Work on custom 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
+

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

@@ -403,19 +403,26 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
 				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;
@@ -426,6 +433,7 @@ 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) {
@@ -487,6 +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-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java

@@ -213,6 +213,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	@Autowired
 	private ISearchParamExtractor mySearchParamExtractor;
 
+	@Autowired
+	private ISearchParamRegistry mySearchParamRegistry;
+
 	@Autowired
 	private ISearchResultDao mySearchResultDao;
 
@@ -943,7 +946,7 @@ 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) {
@@ -956,30 +959,18 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return ids;
 	}
 
+	@Override
+	public RuntimeSearchParam getSearchParamByName(RuntimeResourceDefinition theResourceDef, String theParamName) {
+		Map<String, RuntimeSearchParam> params = mySearchParamRegistry.getActiveSearchParams(theResourceDef.getName());
+		return params.get(theParamName);
+	}
+
 	@SuppressWarnings("unused")
 	@CoverageIgnore
 	public BaseHasResource readEntity(IIdType theValueId) {
 		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;
 	}
@@ -1718,7 +1709,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return parameters;
 	}
 
-	public static SearchParameterMap translateMatchUrl(FhirContext theContext, String theMatchUrl, RuntimeResourceDefinition resourceDef) {
+	public static SearchParameterMap translateMatchUrl(IDao theCallingDao, FhirContext theContext, String theMatchUrl, RuntimeResourceDefinition resourceDef) {
 		SearchParameterMap paramMap = new SearchParameterMap();
 		List<NameValuePair> parameters = translateMatchUrl(theMatchUrl);
 
@@ -1788,7 +1779,7 @@ 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);
 				}

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;
@@ -44,23 +58,42 @@ 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.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;
@@ -697,7 +730,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		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 + "]");
 			}
@@ -1027,7 +1060,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 				throw new InvalidRequestException(msg);
 			}
 
-			aaaa
+			// 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);
+				}
+			}
+			
 		}
 	}
 

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/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

@@ -6,6 +6,8 @@ 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 +75,6 @@ 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);
 }

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

@@ -216,12 +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);
 			}
@@ -241,7 +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);
@@ -552,7 +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";
 						}
@@ -606,7 +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;
@@ -1385,7 +1387,7 @@ public class SearchBuilder {
 	}
 
 	private Predicate createResourceLinkPathPredicate(String theParamName, Root<? extends ResourceLink> from) {
-		return createResourceLinkPathPredicate(myContext, theParamName, from, myResourceType);
+		return createResourceLinkPathPredicate(myCallingDao, myContext, theParamName, from, myResourceType);
 	}
 
 	private TypedQuery<Long> createSearchAllByTypeQuery(DateRangeParam theLastUpdated) {
@@ -1437,7 +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() + "'");
 		}
@@ -1503,7 +1506,8 @@ public class SearchBuilder {
 
 	private String determineSystemIfMissing(String theParamName, String code, String system) {
 		if (system == null) {
-			RuntimeSearchParam param = getSearchParam(theParamName);
+			RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(myResourceName);
+			RuntimeSearchParam param = myCallingDao.getSearchParamByName(resourceDef, theParamName);
 			if (param != null) {
 				Set<String> valueSetUris = Sets.newHashSet();
 				for (String nextPath : param.getPathsSplit()) {
@@ -1612,12 +1616,6 @@ public class SearchBuilder {
 		doSetPids(resultList);
 	}
 
-	private RuntimeSearchParam getSearchParam(String theParamName) {
-		RuntimeResourceDefinition resourceDef = myContext.getResourceDefinition(myResourceType);
-		RuntimeSearchParam param = resourceDef.getSearchParam(theParamName);
-		return param;
-	}
-
 	private void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation) {
 		EntityManager entityManager = myEntityManager;
 		FhirContext context = myContext;
@@ -2042,8 +2040,9 @@ public class SearchBuilder {
 		return likeExpression.replace("%", "[%]") + "%";
 	}
 
-	private static Predicate createResourceLinkPathPredicate(FhirContext theContext, String theParamName, Root<? extends ResourceLink> from, Class<? extends IBaseResource> resourceType) {
+	private static Predicate createResourceLinkPathPredicate(IDao theCallingDao, FhirContext theContext, String theParamName, Root<? extends ResourceLink> from, Class<? extends IBaseResource> resourceType) {
-		RuntimeSearchParam param = theContext.getResourceDefinition(resourceType).getSearchParam(theParamName);
+		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;
@@ -2114,7 +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>();
 		}
@@ -2182,7 +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;
@@ -2283,9 +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/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/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/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/FhirResourceDaoDstu3SearchCustomParamTest.java

@@ -1,70 +1,23 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
 import static org.hamcrest.Matchers.contains;
-import static org.hamcrest.Matchers.containsInAnyOrder;
-import static org.hamcrest.Matchers.containsInRelativeOrder;
 import static org.hamcrest.Matchers.empty;
-import static org.hamcrest.Matchers.endsWith;
-import static org.hamcrest.Matchers.hasItem;
-import static org.hamcrest.Matchers.hasItems;
-import static org.hamcrest.Matchers.not;
-import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.Mockito.mock;
 
-import java.io.IOException;
+import java.util.List;
-import java.math.BigDecimal;
-import java.nio.charset.StandardCharsets;
-import java.util.*;
 
-import javax.servlet.http.HttpServletRequest;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.hl7.fhir.dstu3.model.*;
-import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.dstu3.model.Bundle.BundleType;
-import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
-import org.hl7.fhir.dstu3.model.ContactPoint.ContactPointSystem;
 import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
-import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
+import org.hl7.fhir.dstu3.model.Patient;
-import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
+import org.hl7.fhir.dstu3.model.SearchParameter;
-import org.hl7.fhir.dstu3.model.codesystems.PublicationStatus;
-import org.hl7.fhir.dstu3.model.codesystems.SearchParamType;
-import org.hl7.fhir.instance.model.SearchParameter.XPathUsageType;
-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.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.junit.After;
 import org.junit.AfterClass;
-import org.junit.Ignore;
 import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.TransactionStatus;
-import org.springframework.transaction.support.TransactionCallback;
-import org.springframework.transaction.support.TransactionTemplate;
 
-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.dao.SearchParameterMap.EverythingModeEnum;
+import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.jpa.entity.*;
-import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvc;
-import ca.uhn.fhir.model.api.IQueryParameterType;
-import ca.uhn.fhir.model.api.Include;
-import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
-import ca.uhn.fhir.rest.api.SortOrderEnum;
-import ca.uhn.fhir.rest.api.SortSpec;
-import ca.uhn.fhir.rest.param.*;
-import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.IBundleProvider;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.util.TestUtil;
 
-@SuppressWarnings("unchecked")
 public class FhirResourceDaoDstu3SearchCustomParamTest extends BaseJpaDstu3Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3SearchCustomParamTest.class);
 

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

@@ -1,24 +1,34 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
+import static org.hamcrest.Matchers.contains;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertThat;
 import static org.junit.Assert.fail;
 
 import java.io.IOException;
+import java.util.List;
 
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
+import org.hl7.fhir.dstu3.model.Observation;
+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.Test;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+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.InvalidRequestException;
 import ca.uhn.fhir.util.TestUtil;
 
 public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProviderDstu3Test {
 
-	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderCustomSearchParamDstu3Test.class);
-
 	@Override
 	@After
 	public void after() throws Exception {
@@ -44,10 +54,92 @@ public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProv
 			ourClient.create().resource(sp).execute();
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("", e.getMessage());
+			assertEquals("HTTP 400 Bad Request: Resource.status is missing or invalid: null", e.getMessage());
 		}
 	}
 
+	@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();
+		pat.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()));
+
+	}
+
+	@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-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,
 			
@@ -154,6 +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 {