status = RuntimeSearchParamStatusEnum.ACTIVE;
+				break;
+			case DRAFT:
+				status = RuntimeSearchParamStatusEnum.DRAFT;
+				break;
+			case RETIRED:
+				status = RuntimeSearchParamStatusEnum.RETIRED;
+				break;
+			case NULL:
+				break;
+			}
+		}
+		Set<String> providesMembershipInCompartments = Collections.emptySet();
+		Set<String> targets = toStrings(theNextSp.getTarget());
+
+		if (isBlank(name) || isBlank(path) || paramType == null) {
+			return null;
+		}
+
+		RuntimeSearchParam retVal = new RuntimeSearchParam(name, description, path, paramType, providesMembershipInCompartments, targets, status);
+		return retVal;
+	}
+
+	private Set<String> toStrings(List<CodeType> theTarget) {
+		HashSet<String> retVal = new HashSet<String>();
+		for (CodeType next : theTarget) {
+			if (isNotBlank(next.getValue())) {
+				retVal.add(next.getValue());
+			}
+		}
+		return retVal;
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java

@@ -77,6 +77,7 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 	@Index(name = "IDX_RES_DATE", columnList="RES_UPDATED"), 
 	@Index(name = "IDX_RES_LANG", columnList="RES_TYPE,RES_LANGUAGE"), 
 	@Index(name = "IDX_RES_PROFILE", columnList="RES_PROFILE"),
+	@Index(name = "IDX_RES_TYPE", columnList="RES_TYPE"),
 	@Index(name = "IDX_INDEXSTATUS", columnList="SP_INDEX_STATUS")
 })
 @AnalyzerDefs({

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaConformanceProviderDstu3.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
+import java.util.Collection;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -27,10 +29,15 @@ import javax.servlet.http.HttpServletRequest;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.CapabilityStatement.*;
 import org.hl7.fhir.dstu3.model.Enumerations.SearchParamType;
+import org.springframework.beans.factory.annotation.Autowired;
 
+import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.util.CoverageIgnore;
 import ca.uhn.fhir.util.ExtensionConstants;
@@ -62,7 +69,7 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
 		myDaoConfig = theDaoConfig;
 		super.setCache(false);
 	}
-
+	
 	@Override
 	public CapabilityStatement getServerConformance(HttpServletRequest theRequest) {
 		CapabilityStatement retVal = myCachedValue;
@@ -89,19 +96,48 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
 					nextResource.addExtension(new Extension(ExtensionConstants.CONF_RESOURCE_COUNT, new DecimalType(count)));
 				}
 
-				// Add chained params
+				nextResource.getSearchParam().clear();
-				for (CapabilityStatementRestResourceSearchParamComponent nextParam : nextResource.getSearchParam()) {
+				String resourceName = nextResource.getType();
-					if (nextParam.getType() == SearchParamType.REFERENCE) {
+				RuntimeResourceDefinition resourceDef = myRestfulServer.getFhirContext().getResourceDefinition(resourceName);
-//						List<CodeType> targets = nextParam.getTarget();
+				Collection<RuntimeSearchParam> searchParams = mySystemDao.getSearchParamsByResourceType(resourceDef);
-//						for (CodeType next : targets) {
+				for (RuntimeSearchParam runtimeSp : searchParams) {
-//							RuntimeResourceDefinition def = ctx.getResourceDefinition(next.getValue());
+					CapabilityStatementRestResourceSearchParamComponent confSp = nextResource.addSearchParam();
-//							for (RuntimeSearchParam nextChainedParam : def.getSearchParams()) {
-//								nextParam.addChain(nextChainedParam.getName());
-//							}
-//						}
-					}
-				}
 
+					confSp.setName(runtimeSp.getName());
+					confSp.setDocumentation(runtimeSp.getDescription());
+					confSp.setDefinition(runtimeSp.getUri());
+					switch (runtimeSp.getParamType()) {
+					case COMPOSITE:
+						confSp.setType(SearchParamType.COMPOSITE);
+						break;
+					case DATE:
+						confSp.setType(SearchParamType.DATE);
+						break;
+					case NUMBER:
+						confSp.setType(SearchParamType.NUMBER);
+						break;
+					case QUANTITY:
+						confSp.setType(SearchParamType.QUANTITY);
+						break;
+					case REFERENCE:
+						confSp.setType(SearchParamType.REFERENCE);
+						break;
+					case STRING:
+						confSp.setType(SearchParamType.STRING);
+						break;
+					case TOKEN:
+						confSp.setType(SearchParamType.TOKEN);
+						break;
+					case URI:
+						confSp.setType(SearchParamType.URI);
+						break;
+					case HAS:
+						// Shouldn't happen
+						break;
+					}
+					
+				}
+				
 			}
 		}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java

@@ -141,9 +141,9 @@ public final class PersistedJpaBundleProvider implements IBundleProvider {
 
 		Set<Long> revIncludedPids = new HashSet<Long>();
 		if (mySearchEntity.getSearchType() == SearchTypeEnum.SEARCH) {
-			revIncludedPids.addAll(SearchBuilder.loadReverseIncludes(myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated()));
+			revIncludedPids.addAll(SearchBuilder.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toRevIncludesList(), true, mySearchEntity.getLastUpdated()));
 		}
-		revIncludedPids.addAll(SearchBuilder.loadReverseIncludes(myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));
+		revIncludedPids.addAll(SearchBuilder.loadReverseIncludes(myDao, myContext, myEntityManager, pidsSubList, mySearchEntity.toIncludesList(), false, mySearchEntity.getLastUpdated()));
 
 		// Execute the query and make sure we return distinct results
 		List<IBaseResource> resources = new ArrayList<IBaseResource>();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDaoTest.java

@@ -1,11 +1,16 @@
 package ca.uhn.fhir.jpa.dao;
 
 import static org.junit.Assert.assertEquals;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.eq;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 import org.junit.AfterClass;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
 import ca.uhn.fhir.model.dstu2.resource.Condition;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
@@ -25,7 +30,12 @@ public class BaseHapiFhirDaoTest  extends BaseJpaTest {
 
 	@Test
 	public void testTranslateMatchUrl() {
-		SearchParameterMap match = BaseHapiFhirDao.translateMatchUrl(ourCtx, "Condition?patient=304&_lastUpdated=>2011-01-01T11:12:21.0000Z", ourCtx.getResourceDefinition(Condition.class));
+		RuntimeResourceDefinition resourceDef = ourCtx.getResourceDefinition(Condition.class);
+		
+		IDao dao = mock(IDao.class);
+		when(dao.getSearchParamByName(any(RuntimeResourceDefinition.class), eq("patient"))).thenReturn(resourceDef.getSearchParam("patient"));
+				
+		SearchParameterMap match = BaseHapiFhirDao.translateMatchUrl(dao, ourCtx, "Condition?patient=304&_lastUpdated=>2011-01-01T11:12:21.0000Z", resourceDef);
 		assertEquals("2011-01-01T11:12:21.0000Z", match.getLastUpdated().getLowerBound().getValueAsString());
 		assertEquals(ReferenceParam.class, match.get("patient").get(0).get(0).getClass());
 		assertEquals("304", ((ReferenceParam)match.get("patient").get(0).get(0)).getIdPart());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java

@@ -53,6 +53,12 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
 	private static JpaValidationSupportChainDstu3 ourJpaValidationSupportChainDstu3;
 	private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
 
+	
+	@Autowired
+	@Qualifier("mySearchParameterDaoDstu3")
+	protected IFhirResourceDao<SearchParameter> mySearchParameterDao;
+	@Autowired
+	protected ISearchParamRegistry mySearchParamRegsitry;
 //	@Autowired
 //	protected HapiWorkerContext myHapiWorkerContext;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java

@@ -0,0 +1,202 @@
+package ca.uhn.fhir.jpa.dao.dstu3;
+
+import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.empty;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
+
+import java.util.List;
+
+import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.SearchParameter;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.AfterClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.TestUtil;
+
+public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu3Test {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3SearchCustomSearchParamTest.class);
+
+	@Test
+	public void testCreateInvalidParamInvalidResourceName() {
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("PatientFoo.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		try {
+			mySearchParameterDao.create(fooSp, mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("Invalid path value \"PatientFoo.gender\": Unknown resource name \"PatientFoo\" (this name is not known in FHIR version \"DSTU3\")", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testCreateInvalidParamMismatchedResourceName() {
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("Patient.gender or Observation.code");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		try {
+			mySearchParameterDao.create(fooSp, mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("Invalid path value \"Observation.code\". All paths in a single SearchParameter must match the same resource type", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testCreateInvalidParamNoPath() {
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		try {
+			mySearchParameterDao.create(fooSp, mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("Resource.xpath is missing", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testCreateInvalidParamNoResourceName() {
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		try {
+			mySearchParameterDao.create(fooSp, mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("Invalid path value \"gender\". Must start with a resource name", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testCreateInvalidParamParamNullStatus() {
+
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("Patient.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(null);
+		try {
+			mySearchParameterDao.create(fooSp, mySrd);
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("Resource.status is missing or invalid: null", e.getMessage());
+		}
+
+	}
+
+	@Test
+	public void testSearchWithCustomParam() {
+
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("Patient.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		mySearchParameterDao.create(fooSp, mySrd);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		Patient pat = new Patient();
+		pat.setGender(AdministrativeGender.MALE);
+		IIdType patId = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
+
+		Patient pat2 = new Patient();
+		pat.setGender(AdministrativeGender.FEMALE);
+		IIdType patId2 = myPatientDao.create(pat2, mySrd).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map;
+		IBundleProvider results;
+		List<String> foundResources;
+
+		// Try with custom gender SP
+		map = new SearchParameterMap();
+		map.add("foo", new TokenParam(null, "male"));
+		results = myPatientDao.search(map);
+		foundResources = toUnqualifiedVersionlessIdValues(results);
+		assertThat(foundResources, contains(patId.getValue()));
+
+		// Try with normal gender SP
+		map = new SearchParameterMap();
+		map.add("gender", new TokenParam(null, "male"));
+		results = myPatientDao.search(map);
+		foundResources = toUnqualifiedVersionlessIdValues(results);
+		assertThat(foundResources, contains(patId.getValue()));
+
+	}
+
+	@Test
+	public void testSearchWithCustomParamDraft() {
+
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("Patient.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.DRAFT);
+		mySearchParameterDao.create(fooSp, mySrd);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		Patient pat = new Patient();
+		pat.setGender(AdministrativeGender.MALE);
+		IIdType patId = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
+
+		Patient pat2 = new Patient();
+		pat.setGender(AdministrativeGender.FEMALE);
+		IIdType patId2 = myPatientDao.create(pat2, mySrd).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map;
+		IBundleProvider results;
+		List<String> foundResources;
+
+		// Try with custom gender SP (should find nothing)
+		map = new SearchParameterMap();
+		map.add("foo", new TokenParam(null, "male"));
+		results = myPatientDao.search(map);
+		foundResources = toUnqualifiedVersionlessIdValues(results);
+		assertThat(foundResources, empty());
+
+		// Try with normal gender SP
+		map = new SearchParameterMap();
+		map.add("gender", new TokenParam(null, "male"));
+		results = myPatientDao.search(map);
+		foundResources = toUnqualifiedVersionlessIdValues(results);
+		assertThat(foundResources, contains(patId.getValue()));
+
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/SearchParamExtractorDstu3Test.java

@@ -1,7 +1,10 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
 
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Set;
 
 import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
@@ -12,6 +15,9 @@ import org.junit.BeforeClass;
 import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
@@ -37,7 +43,29 @@ public class SearchParamExtractorDstu3Test {
 		Observation obs = new Observation();
 		obs.addCategory().addCoding().setSystem("SYSTEM").setCode("CODE");
 		
-		SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(ourCtx, ourValidationSupport);
+		ISearchParamRegistry searchParamRegistry = new ISearchParamRegistry() {
+			@Override
+			public Map<String,RuntimeSearchParam> getActiveSearchParams(String theResourceName) {
+				RuntimeResourceDefinition nextResDef = ourCtx.getResourceDefinition(theResourceName);
+				Map<String, RuntimeSearchParam> sps = new HashMap<String, RuntimeSearchParam>();
+				for (RuntimeSearchParam nextSp : nextResDef.getSearchParams()) {
+					sps.put(nextSp.getName(), nextSp);
+				}
+				return sps;
+			}
+
+			@Override
+			public void forceRefresh() {
+				// nothing
+			}
+
+			@Override
+			public Collection<RuntimeSearchParam> getAllSearchParams(String theResourceName) {
+				throw new UnsupportedOperationException();
+			}
+		};
+		
+		SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(ourCtx, ourValidationSupport, searchParamRegistry);
 		Set<BaseResourceIndexedSearchParam> tokens = extractor.extractSearchParamTokens(new ResourceTable(), obs);
 		assertEquals(1, tokens.size());
 		ResourceIndexedSearchParamToken token = (ResourceIndexedSearchParamToken) tokens.iterator().next();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderCustomSearchParamDstu3Test.java

@@ -0,0 +1,319 @@
+package ca.uhn.fhir.jpa.provider.dstu3;
+
+import static org.hamcrest.Matchers.contains;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.CapabilityStatement;
+import org.hl7.fhir.dstu3.model.CapabilityStatement.CapabilityStatementRestComponent;
+import org.hl7.fhir.dstu3.model.CapabilityStatement.CapabilityStatementRestResourceComponent;
+import org.hl7.fhir.dstu3.model.CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent;
+import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
+import org.hl7.fhir.dstu3.model.Observation;
+import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.SearchParameter;
+import org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import ca.uhn.fhir.jpa.entity.ResourceTable;
+import ca.uhn.fhir.rest.gclient.ReferenceClientParam;
+import ca.uhn.fhir.rest.gclient.TokenClientParam;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.TestUtil;
+
+public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProviderDstu3Test {
+
+	@Override
+	@After
+	public void after() throws Exception {
+		super.after();
+
+		myDaoConfig.setDefaultSearchParamsCanBeOverridden(new DaoConfig().isDefaultSearchParamsCanBeOverridden());
+	}
+
+	@Override
+	public void before() throws Exception {
+		super.before();
+	}
+
+	@Test
+	public void saveCreateSearchParamInvalidWithMissingStatus() throws IOException {
+		SearchParameter sp = new SearchParameter();
+		sp.setCode("foo");
+		sp.setXpath("Patient.gender");
+		sp.setXpathUsage(XPathUsageType.NORMAL);
+		sp.setTitle("Foo Param");
+
+		try {
+			ourClient.create().resource(sp).execute();
+			fail();
+		} catch (UnprocessableEntityException e) {
+			assertEquals("HTTP 422 Unprocessable Entity: Resource.status is missing or invalid: null", e.getMessage());
+		}
+	}
+
+	@Override
+	@Before
+	public void beforeResetConfig() {
+		super.beforeResetConfig();
+
+		myDaoConfig.setDefaultSearchParamsCanBeOverridden(new DaoConfig().isDefaultSearchParamsCanBeOverridden());
+		mySearchParamRegsitry.forceRefresh();
+	}
+
+	@Test
+	public void testConformanceOverrideAllowed() {
+		myDaoConfig.setDefaultSearchParamsCanBeOverridden(true);
+
+		CapabilityStatement conformance = ourClient
+				.fetchConformance()
+				.ofType(CapabilityStatement.class)
+				.execute();
+		Map<String, CapabilityStatementRestResourceSearchParamComponent> map = extractSearchParams(conformance, "Patient");
+
+		CapabilityStatementRestResourceSearchParamComponent param = map.get("foo");
+		assertNull(param);
+
+		param = map.get("gender");
+		assertNotNull(param);
+
+		// Add a custom search parameter
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("Patient.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		mySearchParameterDao.create(fooSp, mySrd);
+
+		// Disable an existing parameter
+		fooSp = new SearchParameter();
+		fooSp.setCode("gender");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("Gender");
+		fooSp.setXpath("Patient.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.RETIRED);
+		mySearchParameterDao.create(fooSp, mySrd);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		conformance = ourClient
+				.fetchConformance()
+				.ofType(CapabilityStatement.class)
+				.execute();
+		map = extractSearchParams(conformance, "Patient");
+
+		param = map.get("foo");
+		assertEquals("foo", param.getName());
+
+		param = map.get("gender");
+		assertNull(param);
+
+	}
+
+	@Test
+	public void testConformanceOverrideNotAllowed() {
+		myDaoConfig.setDefaultSearchParamsCanBeOverridden(false);
+		
+		CapabilityStatement conformance = ourClient
+				.fetchConformance()
+				.ofType(CapabilityStatement.class)
+				.execute();
+		Map<String, CapabilityStatementRestResourceSearchParamComponent> map = extractSearchParams(conformance, "Patient");
+
+		CapabilityStatementRestResourceSearchParamComponent param = map.get("foo");
+		assertNull(param);
+
+		param = map.get("gender");
+		assertNotNull(param);
+
+		// Add a custom search parameter
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("Patient.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		mySearchParameterDao.create(fooSp, mySrd);
+
+		// Disable an existing parameter
+		fooSp = new SearchParameter();
+		fooSp.setCode("gender");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("Gender");
+		fooSp.setXpath("Patient.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.RETIRED);
+		mySearchParameterDao.create(fooSp, mySrd);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		conformance = ourClient
+				.fetchConformance()
+				.ofType(CapabilityStatement.class)
+				.execute();
+		map = extractSearchParams(conformance, "Patient");
+
+		param = map.get("foo");
+		assertEquals("foo", param.getName());
+
+		param = map.get("gender");
+		assertNotNull(param);
+
+	}
+
+	private Map<String, CapabilityStatementRestResourceSearchParamComponent> extractSearchParams(CapabilityStatement conformance, String resType) {
+		Map<String, CapabilityStatementRestResourceSearchParamComponent> map = new HashMap<String, CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent>();
+		for (CapabilityStatementRestComponent nextRest : conformance.getRest()) {
+			for (CapabilityStatementRestResourceComponent nextResource : nextRest.getResource()) {
+				if (!resType.equals(nextResource.getType())) {
+					continue;
+				}
+				for (CapabilityStatementRestResourceSearchParamComponent nextParam : nextResource.getSearchParam()) {
+					map.put(nextParam.getName(), nextParam);
+				}
+			}
+		}
+		return map;
+	}
+
+	@SuppressWarnings("unused")
+	@Test
+	public void testSearchWithCustomParam() {
+
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("Patient.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		mySearchParameterDao.create(fooSp, mySrd);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		Patient pat = new Patient();
+		pat.setGender(AdministrativeGender.MALE);
+		IIdType patId = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
+
+		Patient pat2 = new Patient();
+		pat2.setGender(AdministrativeGender.FEMALE);
+		IIdType patId2 = myPatientDao.create(pat2, mySrd).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map;
+		IBundleProvider results;
+		List<String> foundResources;
+		Bundle result;
+
+		result = ourClient
+				.search()
+				.forResource(Patient.class)
+				.where(new TokenClientParam("foo").exactly().code("male"))
+				.returnBundle(Bundle.class)
+				.execute();
+		foundResources = toUnqualifiedVersionlessIdValues(result);
+		assertThat(foundResources, contains(patId.getValue()));
+
+	}
+
+	@Test
+	public void testCreatingParamMarksCorrectResourcesForReindexing() {
+		Patient pat = new Patient();
+		pat.setGender(AdministrativeGender.MALE);
+		IIdType patId = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
+
+		Observation obs2 = new Observation();
+		obs2.setStatus(ObservationStatus.FINAL);
+		IIdType obsId = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
+
+		ResourceTable res = myResourceTableDao.findOne(patId.getIdPartAsLong());
+		assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, res.getIndexStatus().longValue());
+		res = myResourceTableDao.findOne(obsId.getIdPartAsLong());
+		assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, res.getIndexStatus().longValue());
+
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.TOKEN);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("Patient.gender");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		mySearchParameterDao.create(fooSp, mySrd);
+
+		res = myResourceTableDao.findOne(patId.getIdPartAsLong());
+		assertEquals(null, res.getIndexStatus());
+		res = myResourceTableDao.findOne(obsId.getIdPartAsLong());
+		assertEquals(BaseHapiFhirDao.INDEX_STATUS_INDEXED, res.getIndexStatus().longValue());
+
+	}
+
+	@SuppressWarnings("unused")
+	@Test
+	public void testSearchQualifiedWithCustomReferenceParam() {
+
+		SearchParameter fooSp = new SearchParameter();
+		fooSp.setCode("foo");
+		fooSp.setType(org.hl7.fhir.dstu3.model.Enumerations.SearchParamType.REFERENCE);
+		fooSp.setTitle("FOO SP");
+		fooSp.setXpath("Observation.subject");
+		fooSp.setXpathUsage(org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType.NORMAL);
+		fooSp.setStatus(org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus.ACTIVE);
+		mySearchParameterDao.create(fooSp, mySrd);
+
+		mySearchParamRegsitry.forceRefresh();
+
+		Patient pat = new Patient();
+		pat.setGender(AdministrativeGender.MALE);
+		IIdType patId = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
+
+		Observation obs1 = new Observation();
+		obs1.getSubject().setReferenceElement(patId);
+		IIdType obsId1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
+
+		Observation obs2 = new Observation();
+		obs2.setStatus(org.hl7.fhir.dstu3.model.Observation.ObservationStatus.FINAL);
+		IIdType obsId2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map;
+		IBundleProvider results;
+		List<String> foundResources;
+		Bundle result;
+
+		result = ourClient
+				.search()
+				.forResource(Observation.class)
+				.where(new ReferenceClientParam("foo").hasChainedProperty(Patient.GENDER.exactly().code("male")))
+				.returnBundle(Bundle.class)
+				.execute();
+		foundResources = toUnqualifiedVersionlessIdValues(result);
+		assertThat(foundResources, contains(obsId1.getValue()));
+
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/DynamicSearchTest.java

@@ -22,6 +22,7 @@ import org.junit.Test;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeSearchParam;
+import ca.uhn.fhir.context.RuntimeSearchParam.RuntimeSearchParamStatusEnum;
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
 import ca.uhn.fhir.model.dstu.resource.Conformance;
@@ -175,8 +176,8 @@ public class DynamicSearchTest {
 		@Override
 		public List<RuntimeSearchParam> getSearchParameters() {
 			ArrayList<RuntimeSearchParam> retVal = new ArrayList<RuntimeSearchParam>();
-			retVal.add(new RuntimeSearchParam("param1", "This is the first parameter", "Patient.param1", RestSearchParameterTypeEnum.STRING, null, null));
+			retVal.add(new RuntimeSearchParam("param1", "This is the first parameter", "Patient.param1", RestSearchParameterTypeEnum.STRING, null, null, RuntimeSearchParamStatusEnum.ACTIVE));
-			retVal.add(new RuntimeSearchParam("param2", "This is the second parameter", "Patient.param2", RestSearchParameterTypeEnum.DATE, null, null));
+			retVal.add(new RuntimeSearchParam("param2", "This is the second parameter", "Patient.param2", RestSearchParameterTypeEnum.DATE, null, null, RuntimeSearchParamStatusEnum.ACTIVE));
 			return retVal;
 		}
 

hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/rest/server/ValidateDstu2_1Test.java

@@ -96,8 +96,11 @@ public class ValidateDstu2_1Test {
 		params.addParameter().setName("resource").setResource(patient);
 		params.addParameter().setName("mode").setValue(new CodeType(" "));
 
+
+		String encodedResource = ourCtx.newXmlParser().encodeResourceToString(params);
+		
 		HttpPost httpPost = new HttpPost("http://localhost:" + ourPort + "/Patient/$validate");
-		httpPost.setEntity(new StringEntity(ourCtx.newXmlParser().encodeResourceToString(params), ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
+		httpPost.setEntity(new StringEntity(encodedResource, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
 
 		HttpResponse status = ourClient.execute(httpPost);
 		String resp = IOUtils.toString(status.getEntity().getContent());

hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/server/SearchDefaultMethodDstu3Test.java

@@ -0,0 +1,261 @@
+package ca.uhn.fhir.rest.server;
+
+import static org.hamcrest.Matchers.either;
+import static org.hamcrest.Matchers.equalTo;
+import static org.hamcrest.Matchers.hasSize;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
+
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.dstu3.model.HumanName;
+import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.annotation.OptionalParam;
+import ca.uhn.fhir.rest.annotation.RawParam;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.param.StringAndListParam;
+import ca.uhn.fhir.util.PortUtil;
+import ca.uhn.fhir.util.TestUtil;
+
+public class SearchDefaultMethodDstu3Test {
+
+	private static CloseableHttpClient ourClient;
+	private static FhirContext ourCtx = FhirContext.forDstu3();
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchDefaultMethodDstu3Test.class);
+	private static int ourPort;
+	private static Server ourServer;
+	private static String ourLastMethod;
+	private static StringAndListParam ourLastParam1;
+	private static StringAndListParam ourLastParam2;
+
+	@Before
+	public void before() {
+		ourLastMethod = null;
+		ourLastParam1 = null;
+		ourLastParam2 = null;
+		ourLastAdditionalParams = null;
+	}
+
+	@Test
+	public void testSearchNoParams() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient");
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertThat(ourLastMethod, either(equalTo("search01")).or(equalTo("search02")));
+			assertEquals(null, ourLastParam1);
+			assertEquals(null, ourLastParam2);
+			assertEquals(null, ourLastAdditionalParams);
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@Test
+	public void testSearchOneOptionalParam() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?param1=val1");
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertThat(ourLastParam1.getValuesAsQueryTokens(), hasSize(1));
+			assertThat(ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens(), hasSize(1));
+			assertEquals("val1", ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
+			assertEquals(null, ourLastParam2);
+			assertEquals(null, ourLastAdditionalParams);
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@Test
+	public void testSearchTwoOptionalParams() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?param1=val1&param2=val2");
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertThat(ourLastParam1.getValuesAsQueryTokens(), hasSize(1));
+			assertThat(ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens(), hasSize(1));
+			assertEquals("val1", ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
+
+			assertThat(ourLastParam2.getValuesAsQueryTokens(), hasSize(1));
+			assertThat(ourLastParam2.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens(), hasSize(1));
+			assertEquals("val2", ourLastParam2.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
+
+			assertEquals(null, ourLastAdditionalParams);
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@Test
+	public void testSearchTwoOptionalParamsAndExtraParam() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?param1=val1&param2=val2&param3=val3&_pretty=true");
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertEquals("search03", ourLastMethod);
+
+			assertThat(ourLastParam1.getValuesAsQueryTokens(), hasSize(1));
+			assertThat(ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens(), hasSize(1));
+			assertEquals("val1", ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
+
+			assertThat(ourLastParam2.getValuesAsQueryTokens(), hasSize(1));
+			assertThat(ourLastParam2.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens(), hasSize(1));
+			assertEquals("val2", ourLastParam2.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
+
+			ourLog.info(ourLastAdditionalParams.toString());
+			assertEquals(1, ourLastAdditionalParams.size());
+			assertEquals("val3", ourLastAdditionalParams.get("param3").get(0));
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@Test
+	public void testSearchTwoOptionalParamsWithQualifierAndExtraParam() throws Exception {
+		HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?param1=val1&param2=val2&param2:exact=val2e&param3=val3&_pretty=true");
+		CloseableHttpResponse status = ourClient.execute(httpGet);
+		try {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(responseContent);
+			assertEquals(200, status.getStatusLine().getStatusCode());
+
+			assertEquals("search03", ourLastMethod);
+
+			assertThat(ourLastParam1.getValuesAsQueryTokens(), hasSize(1));
+			assertThat(ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens(), hasSize(1));
+			assertEquals("val1", ourLastParam1.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
+
+			assertThat(ourLastParam2.getValuesAsQueryTokens(), hasSize(2));
+			assertThat(ourLastParam2.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens(), hasSize(1));
+			assertEquals("val2", ourLastParam2.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
+			assertEquals("val2e", ourLastParam2.getValuesAsQueryTokens().get(1).getValuesAsQueryTokens().get(0).getValue());
+
+			ourLog.info(ourLastAdditionalParams.toString());
+			assertEquals(1, ourLastAdditionalParams.size());
+			assertEquals("val3", ourLastAdditionalParams.get("param3").get(0));
+
+		} finally {
+			IOUtils.closeQuietly(status.getEntity().getContent());
+		}
+
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() throws Exception {
+		ourServer.stop();
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+	@BeforeClass
+	public static void beforeClass() throws Exception {
+		ourPort = PortUtil.findFreePort();
+		ourServer = new Server(ourPort);
+
+		DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
+
+		ServletHandler proxyHandler = new ServletHandler();
+		RestfulServer servlet = new RestfulServer(ourCtx);
+		servlet.setPagingProvider(new FifoMemoryPagingProvider(10));
+
+		servlet.setResourceProviders(patientProvider);
+		ServletHolder servletHolder = new ServletHolder(servlet);
+		proxyHandler.addServletWithMapping(servletHolder, "/*");
+		ourServer.setHandler(proxyHandler);
+		ourServer.start();
+
+		PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
+		HttpClientBuilder builder = HttpClientBuilder.create();
+		builder.setConnectionManager(connectionManager);
+		ourClient = builder.build();
+
+	}
+
+	private static Map<String, List<String>> ourLastAdditionalParams;
+
+	public static class DummyPatientResourceProvider implements IResourceProvider {
+
+		@Override
+		public Class<? extends IBaseResource> getResourceType() {
+			return Patient.class;
+		}
+
+		@Search()
+		public List<Patient> search01(
+				@OptionalParam(name = "param1") StringAndListParam theParam1) {
+			ourLastMethod = "search01";
+			ourLastParam1 = theParam1;
+			ArrayList<Patient> retVal = new ArrayList<Patient>();
+			retVal.add((Patient) new Patient().addName(new HumanName().setFamily("FAMILY")).setId("1"));
+			return retVal;
+		}
+
+		@Search()
+		public List<Patient> search02(
+				@OptionalParam(name = "param1") StringAndListParam theParam1,
+				@OptionalParam(name = "param2") StringAndListParam theParam2) {
+			ourLastMethod = "search02";
+			ourLastParam1 = theParam1;
+			ourLastParam2 = theParam2;
+			ArrayList<Patient> retVal = new ArrayList<Patient>();
+			retVal.add((Patient) new Patient().addName(new HumanName().setFamily("FAMILY")).setId("1"));
+			return retVal;
+		}
+
+		@Search(allowUnknownParams = true)
+		public List<Patient> search03(
+				@OptionalParam(name = "param1") StringAndListParam theParam1,
+				@OptionalParam(name = "param2") StringAndListParam theParam2,
+				@RawParam() Map<String, List<String>> theAdditionalParams) {
+			ourLastMethod = "search03";
+			ourLastParam1 = theParam1;
+			ourLastParam2 = theParam2;
+			ourLastAdditionalParams = theAdditionalParams;
+			ArrayList<Patient> retVal = new ArrayList<Patient>();
+			retVal.add((Patient) new Patient().addName(new HumanName().setFamily("FAMILY")).setId("1"));
+			return retVal;
+		}
+
+	}
+
+}

hapi-fhir-validation-resources-dstu2.1/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

hapi-tinder-plugin/src/main/resources/vm/jpa_resource_provider.vm

@@ -39,7 +39,7 @@ public class ${className}ResourceProvider extends
 		return ${className}.class;
 	}
 
-	@Search()
+	@Search(allowUnknownParams=true)
 	public ca.uhn.fhir.rest.server.IBundleProvider search(
 			javax.servlet.http.HttpServletRequest theServletRequest,
 			
@@ -99,6 +99,9 @@ public class ${className}ResourceProvider extends
 #end
 #end	
 
+			@RawParam
+			Map<String, List<String>> theAdditionalRawParams,
+
 #if ( $version != 'dstu' )
 			@IncludeParam(reverse=true)
 			Set<Include> theRevIncludes,
@@ -151,6 +154,8 @@ public class ${className}ResourceProvider extends
 			paramMap.setCount(theCount);
 			paramMap.setRequestDetails(theRequestDetails);
 
+			getDao().translateRawParameters(theAdditionalRawParams, paramMap);
+
 			ca.uhn.fhir.rest.server.IBundleProvider retVal = getDao().search(paramMap);
 			return retVal;
 		} finally {

src/changes/changes.xml

@@ -19,6 +19,11 @@
 					</ul>
 				]]>
 			</action>
+			<action type="add">
+				The JPA server now supports custom search parameters in DSTU3
+				mode. This allows users to create search parameters which contain
+				custom paths, or even override and disable existing search
+				parameters.
 			<action type="fix">
 				CLI example uploader couldn't find STU3 examples after CI server
 				was moved to build.fhir.org
@@ -133,7 +138,7 @@
 					</ul>
 				]]>
 			</action>
-			<action type="fix">
+		<action type="fix">
 				Fix issue in AuthorizationIntetceptor where
 				transactions are blocked even when they
 				should not be
@@ -284,6 +289,101 @@
 				return CapabilityStatement instead of the previously used
 				"Conformance" resource
 			</action>
+			<action type="fix">
+				CLI example uploader couldn't find STU3 examples after CI server
+				was moved to build.fhir.org
+			</action>
+			<action type="fix">
+				Fix issue in JPA subscription module that prevented purging stale
+				subscriptions when many were present on Postgres
+			</action>
+			<action type="fix" issue="532">
+				Server interceptor methods were being called twice unnecessarily
+				by the JPA server, and the DaoConfig interceptor registration 
+				framework was not actually useful. Thanks to GitHub user
+				@mattiuusitalo for reporting!
+			</action>
+			<action type="fix" issue="503">
+				AuthorizationInterceptor on JPA server did not correctly
+				apply rules on deleting resources in a specific compartment
+				because the resource metadata was stripped by the JPA server
+				before the interceptor could see it. Thanks to
+				Eeva Turkka for reporting!
+			</action>
+			<action type="fix" issue="519">
+				JPA server exported CapabilityStatement includes 
+				double entries for the _id parameter and uses the
+				wrong type (string instead of token). Thanks to 
+				Robert Lichtenberger for reporting!
+			</action>
+			<action type="add" issue="504">
+				Custom resource types which extend Binary must not
+				have declared extensions since this is invalid in 
+				FHIR (and HAPI would just ignore them anyhow). Thanks 
+				to Thomas S Berg for reporting!
+			</action>
+			<action type="add">
+				Standard HAPI zip/tar distributions did not include the project
+				sources and JavaDoc JARs. Thanks to Keith Boone for pointing
+				this out!
+			</action>
+			<action type="fix">
+				Server AuthorizationInterceptor always rejects history operation 
+				at the type level even if rules should allow it.
+			</action>
+			<action type="fix">
+				JPA server terminology service was not correctly validating or expanding codes 
+				in SNOMED CT or LOINC code systems. Thanks to David Hay for reporting!
+			</action>
+			<action type="fix" issue="539">
+				Attempting to search for an invalid resource type (e.g. GET base/FooResource) should 
+				return an HTTP 404 and not a 400, per the HTTP spec. Thanks to 
+				GitHub user @CarthageKing for the pull request!
+			</action>
+			<action type="fix" issue="544">
+				When parsing a Bundle containing placeholder fullUrls and references
+				(e.g. "urn:uuid:0000-0000") the resource reference targets did not get
+				populated with the given resources. Note that as a part of this
+				change, <![CDATA[<code>IdType</code> and <code>IdDt</code>]]> have been modified
+				so that when parsing a placeholder ID, the complete placeholder including the
+				"urn:uuid:" or "urn:oid:" prefix will be placed into the ID part. Previously,
+				the prefix was treated as the base URL, which led to strange behaviour
+				like the placeholder being treated as a real IDs. Thanks to GitHub
+				user @jodue for reporting!
+			</action>
+			<action type="add">
+				Declared extensions with multiple type() options listed in the @Child
+				annotation caused a crash on startup. Now this is supported.
+			</action>
+			<action type="add">
+				STU3 XHTML parser for narrative choked if the narrative contained
+				an <![CDATA[<code>&amp;rsquot;</code>]]> entity string.
+			</action>
+			<action type="fix" issue="538">
+				When parsing a quantity parameter on the server with a 
+				value and units but no system (e.g. 
+				<![CDATA[<code>GET [base]/Observation?value=5.4||mg</code>]]>)
+				the unit was incorrectly treated as the system. Thanks to
+				@CarthageKing for the pull request!
+			</action>
+			<action type="533">
+				Correct a typo in the JPA ValueSet ResourceProvider which prevented
+				successful operation under Spring 4.3. Thanks to 
+				Robbert van Waveren for the pull request!
+			</action>
+			<action type="remove">
+				Deprecate the method
+				<![CDATA[<code>ICompositeElement#getAllPopulatedChildElementsOfType(Class)</code>]]>
+				as it is no longer used by HAPI and is just an annoying step
+				in creating custom structures. Thanks to Allan Bro Hansen
+				for pointing this out.
+			</action>
+			<action type="fix" issue="547">
+				CapturingInterceptor did not buffer the response meaning
+				that in many circumstances it did not actually capture
+				the response. Thanks to Jenny Syed of Cerner for
+				the pull request and contribution!
+			</action>
 		</release>
 		<release version="2.1" date="2016-11-11">
 			<action type="add">