Fix #148 - Add _count support to everything operation

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

@@ -246,12 +246,11 @@ abstract class BaseResourceReturningMethodBinding extends BaseMethodBinding<Obje
 			}
 		}
 
-		Integer count = RestfulServerUtils.extractCountParameter(theRequest.getServletRequest());
-
-		boolean respondGzip = theRequest.isRespondGzip();
-
-		HttpServletResponse response = theRequest.getServletResponse();
 		Object resultObj = invokeServer(theRequest, params);
+
+		Integer count = RestfulServerUtils.extractCountParameter(theRequest.getServletRequest());
+		boolean respondGzip = theRequest.isRespondGzip();
+		HttpServletResponse response = theRequest.getServletResponse();
 		switch (getReturnType()) {
 		case BUNDLE: {
 
@@ -283,12 +282,15 @@ abstract class BaseResourceReturningMethodBinding extends BaseMethodBinding<Obje
 				RestfulServerUtils.streamResponseAsResource(theServer, response, resource, responseEncoding, prettyPrint, requestIsBrowser, narrativeMode, respondGzip, theRequest.getFhirServerBase());
 				break;
 			} else {
-                Set<Include> includes = getRequestIncludesFromParams(params);
+				Set<Include> includes = getRequestIncludesFromParams(params);
 
 				IBundleProvider result = (IBundleProvider) resultObj;
+				if (count == null) {
+					count = result.preferredPageSize();
+				}
+
 				IVersionSpecificBundleFactory bundleFactory = theServer.getFhirContext().newBundleFactory();
-				bundleFactory.initializeBundleFromBundleProvider(theServer, result, responseEncoding, theRequest.getFhirServerBase(), theRequest.getCompleteUrl(), prettyPrint, 0, count, null,
+				bundleFactory.initializeBundleFromBundleProvider(theServer, result, responseEncoding, theRequest.getFhirServerBase(), theRequest.getCompleteUrl(), prettyPrint, 0, count, null, getResponseBundleType(), includes);
-						getResponseBundleType(), includes);
 				Bundle bundle = bundleFactory.getDstu1Bundle();
 				if (bundle != null) {
 					for (int i = theServer.getInterceptors().size() - 1; i >= 0; i--) {

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

@@ -208,6 +208,11 @@ public class HistoryMethodBinding extends BaseResourceReturningMethodBinding {
 			public int size() {
 				return resources.size();
 			}
+
+			@Override
+			public Integer preferredPageSize() {
+				return null;
+			}
 		};
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/BundleProviders.java

@@ -56,6 +56,11 @@ public class BundleProviders {
 			public InstantDt getPublished() {
 				return published;
 			}
+
+			@Override
+			public Integer preferredPageSize() {
+				return null;
+			}
 		};
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/Dstu1BundleFactory.java

@@ -26,21 +26,24 @@ import java.util.List;
 import java.util.Set;
 import java.util.UUID;
 
-import ca.uhn.fhir.model.api.*;
-import ca.uhn.fhir.util.ResourceReferenceInfo;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
-import org.hl7.fhir.instance.model.IBaseResource;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.context.RuntimeResourceDefinition;
+import ca.uhn.fhir.model.api.Bundle;
+import ca.uhn.fhir.model.api.BundleEntry;
+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.base.composite.BaseResourceReferenceDt;
 import ca.uhn.fhir.model.base.resource.BaseOperationOutcome;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.util.ResourceReferenceInfo;
 
 public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 
@@ -253,7 +256,7 @@ public class Dstu1BundleFactory implements IVersionSpecificBundleFactory {
 	}
 
 	@Override
-	public IBaseResource getResourceBundle() {
+	public IResource getResourceBundle() {
 		return null;
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/IBundleProvider.java

@@ -28,14 +28,37 @@ import ca.uhn.fhir.model.primitive.InstantDt;
 public interface IBundleProvider {
 
 	/**
+	 * Load the given collection of resources by index, plus any additional resources per the
+	 * server's processing rules (e.g. _include'd resources, OperationOutcome, etc.). For example,
+	 * if the method is invoked with index 0,10 the method might return 10 search results, plus an 
+	 * additional 20 resources which matched a client's _include specification.
+	 * 
 	 * @param theFromIndex The low index (inclusive) to return
 	 * @param theToIndex The high index (exclusive) to return
 	 * @return A list of resources. The size of this list must be at least <code>theToIndex - theFromIndex</code>.
 	 */
 	List<IResource> getResources(int theFromIndex, int theToIndex);
 	
+	/**
+	 * Optionally may be used to signal a preferred page size to the server, e.g. because
+	 * the implementing code recognizes that the resources which will be returned by this
+	 * implementation are expensive to load so a smaller page size should be used. The value
+	 * returned by this method will only be used if the client has not explicitly requested
+	 * a page size.
+	 * 
+	 * @return Returns the preferred page size or <code>null</code>
+	 */
+	Integer preferredPageSize();
+	
+	/**
+	 * Returns the total number of results which match the given query (exclusive of any
+	 * _include's or OperationOutcome)
+	 */
 	int size();
 	
+	/**
+	 * Returns the instant as of which this result was valid
+	 */
 	InstantDt getPublished();
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/IVersionSpecificBundleFactory.java

@@ -23,11 +23,9 @@ package ca.uhn.fhir.rest.server;
 import java.util.List;
 import java.util.Set;
 
-import ca.uhn.fhir.model.api.Include;
-import org.hl7.fhir.instance.model.IBaseResource;
-
 import ca.uhn.fhir.model.api.Bundle;
 import ca.uhn.fhir.model.api.IResource;
+import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
 
 /**
@@ -41,11 +39,11 @@ public interface IVersionSpecificBundleFactory {
 	void addRootPropertiesToBundle(String theAuthor, String theServerBase, String theCompleteUrl, Integer theTotalResults, BundleTypeEnum theBundleType);
 
 	void initializeBundleFromBundleProvider(RestfulServer theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl, boolean thePrettyPrint,
-			int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes);
+			int theOffset, Integer theCount, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes);
 
 	Bundle getDstu1Bundle();
 
-	IBaseResource getResourceBundle();
+	IResource getResourceBundle();
 
 	void initializeBundleFromResourceList(String theAuthor, List<IResource> theResult, String theServerBase, String theCompleteUrl, int theTotalResults, BundleTypeEnum theBundleType);
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/ResponseResourceList.java

@@ -0,0 +1,98 @@
+package ca.uhn.fhir.rest.server;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.instance.model.IBaseResource;
+
+/**
+ * Used by {@link IBundleProvider} to provide a single page worth of results.
+ * 
+ * If the server chooses to, it may return a different number of matching results to the number that the user requested.
+ * For example, if the client requested 100 results but the server decided to return only 10 (perhaps because they were
+ * very large), this value should be set to 10. Note that this count refers only to resources which are included in the
+ * indexes provided to {@link IBundleProvider#getResources(int, int)}, so it should not reflect any additional results
+ * added to the response as a result of _include parameters, OperationOutcome's etc.
+ */
+public class ResponseResourceList {
+	/**
+	 * Singleton unmodifiable empty list
+	 */
+	public static final ResponseResourceList EMPTY = new EmptyResponseResourceList();
+
+	private List<IBaseResource> myIncludeResults;	
+	private List<IBaseResource> myMatchResults;
+	
+	/**
+	 * Adds an "include" results. Include results are results which are added as a result of <code>_include</code>
+	 * directives in search requests.
+	 */
+	public void addIncludeResults(IBaseResource theIncludeResult) {
+		if (myIncludeResults == null) {
+			myIncludeResults = new ArrayList<IBaseResource>();
+		}
+		myIncludeResults.add(theIncludeResult);
+	}
+
+	/**
+	 * Adds a "match" result. A match result is a result added as a direct result of the operation in question. E.g. for
+	 * a search invocation a match result would be a result which directly matched the search criteria. For a history
+	 * invocation it would be a historical version of a resource or the current version.
+	 */
+	public void addMatchResult(IBaseResource theResource) {
+		Validate.notNull(theResource, "theResource must not be null");
+		if (myMatchResults == null) {
+			myMatchResults = new ArrayList<IBaseResource>();
+		}
+		myMatchResults.add(theResource);
+	}
+
+	public List<IBaseResource> getIncludeResults() {
+		return myIncludeResults;
+	}
+
+	public List<IBaseResource> getMatchResults() {
+		return myMatchResults;
+	}
+
+	/**
+	 * Sets the "include" results. Include results are results which are added as a result of <code>_include</code>
+	 * directives in search requests.
+	 */
+	public void setIncludeResults(List<IBaseResource> theIncludeResults) {
+		myIncludeResults = theIncludeResults;
+	}
+
+	/**
+	 * Sets the "match" results. A match result is a result added as a direct result of the operation in question. E.g.
+	 * for a search invocation a match result would be a result which directly matched the search criteria. For a
+	 * history invocation it would be a historical version of a resource or the current version.
+	 */
+	public void setMatchResults(List<IBaseResource> theMatchResults) {
+		myMatchResults = theMatchResults;
+	}
+
+	private static final class EmptyResponseResourceList extends ResponseResourceList {
+		@Override
+		public void addIncludeResults(IBaseResource theIncludeResult) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void addMatchResult(IBaseResource theResource) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void setIncludeResults(List<IBaseResource> theIncludeResults) {
+			throw new UnsupportedOperationException();
+		}
+
+		@Override
+		public void setMatchResults(List<IBaseResource> theMatchResults) {
+			throw new UnsupportedOperationException();
+		}
+	}
+
+}

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/SimpleBundleProvider.java

@@ -60,4 +60,9 @@ public class SimpleBundleProvider implements IBundleProvider {
 		return InstantDt.withCurrentTime();
 	}
 
+	@Override
+	public Integer preferredPageSize() {
+		return null;
+	}
+	
 }

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

@@ -494,6 +494,11 @@ public abstract class BaseFhirDao implements IDao {
 			public int size() {
 				return tuples.size();
 			}
+
+			@Override
+			public Integer preferredPageSize() {
+				return null;
+			}
 		};
 	}
 

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

@@ -659,6 +659,18 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		return new HashSet<Long>(q.getResultList());
 	}
 
+	private List<IResource> addResourcesAsIncludesById(List<IResource> theListToPopulate, Set<IdDt> includePids, List<IResource> resources) {
+		if (!includePids.isEmpty()) {
+			ourLog.info("Loading {} included resources", includePids.size());
+			resources = loadResourcesById(includePids);
+			for (IResource next : resources) {
+				ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(next, BundleEntrySearchModeEnum.INCLUDE);
+			}
+			theListToPopulate.addAll(resources);
+		}
+		return resources;
+	}
+
 	@Override
 	public void addTag(IdDt theId, TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) {
 		StopWatch w = new StopWatch();
@@ -713,50 +725,6 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		return doCreate(theResource, theIfNoneExist, thePerformIndexing);
 	}
 
-	private DaoMethodOutcome doCreate(T theResource, String theIfNoneExist, boolean thePerformIndexing) {
-		StopWatch w = new StopWatch();
-		ResourceTable entity = new ResourceTable();
-		entity.setResourceType(toResourceName(theResource));
-
-		if (isNotBlank(theIfNoneExist)) {
-			Set<Long> match = processMatchUrl(theIfNoneExist, myResourceType);
-			if (match.size() > 1) {
-				String msg = getContext().getLocalizer().getMessage(BaseFhirDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theIfNoneExist, match.size());
-				throw new PreconditionFailedException(msg);
-			} else if (match.size() == 1) {
-				Long pid = match.iterator().next();
-				entity = myEntityManager.find(ResourceTable.class, pid);
-				return toMethodOutcome(entity, theResource).setCreated(false);
-			}
-		}
-
-		if (theResource.getId().isEmpty() == false) {
-			if (isValidPid(theResource.getId())) {
-				throw new UnprocessableEntityException(
-						"This server cannot create an entity with a user-specified numeric ID - Client should not specify an ID when creating a new resource, or should include at least one letter in the ID to force a client-defined ID");
-			}
-			createForcedIdIfNeeded(entity, theResource.getId());
-
-			if (entity.getForcedId() != null) {
-				try {
-					translateForcedIdToPid(theResource.getId());
-					throw new UnprocessableEntityException(getContext().getLocalizer().getMessage(BaseFhirResourceDao.class, "duplicateCreateForcedId", theResource.getId().getIdPart()));
-				} catch (ResourceNotFoundException e) {
-					// good, this ID doesn't exist so we can create it
-				}
-			}
-
-		}
-
-		updateEntity(theResource, entity, false, null, thePerformIndexing, true);
-
-		DaoMethodOutcome outcome = toMethodOutcome(entity, theResource).setCreated(true);
-
-		notifyWriteCompleted();
-		ourLog.info("Processed create on {} in {}ms", myResourceName, w.getMillisAndRestart());
-		return outcome;
-	}
-
 	private Predicate createCompositeParamPart(CriteriaBuilder builder, Root<ResourceTable> from, RuntimeSearchParam left, IQueryParameterType leftValue) {
 		Predicate retVal = null;
 		switch (left.getParamType()) {
@@ -979,6 +947,50 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		return toMethodOutcome(savedEntity, null);
 	}
 
+	private DaoMethodOutcome doCreate(T theResource, String theIfNoneExist, boolean thePerformIndexing) {
+		StopWatch w = new StopWatch();
+		ResourceTable entity = new ResourceTable();
+		entity.setResourceType(toResourceName(theResource));
+
+		if (isNotBlank(theIfNoneExist)) {
+			Set<Long> match = processMatchUrl(theIfNoneExist, myResourceType);
+			if (match.size() > 1) {
+				String msg = getContext().getLocalizer().getMessage(BaseFhirDao.class, "transactionOperationWithMultipleMatchFailure", "CREATE", theIfNoneExist, match.size());
+				throw new PreconditionFailedException(msg);
+			} else if (match.size() == 1) {
+				Long pid = match.iterator().next();
+				entity = myEntityManager.find(ResourceTable.class, pid);
+				return toMethodOutcome(entity, theResource).setCreated(false);
+			}
+		}
+
+		if (theResource.getId().isEmpty() == false) {
+			if (isValidPid(theResource.getId())) {
+				throw new UnprocessableEntityException(
+						"This server cannot create an entity with a user-specified numeric ID - Client should not specify an ID when creating a new resource, or should include at least one letter in the ID to force a client-defined ID");
+			}
+			createForcedIdIfNeeded(entity, theResource.getId());
+
+			if (entity.getForcedId() != null) {
+				try {
+					translateForcedIdToPid(theResource.getId());
+					throw new UnprocessableEntityException(getContext().getLocalizer().getMessage(BaseFhirResourceDao.class, "duplicateCreateForcedId", theResource.getId().getIdPart()));
+				} catch (ResourceNotFoundException e) {
+					// good, this ID doesn't exist so we can create it
+				}
+			}
+
+		}
+
+		updateEntity(theResource, entity, false, null, thePerformIndexing, true);
+
+		DaoMethodOutcome outcome = toMethodOutcome(entity, theResource).setCreated(true);
+
+		notifyWriteCompleted();
+		ourLog.info("Processed create on {} in {}ms", myResourceName, w.getMillisAndRestart());
+		return outcome;
+	}
+
 	@Override
 	public TagList getAllResourceTags() {
 		StopWatch w = new StopWatch();
@@ -987,6 +999,8 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		return tags;
 	}
 
+	protected abstract List<Object> getIncludeValues(FhirTerser theTerser, Include theInclude, IResource theResource, RuntimeResourceDefinition theResourceDef);
+
 	public Class<T> getResourceType() {
 		return myResourceType;
 	}
@@ -1092,6 +1106,11 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 				return retVal;
 			}
 
+			@Override
+			public Integer preferredPageSize() {
+				return null;
+			}
+
 			@Override
 			public int size() {
 				return count;
@@ -1140,6 +1159,159 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		}
 	}
 
+	protected void loadReverseIncludes(List<Long> theMatches, Set<Include> theRevIncludes) {
+		if (theMatches.size() == 0) {
+			return;
+		}
+
+		HashSet<Long> pidsToInclude = new HashSet<Long>();
+		
+		for (Include nextInclude : theRevIncludes) {
+			boolean matchAll = "*".equals(nextInclude.getValue());
+			if (matchAll) {
+				String sql = "SELECT r FROM ResourceLink r WHERE r.myTargetResourcePid IN (:target_pids)";
+				TypedQuery<ResourceLink> q = myEntityManager.createQuery(sql, ResourceLink.class);
+				q.setParameter("target_pids", theMatches);
+				List<ResourceLink> results = q.getResultList();
+				for (ResourceLink resourceLink : results) {
+					pidsToInclude.add(resourceLink.getSourceResourcePid());
+				}
+			} else {
+				int colonIdx = nextInclude.getValue().indexOf(':');
+				if (colonIdx < 2) {
+					continue;
+				}
+				String resType = nextInclude.getValue().substring(0, colonIdx);
+				RuntimeResourceDefinition def = getContext().getResourceDefinition(resType);
+				if (def == null) {
+					ourLog.warn("Unknown resource type in _revinclude=" + nextInclude.getValue());
+					continue;
+				}
+
+				String paramName = nextInclude.getValue().substring(colonIdx + 1);
+				RuntimeSearchParam param = def.getSearchParam(paramName);
+				if (param == null) {
+					ourLog.warn("Unknown param name in _revinclude=" + nextInclude.getValue());
+					continue;
+				}
+
+				for (String nextPath : param.getPathsSplit()) {
+					String sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r.myTargetResourcePid IN (:target_pids)";
+					TypedQuery<ResourceLink> q = myEntityManager.createQuery(sql, ResourceLink.class);
+					q.setParameter("src_path", nextPath);
+					q.setParameter("target_pids", theMatches);
+					List<ResourceLink> results = q.getResultList();
+					for (ResourceLink resourceLink : results) {
+						pidsToInclude.add(resourceLink.getSourceResourcePid());
+					}
+				}
+			}
+		}
+		
+		theMatches.addAll(pidsToInclude);
+	}
+
+	@Override
+	public MetaDt metaAddOperation(IdDt theResourceId, MetaDt theMetaAdd) {
+		StopWatch w = new StopWatch();
+		BaseHasResource entity = readEntity(theResourceId);
+		if (entity == null) {
+			throw new ResourceNotFoundException(theResourceId);
+		}
+
+		List<TagDefinition> tags = toTagList(theMetaAdd);
+
+		//@formatter:off
+		for (TagDefinition nextDef : tags) {
+			
+			boolean hasTag = false;
+			for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
+				if (ObjectUtil.equals(next.getTag().getTagType(), nextDef.getTagType()) && 
+						ObjectUtil.equals(next.getTag().getSystem(), nextDef.getSystem()) && 
+						ObjectUtil.equals(next.getTag().getCode(), nextDef.getCode())) {
+					hasTag = true;
+					break;
+				}
+			}
+
+			if (!hasTag) {
+				entity.setHasTags(true);
+				
+				TagDefinition def = getTag(nextDef.getTagType(), nextDef.getSystem(), nextDef.getCode(), nextDef.getDisplay());
+				BaseTag newEntity = entity.addTag(def);
+				myEntityManager.persist(newEntity);
+			}
+		}
+		//@formatter:on
+
+		myEntityManager.merge(entity);
+		notifyWriteCompleted();
+		ourLog.info("Processed metaAddOperation on {} in {}ms", new Object[] { theResourceId, w.getMillisAndRestart() });
+
+		return metaGetOperation(theResourceId);
+	}
+
+	@Override
+	public MetaDt metaDeleteOperation(IdDt theResourceId, MetaDt theMetaDel) {
+		StopWatch w = new StopWatch();
+		BaseHasResource entity = readEntity(theResourceId);
+		if (entity == null) {
+			throw new ResourceNotFoundException(theResourceId);
+		}
+
+		List<TagDefinition> tags = toTagList(theMetaDel);
+
+		//@formatter:off
+		for (TagDefinition nextDef : tags) {
+			for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
+				if (ObjectUtil.equals(next.getTag().getTagType(), nextDef.getTagType()) && 
+						ObjectUtil.equals(next.getTag().getSystem(), nextDef.getSystem()) && 
+						ObjectUtil.equals(next.getTag().getCode(), nextDef.getCode())) {
+					myEntityManager.remove(next);
+					entity.getTags().remove(next);
+				}
+			}
+		}
+		//@formatter:on
+
+		if (entity.getTags().isEmpty()) {
+			entity.setHasTags(false);
+		}
+
+		myEntityManager.merge(entity);
+
+		ourLog.info("Processed metaDeleteOperation on {} in {}ms", new Object[] { theResourceId.getValue(), w.getMillisAndRestart() });
+
+		return metaGetOperation(theResourceId);
+	}
+
+	@Override
+	public MetaDt metaGetOperation() {
+		String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t WHERE t.myResourceType = :res_type)";
+		TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
+		q.setParameter("res_type", myResourceName);
+		List<TagDefinition> tagDefinitions = q.getResultList();
+
+		MetaDt retVal = super.toMetaDt(tagDefinitions);
+
+		return retVal;
+	}
+
+	@Override
+	public MetaDt metaGetOperation(IdDt theId) {
+		Long pid = super.translateForcedIdToPid(theId);
+
+		String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t WHERE t.myResourceType = :res_type AND t.myResourceId = :res_id)";
+		TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
+		q.setParameter("res_type", myResourceName);
+		q.setParameter("res_id", pid);
+		List<TagDefinition> tagDefinitions = q.getResultList();
+
+		MetaDt retVal = super.toMetaDt(tagDefinitions);
+
+		return retVal;
+	}
+
 	@PostConstruct
 	public void postConstruct() {
 		RuntimeResourceDefinition def = getContext().getResourceDefinition(myResourceType);
@@ -1341,7 +1513,6 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		}
 
 		IBundleProvider retVal = new IBundleProvider() {
-
 			@Override
 			public InstantDt getPublished() {
 				return now;
@@ -1422,6 +1593,11 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 				});
 			}
 
+			@Override
+			public Integer preferredPageSize() {
+				return theParams.getCount();
+			}
+
 			@Override
 			public int size() {
 				return pids.size();
@@ -1433,77 +1609,11 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		return retVal;
 	}
 
-	private List<IResource> addResourcesAsIncludesById(List<IResource> theListToPopulate, Set<IdDt> includePids, List<IResource> resources) {
-		if (!includePids.isEmpty()) {
-			ourLog.info("Loading {} included resources", includePids.size());
-			resources = loadResourcesById(includePids);
-			for (IResource next : resources) {
-				ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.put(next, BundleEntrySearchModeEnum.INCLUDE);
-			}
-			theListToPopulate.addAll(resources);
-		}
-		return resources;
-	}
-
-	protected void loadReverseIncludes(List<Long> theMatches, Set<Include> theRevIncludes) {
-		if (theMatches.size() == 0) {
-			return;
-		}
-
-		HashSet<Long> pidsToInclude = new HashSet<Long>();
-		
-		for (Include nextInclude : theRevIncludes) {
-			boolean matchAll = "*".equals(nextInclude.getValue());
-			if (matchAll) {
-				String sql = "SELECT r FROM ResourceLink r WHERE r.myTargetResourcePid IN (:target_pids)";
-				TypedQuery<ResourceLink> q = myEntityManager.createQuery(sql, ResourceLink.class);
-				q.setParameter("target_pids", theMatches);
-				List<ResourceLink> results = q.getResultList();
-				for (ResourceLink resourceLink : results) {
-					pidsToInclude.add(resourceLink.getSourceResourcePid());
-				}
-			} else {
-				int colonIdx = nextInclude.getValue().indexOf(':');
-				if (colonIdx < 2) {
-					continue;
-				}
-				String resType = nextInclude.getValue().substring(0, colonIdx);
-				RuntimeResourceDefinition def = getContext().getResourceDefinition(resType);
-				if (def == null) {
-					ourLog.warn("Unknown resource type in _revinclude=" + nextInclude.getValue());
-					continue;
-				}
-
-				String paramName = nextInclude.getValue().substring(colonIdx + 1);
-				RuntimeSearchParam param = def.getSearchParam(paramName);
-				if (param == null) {
-					ourLog.warn("Unknown param name in _revinclude=" + nextInclude.getValue());
-					continue;
-				}
-
-				for (String nextPath : param.getPathsSplit()) {
-					String sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r.myTargetResourcePid IN (:target_pids)";
-					TypedQuery<ResourceLink> q = myEntityManager.createQuery(sql, ResourceLink.class);
-					q.setParameter("src_path", nextPath);
-					q.setParameter("target_pids", theMatches);
-					List<ResourceLink> results = q.getResultList();
-					for (ResourceLink resourceLink : results) {
-						pidsToInclude.add(resourceLink.getSourceResourcePid());
-					}
-				}
-			}
-		}
-		
-		theMatches.addAll(pidsToInclude);
-	}
-
 	@Override
 	public IBundleProvider search(String theParameterName, IQueryParameterType theValue) {
 		return search(Collections.singletonMap(theParameterName, theValue));
 	}
 
-	protected abstract List<Object> getIncludeValues(FhirTerser theTerser, Include theInclude, IResource theResource, RuntimeResourceDefinition theResourceDef);
-
 	@Override
 	public Set<Long> searchForIds(Map<String, IQueryParameterType> theParams) {
 		SearchParameterMap map = new SearchParameterMap();
@@ -1708,6 +1818,22 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		return qp;
 	}
 
+	private ArrayList<TagDefinition> toTagList(MetaDt theMeta) {
+		ArrayList<TagDefinition> retVal = new ArrayList<TagDefinition>();
+
+		for (CodingDt next : theMeta.getTag()) {
+			retVal.add(new TagDefinition(TagTypeEnum.TAG, next.getSystem(), next.getCode(), next.getDisplay()));
+		}
+		for (CodingDt next : theMeta.getSecurity()) {
+			retVal.add(new TagDefinition(TagTypeEnum.SECURITY_LABEL, next.getSystem(), next.getCode(), next.getDisplay()));
+		}
+		for (UriDt next : theMeta.getProfile()) {
+			retVal.add(new TagDefinition(TagTypeEnum.PROFILE, BaseFhirDao.NS_JPA_PROFILE, next.getValue(), null));
+		}
+
+		return retVal;
+	}
+
 	@Override
 	public DaoMethodOutcome update(T theResource) {
 		return update(theResource, null);
@@ -1788,121 +1914,4 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
 		}
 	}
 
-	@Override
-	public MetaDt metaGetOperation() {
-		String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t WHERE t.myResourceType = :res_type)";
-		TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
-		q.setParameter("res_type", myResourceName);
-		List<TagDefinition> tagDefinitions = q.getResultList();
-
-		MetaDt retVal = super.toMetaDt(tagDefinitions);
-
-		return retVal;
-	}
-
-	@Override
-	public MetaDt metaGetOperation(IdDt theId) {
-		Long pid = super.translateForcedIdToPid(theId);
-
-		String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t WHERE t.myResourceType = :res_type AND t.myResourceId = :res_id)";
-		TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
-		q.setParameter("res_type", myResourceName);
-		q.setParameter("res_id", pid);
-		List<TagDefinition> tagDefinitions = q.getResultList();
-
-		MetaDt retVal = super.toMetaDt(tagDefinitions);
-
-		return retVal;
-	}
-
-	@Override
-	public MetaDt metaDeleteOperation(IdDt theResourceId, MetaDt theMetaDel) {
-		StopWatch w = new StopWatch();
-		BaseHasResource entity = readEntity(theResourceId);
-		if (entity == null) {
-			throw new ResourceNotFoundException(theResourceId);
-		}
-
-		List<TagDefinition> tags = toTagList(theMetaDel);
-
-		//@formatter:off
-		for (TagDefinition nextDef : tags) {
-			for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
-				if (ObjectUtil.equals(next.getTag().getTagType(), nextDef.getTagType()) && 
-						ObjectUtil.equals(next.getTag().getSystem(), nextDef.getSystem()) && 
-						ObjectUtil.equals(next.getTag().getCode(), nextDef.getCode())) {
-					myEntityManager.remove(next);
-					entity.getTags().remove(next);
-				}
-			}
-		}
-		//@formatter:on
-
-		if (entity.getTags().isEmpty()) {
-			entity.setHasTags(false);
-		}
-
-		myEntityManager.merge(entity);
-
-		ourLog.info("Processed metaDeleteOperation on {} in {}ms", new Object[] { theResourceId.getValue(), w.getMillisAndRestart() });
-
-		return metaGetOperation(theResourceId);
-	}
-
-	@Override
-	public MetaDt metaAddOperation(IdDt theResourceId, MetaDt theMetaAdd) {
-		StopWatch w = new StopWatch();
-		BaseHasResource entity = readEntity(theResourceId);
-		if (entity == null) {
-			throw new ResourceNotFoundException(theResourceId);
-		}
-
-		List<TagDefinition> tags = toTagList(theMetaAdd);
-
-		//@formatter:off
-		for (TagDefinition nextDef : tags) {
-			
-			boolean hasTag = false;
-			for (BaseTag next : new ArrayList<BaseTag>(entity.getTags())) {
-				if (ObjectUtil.equals(next.getTag().getTagType(), nextDef.getTagType()) && 
-						ObjectUtil.equals(next.getTag().getSystem(), nextDef.getSystem()) && 
-						ObjectUtil.equals(next.getTag().getCode(), nextDef.getCode())) {
-					hasTag = true;
-					break;
-				}
-			}
-
-			if (!hasTag) {
-				entity.setHasTags(true);
-				
-				TagDefinition def = getTag(nextDef.getTagType(), nextDef.getSystem(), nextDef.getCode(), nextDef.getDisplay());
-				BaseTag newEntity = entity.addTag(def);
-				myEntityManager.persist(newEntity);
-			}
-		}
-		//@formatter:on
-
-		myEntityManager.merge(entity);
-		notifyWriteCompleted();
-		ourLog.info("Processed metaAddOperation on {} in {}ms", new Object[] { theResourceId, w.getMillisAndRestart() });
-
-		return metaGetOperation(theResourceId);
-	}
-
-	private ArrayList<TagDefinition> toTagList(MetaDt theMeta) {
-		ArrayList<TagDefinition> retVal = new ArrayList<TagDefinition>();
-
-		for (CodingDt next : theMeta.getTag()) {
-			retVal.add(new TagDefinition(TagTypeEnum.TAG, next.getSystem(), next.getCode(), next.getDisplay()));
-		}
-		for (CodingDt next : theMeta.getSecurity()) {
-			retVal.add(new TagDefinition(TagTypeEnum.SECURITY_LABEL, next.getSystem(), next.getCode(), next.getDisplay()));
-		}
-		for (UriDt next : theMeta.getProfile()) {
-			retVal.add(new TagDefinition(TagTypeEnum.PROFILE, BaseFhirDao.NS_JPA_PROFILE, next.getValue(), null));
-		}
-
-		return retVal;
-	}
-
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java

@@ -15,6 +15,7 @@ import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.TreeSet;
 import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
@@ -50,6 +51,7 @@ import ca.uhn.fhir.model.dstu.resource.Practitioner;
 import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
 import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
 import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
+import ca.uhn.fhir.model.dstu2.resource.Condition;
 import ca.uhn.fhir.model.dstu2.resource.DiagnosticOrder;
 import ca.uhn.fhir.model.dstu2.resource.DocumentManifest;
 import ca.uhn.fhir.model.dstu2.resource.DocumentReference;
@@ -62,7 +64,9 @@ import ca.uhn.fhir.model.dstu2.resource.Parameters;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.dstu2.valueset.EncounterClassEnum;
 import ca.uhn.fhir.model.dstu2.valueset.EncounterStateEnum;
+import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.IntegerDt;
 import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
 import ca.uhn.fhir.model.valueset.BundleTypeEnum;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
@@ -277,11 +281,10 @@ public class ResourceProviderDstu2Test {
 		}
 	}
 
-	
 	@Test
 	public void testSearchWithInclude() throws Exception {
 		Organization org = new Organization();
-		org.addIdentifier().setSystem("urn:system:rpdstu2").setValue( "testSearchWithInclude01");
+		org.addIdentifier().setSystem("urn:system:rpdstu2").setValue("testSearchWithInclude01");
 		IdDt orgId = ourClient.create().resource(org).prettyPrint().encodedXml().execute().getId();
 
 		Patient pat = new Patient();
@@ -347,7 +350,6 @@ public class ResourceProviderDstu2Test {
 			ids.add(next.getResource().getId());
 		}
 
-		
 		assertThat(ids, containsInAnyOrder(patientId, devId, obsId, encId, orgId1, orgId2));
 
 		// _revinclude's are counted but not _include's
@@ -360,10 +362,80 @@ public class ResourceProviderDstu2Test {
 	 * See #147
 	 */
 	@Test
-	public void testEverythingDoesnRepeatPatient() throws Exception {
+	public void testEverythingDoesntRepeatPatient() throws Exception {
 		ca.uhn.fhir.model.dstu2.resource.Bundle b;
 		b = ourFhirCtx.newJsonParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, new InputStreamReader(ResourceProviderDstu2Test.class.getResourceAsStream("/bug147-bundle.json")));
 
+		ca.uhn.fhir.model.dstu2.resource.Bundle resp = ourClient.transaction().withBundle(b).execute();
+		List<IdDt> ids = new ArrayList<IdDt>();
+		for (Entry next : resp.getEntry()) {
+			IdDt toAdd = new IdDt(next.getTransactionResponse().getLocation()).toUnqualifiedVersionless();
+			ids.add(toAdd);
+		}
+		ourLog.info("Created: " + ids.toString());
+
+		IdDt patientId = new IdDt(resp.getEntry().get(1).getTransactionResponse().getLocation());
+		assertEquals("Patient", patientId.getResourceType());
+
+		{
+			Parameters output = ourClient.operation().onInstance(patientId).named("everything").withNoParameters(Parameters.class).execute();
+			b = (ca.uhn.fhir.model.dstu2.resource.Bundle) output.getParameterFirstRep().getResource();
+
+			ids = new ArrayList<IdDt>();
+			boolean dupes = false;
+			for (Entry next : b.getEntry()) {
+				IdDt toAdd = next.getResource().getId().toUnqualifiedVersionless();
+				dupes = dupes | ids.contains(toAdd);
+				ids.add(toAdd);
+			}
+			ourLog.info("$everything: " + ids.toString());
+
+			assertFalse(ids.toString(), dupes);
+
+			/*
+			 * Condition/11 is the 11th resource and the default page size is 10 so we don't show the 11th.
+			 */
+			assertThat(ids.toString(), not(containsString("Condition")));
+		}
+
+		/*
+		 * Now try with a size specified
+		 */
+		{
+			Parameters input = new Parameters();
+			input.addParameter().setName(Constants.PARAM_COUNT).setValue(new IntegerDt(100));
+			Parameters output = ourClient.operation().onInstance(patientId).named("everything").withParameters(input).execute();
+			b = (ca.uhn.fhir.model.dstu2.resource.Bundle) output.getParameterFirstRep().getResource();
+
+			ids = new ArrayList<IdDt>();
+			boolean dupes = false;
+			for (Entry next : b.getEntry()) {
+				IdDt toAdd = next.getResource().getId().toUnqualifiedVersionless();
+				dupes = dupes | ids.contains(toAdd);
+				ids.add(toAdd);
+			}
+			ourLog.info("$everything: " + ids.toString());
+
+			assertFalse(ids.toString(), dupes);
+			assertThat(ids.toString(), containsString("Condition"));
+
+		}
+	}
+
+	/**
+	 * See #148
+	 */
+	@Test
+	public void testEverythingIncludesCondition() throws Exception {
+		ca.uhn.fhir.model.dstu2.resource.Bundle b = new ca.uhn.fhir.model.dstu2.resource.Bundle();
+		Patient p = new Patient();
+		p.setId("1");
+		b.addEntry().setResource(p).getTransaction().setMethod(HTTPVerbEnum.POST);
+
+		Condition c = new Condition();
+		c.getPatient().setReference("Patient/1");
+		b.addEntry().setResource(c).getTransaction().setMethod(HTTPVerbEnum.POST);
+
 		ca.uhn.fhir.model.dstu2.resource.Bundle resp = ourClient.transaction().withBundle(b).execute();
 
 		ourLog.info(ourFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
@@ -375,16 +447,14 @@ public class ResourceProviderDstu2Test {
 		b = (ca.uhn.fhir.model.dstu2.resource.Bundle) output.getParameterFirstRep().getResource();
 
 		List<IdDt> ids = new ArrayList<IdDt>();
-		boolean dupes = false;
 		for (Entry next : b.getEntry()) {
 			IdDt toAdd = next.getResource().getId().toUnqualifiedVersionless();
-			dupes = dupes | ids.contains(toAdd);
 			ids.add(toAdd);
 		}
 
-		ourLog.info(ids.toString());
+		assertThat(ids.toString(), containsString("Patient/"));
+		assertThat(ids.toString(), containsString("Condition/"));
 
-		assertFalse(ids.toString(), dupes);
 	}
 
 	@Test
@@ -477,7 +547,7 @@ public class ResourceProviderDstu2Test {
 		int initialSize = client.search().forResource(DiagnosticOrder.class).execute().size();
 
 		DiagnosticOrder res = new DiagnosticOrder();
-		res.addIdentifier().setSystem("urn:foo").setValue( "123");
+		res.addIdentifier().setSystem("urn:foo").setValue("123");
 
 		client.create().resource(res).execute();
 

hapi-fhir-jpaserver-base/src/test/resources/bug147-bundle.json

@@ -24,7 +24,11 @@
 	"entry": 
 	[
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "Patient",
@@ -114,7 +118,11 @@
 		},
 
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "Encounter",
@@ -148,7 +156,11 @@
 		},
 
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "ClinicalImpression",
@@ -193,7 +205,11 @@
 		},
 
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "ClinicalImpression",
@@ -238,7 +254,11 @@
 		},
 
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "Encounter",
@@ -267,7 +287,11 @@
 		},
 
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "ClinicalImpression",
@@ -311,7 +335,11 @@
 		},
 
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "Encounter",
@@ -340,7 +368,11 @@
 		},
 
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "ClinicalImpression",
@@ -384,7 +416,11 @@
 		},
 
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "Observation",
@@ -417,7 +453,11 @@
 		},
 
 		{
-			"transaction": { "method":"POST" },
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
 			"resource": 
 			{
 				"resourceType": "Observation",
@@ -447,7 +487,50 @@
 			{
 				"mode": "match"
 			}
-		}
+		},
 
+		{
+			"transaction": 
+			{
+				"method": "POST"
+			},
+
+			"resource": 
+			{
+				"resourceType": "Condition",
+				"id": "20443",
+				"meta": 
+				{
+					"versionId": "1",
+					"lastUpdated": "2015-04-03T22:56:49.886-04:00"
+				},
+
+				"text": 
+				{
+					"status": "generated",
+					"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">pharyngitis working </div>"
+				},
+
+				"patient": 
+				{
+					"reference": "Patient/1702",
+					"display": "Eve Everywoman "
+				},
+
+				"code": 
+				{
+					"coding": 
+					[
+						{
+							"system": "http://loinc.org",
+							"code": "28397-8",
+							"display": "pharyngitis"
+						}
+					],
+
+					"text": "pharyngitis"
+				}
+			}
+		}
 	]
 }

hapi-fhir-jpaserver-base/src/test/resources/fhir-jpabase-spring-test-config.xml

@@ -35,7 +35,7 @@
 		<property name="persistenceUnitName" value="FHIR_UT" />
 		<property name="jpaVendorAdapter">
 			<bean class="org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter">
-				<property name="showSql" value="true" />
+				<property name="showSql" value="false" />
 				<property name="generateDdl" value="true" />
 				<!-- <property name="databasePlatform" value="org.hibernate.dialect.HSQLDialect" />  -->
 				<property name="databasePlatform" value="org.hibernate.dialect.DerbyTenSevenDialect" />

hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2/Dstu2BundleFactory.java

@@ -268,7 +268,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
 	}
 
 	@Override
-	public IBaseResource getResourceBundle() {
+	public IResource getResourceBundle() {
 		return myBundle;
 	}
 

src/changes/changes.xml

@@ -123,6 +123,9 @@
 				the main focus resource if it was referred to in a deep chain. Thanks
 				to David Hay for reporting!
 			</action>
+			<action type="add" issue="148">
+				JPA Server $everything operation now allows a _count parameter
+			</action>
 		</release>
 		<release version="0.9" date="2015-Mar-14">
 			<action type="add">