Merge 663125f into e53d747

hapifhir · May 9, 2017 · d44cca3 · d44cca3
2 parents e53d747 + 663125f
commit d44cca3
Show file tree

Hide file tree

Showing 50 changed files with 5,630 additions and 14 deletions.
diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeResourceDefinition.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeResourceDefinition.java
@@ -28,6 +28,7 @@
 import java.util.List;
 import java.util.Map;
 
+import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -48,7 +49,9 @@ public class RuntimeResourceDefinition extends BaseRuntimeElementCompositeDefini
 	private List<RuntimeSearchParam> mySearchParams;
 	private final FhirVersionEnum myStructureVersion;
 	private volatile RuntimeResourceDefinition myBaseDefinition;
-
+
+
+
 	public RuntimeResourceDefinition(FhirContext theContext, String theResourceName, Class<? extends IBaseResource> theClass, ResourceDef theResourceAnnotation, boolean theStandardType, Map<Class<? extends IBase>, BaseRuntimeElementDefinition<?>> theClassToElementDefinitions) {
 		super(theResourceName, theClass, theStandardType, theContext, theClassToElementDefinitions);
 		myContext = theContext;
@@ -68,6 +71,7 @@ public RuntimeResourceDefinition(FhirContext theContext, String theResourceName,
 
 	}
 
+
 	public void addSearchParam(RuntimeSearchParam theParam) {
 		myNameToSearchParam.put(theParam.getName(), theParam);
 	}

diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml
@@ -14,6 +14,28 @@
 	<name>HAPI FHIR JPA Server</name>
 
 	<dependencies>
+		<dependency>
+			<groupId>com.fasterxml.jackson.jaxrs</groupId>
+			<artifactId>jackson-jaxrs-json-provider</artifactId>
+			<version>${jackson.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>com.fasterxml.jackson.datatype</groupId>
+			<artifactId>jackson-datatype-hibernate4</artifactId>
+			<version>${jackson.version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-lang3</artifactId>
+			<version>3.5</version>
+		</dependency>
+		<dependency>
+			<groupId>net.sf.saxon</groupId>
+			<artifactId>Saxon-HE</artifactId>
+			<version>9.5.1-5</version>
+		</dependency>
+
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-csv</artifactId>
@@ -363,6 +385,7 @@
 
 	<properties>
 		<skip-hib4>false</skip-hib4>
+		<jackson.version>2.7.1</jackson.version>
 	</properties>
 
 	<build>

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
@@ -886,6 +886,7 @@ public IBundleProvider search(final SearchParameterMap theParams, RequestDetails
 
 			if (theRequestDetails.isSubRequest()) {
 				theParams.setLoadSynchronous(true);
+				int max =  myDaoConfig.getMaximumSearchResultCountInTransaction();
 				theParams.setLoadSynchronousUpTo(myDaoConfig.getMaximumSearchResultCountInTransaction());
 			}
 

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
@@ -180,7 +180,7 @@ public int getIncludeLimit() {
 	@Deprecated
 	public List<IServerInterceptor> getInterceptors() {
 		if (myInterceptors == null) {
-			return Collections.emptyList();
+			myInterceptors = new ArrayList<IServerInterceptor>();
 		}
 		return myInterceptors;
 	}

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu1.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu1.java
@@ -41,6 +41,11 @@
 
 public class FhirResourceDaoDstu1<T extends IResource> extends BaseHapiFhirResourceDao<T> {
 
+	@Override
+	public RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(String criteria) {
+		return null;
+	}
+
 	@Override
 	protected List<Object> getIncludeValues(FhirTerser t, Include next, IBaseResource nextResource, RuntimeResourceDefinition def) {
 		List<Object> values;

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2.java
@@ -145,6 +145,11 @@ public MethodOutcome validate(T theResource, IIdType theId, String theRawResourc
 
 	}
 
+	@Override
+	public RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(String criteria) {
+		return null;
+	}
+
 	private class IdChecker implements IValidatorModule {
 
 		private ValidationModeEnum myMode;

diff --git a/...ir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java b/...ir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoSubscriptionDstu2.java
@@ -29,6 +29,7 @@
 
 import javax.persistence.Query;
 
+import ca.uhn.fhir.model.dstu2.valueset.SubscriptionChannelTypeEnum;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
@@ -116,8 +117,12 @@ public synchronized List<IBaseResource> getUndeliveredResourcesAndPurge(Long the
 	}
 
 	@Override
+	public int pollForNewUndeliveredResources() {
+		return pollForNewUndeliveredResources((String) null);
+	}
+
 	@Transactional(propagation = Propagation.NOT_SUPPORTED)
-	public synchronized int pollForNewUndeliveredResources() {
+	public synchronized int pollForNewUndeliveredResources(final String resourceType) {
 		if (getConfig().isSubscriptionEnabled() == false) {
 			return 0;
 		}
@@ -141,16 +146,28 @@ public Collection<Long> doInTransaction(TransactionStatus theStatus) {
 				@Override
 				public Integer doInTransaction(TransactionStatus theStatus) {
 					SubscriptionTable nextSubscriptionTable = mySubscriptionTableDao.findOne(nextSubscriptionTablePid);
-					return pollForNewUndeliveredResources(nextSubscriptionTable);
+					return pollForNewUndeliveredResources(nextSubscriptionTable, resourceType);
 				}
 			});
 		}
 
 		return retVal;
 	}
 
-	private int pollForNewUndeliveredResources(SubscriptionTable theSubscriptionTable) {
+	private int pollForNewUndeliveredResources(SubscriptionTable theSubscriptionTable, String resourceType) {
 		Subscription subscription = toResource(Subscription.class, theSubscriptionTable.getSubscriptionResource(), false);
+		ourLog.info("subscription for " + resourceType + " with criteria " + subscription.getCriteria());
+
+		if (!subscription.getChannel().getType().equals(SubscriptionChannelTypeEnum.WEBSOCKET.getCode())){
+			ourLog.info("Skipping non web socket subscription");
+			return 0;
+		}
+
+		if (resourceType != null && subscription.getCriteria() != null && !subscription.getCriteria().startsWith(resourceType)) {
+			ourLog.info("Skipping subscription search for " + resourceType + " because it does not match the criteria " + subscription.getCriteria());
+			return 0;
+		}
+
 		RuntimeResourceDefinition resourceDef = validateCriteriaAndReturnResourceDefinition(subscription);
 		SearchParameterMap criteriaUrl = translateMatchUrl(this, getContext(), subscription.getCriteria(), resourceDef);
 
@@ -297,7 +314,7 @@ protected ResourceTable updateEntity(IBaseResource theResource, ResourceTable th
 		return retVal;
 	}
 
-	private RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(Subscription theResource) {
+	public RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(Subscription theResource) {
 		String query = theResource.getCriteria();
 		if (isBlank(query)) {
 			throw new UnprocessableEntityException("Subscription.criteria must be populated");

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDao.java
@@ -25,6 +25,7 @@
 import java.util.Map;
 import java.util.Set;
 
+import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import org.hl7.fhir.dstu3.model.CodeSystem;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.instance.model.api.IBaseMetaType;
@@ -243,6 +244,10 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 	 */
 	MethodOutcome validate(T theResource, IIdType theId, String theRawResource, EncodingEnum theEncoding, ValidationModeEnum theMode, String theProfile, RequestDetails theRequestDetails);
 
+	RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(String criteria);
+
+	<R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) ;
+
 	// /**
 	// * Invoke the everything operation
 	// */

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoSubscription.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoSubscription.java
@@ -37,4 +37,5 @@ public interface IFhirResourceDaoSubscription<T extends IBaseResource> extends I
 
 	void pollForNewUndeliveredResourcesScheduler();
 
+	int pollForNewUndeliveredResources(String resourceType);
 }
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
@@ -1474,7 +1474,8 @@ private String determineSystemIfMissing(String theParamName, String code, String
 	public void loadResourcesByPid(Collection<Long> theIncludePids, List<IBaseResource> theResourceListToPopulate, Set<Long> theRevIncludedPids, boolean theForHistoryOperation,
 			EntityManager entityManager, FhirContext context, IDao theDao) {
 		if (theIncludePids.isEmpty()) {
-			return;
+			ourLog.info("The include pids are empty");
+			//return;
 		}
 
 		// Dupes will cause a crash later anyhow, but this is expensive so only do it

diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3.java
@@ -26,6 +26,7 @@
 import java.util.Collections;
 import java.util.List;
 
+import ca.uhn.fhir.context.FhirContext;
 import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.OperationOutcome;
 import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
@@ -71,6 +72,9 @@ public class FhirResourceDaoDstu3<T extends IAnyResource> extends BaseHapiFhirRe
 	@Qualifier("myInstanceValidatorDstu3")
 	private IValidatorModule myInstanceValidator;
 
+	@Autowired
+	private FhirContext fhirContext;
+
 	@Override
 	protected IBaseOperationOutcome createOperationOutcome(String theSeverity, String theMessage, String theCode) {
 		OperationOutcome oo = new OperationOutcome();
@@ -163,6 +167,26 @@ public MethodOutcome validate(T theResource, IIdType theId, String theRawResourc
 
 	}
 
+	/**
+	 * Get the resource definition from the criteria which specifies the resource type
+	 * @param criteria
+	 * @return
+	 */
+	@Override
+	public RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(String criteria) {
+		String resourceName;
+		if(criteria == null || criteria.trim().isEmpty()){
+			throw new IllegalArgumentException("Criteria cannot be empty");
+		}
+		if(criteria.contains("?")){
+			resourceName = criteria.substring(0, criteria.indexOf("?"));
+		}else{
+			resourceName = criteria;
+		}
+
+		return fhirContext.getResourceDefinition(resourceName);
+	}
+
 	private class IdChecker implements IValidatorModule {
 
 		private ValidationModeEnum myMode;

diff --git a/...server-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSubscriptionDstu3.java b/...server-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSubscriptionDstu3.java
@@ -119,9 +119,13 @@ public synchronized List<IBaseResource> getUndeliveredResourcesAndPurge(Long the
 		return retVal;
 	}
 
+	public int pollForNewUndeliveredResources() {
+      return pollForNewUndeliveredResources((String) null);
+  }
+
 	@Override
 	@Transactional(propagation = Propagation.NOT_SUPPORTED)
-	public synchronized int pollForNewUndeliveredResources() {
+    public synchronized int pollForNewUndeliveredResources(final String resourceType) {
 		if (getConfig().isSubscriptionEnabled() == false) {
 			return 0;
 		}
@@ -145,16 +149,27 @@ public Collection<Long> doInTransaction(TransactionStatus theStatus) {
 				@Override
 				public Integer doInTransaction(TransactionStatus theStatus) {
 					SubscriptionTable nextSubscriptionTable = mySubscriptionTableDao.findOne(nextSubscriptionTablePid);
-					return pollForNewUndeliveredResources(nextSubscriptionTable);
+                    return pollForNewUndeliveredResources(nextSubscriptionTable, resourceType);
 				}
 			});
 		}
 
 		return retVal;
 	}
 
-	private int pollForNewUndeliveredResources(SubscriptionTable theSubscriptionTable) {
+    private int pollForNewUndeliveredResources(SubscriptionTable theSubscriptionTable, String resourceType) {
 		Subscription subscription = toResource(Subscription.class, theSubscriptionTable.getSubscriptionResource(), false);
+        if (subscription.getChannel().getType() != Subscription.SubscriptionChannelType.WEBSOCKET){
+            ourLog.info("Skipping non web socket subscription");
+            return 0;
+        }
+
+        ourLog.info("subscription for " + resourceType + " with criteria " + subscription.getCriteria());
+        if (resourceType != null && subscription.getCriteria() != null && !subscription.getCriteria().startsWith(resourceType)) {
+            ourLog.info("Skipping subscription search for " + resourceType + " because it does not match the criteria " + subscription.getCriteria());
+            return 0;
+        }
+
 		RuntimeResourceDefinition resourceDef = validateCriteriaAndReturnResourceDefinition(subscription);
 		SearchParameterMap criteriaUrl = translateMatchUrl(this, getContext(), subscription.getCriteria(), resourceDef);
 
@@ -302,7 +317,7 @@ protected ResourceTable updateEntity(IBaseResource theResource, ResourceTable th
 		return retVal;
 	}
 
-	private RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(Subscription theResource) {
+	public RuntimeResourceDefinition validateCriteriaAndReturnResourceDefinition(Subscription theResource) {
 		String query = theResource.getCriteria();
 		if (isBlank(query)) {
 			throw new UnprocessableEntityException("Subscription.criteria must be populated");