Work on JPA

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

@@ -57,6 +57,8 @@ import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 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.interceptor.IServerInterceptor;
@@ -73,6 +75,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 	@Autowired
 	private DaoConfig myDaoConfig;
+
 	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
 	@Autowired
@@ -86,6 +89,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Autowired()
 	protected ISearchResultDao mySearchResultDao;
 	private String mySecondaryPrimaryKeyParamName;
+	@Autowired
+	private ISearchParamRegistry mySerarchParamRegistry;
 	@Autowired()
 	protected IHapiTerminologySvc myTerminologySvc;
 
@@ -662,6 +667,30 @@ 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);
@@ -863,9 +892,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return search(map);
 	}
 
-	@Autowired
-	private ISearchParamRegistry mySerarchParamRegistry;
-
 	@Override
 	public IBundleProvider search(final SearchParameterMap theParams) {
 		// Notify interceptors
@@ -988,6 +1014,23 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		return retVal;
 	}
 
+	@Override
+	public void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget) {
+		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);
+			}
+			
+			aaaa
+		}
+	}
+
 	@Override
 	public DaoMethodOutcome update(T theResource) {
 		return update(theResource, null, null);
@@ -1078,30 +1121,6 @@ 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/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/dstu3/FhirResourceDaoSearchParameterDstu3.java

@@ -29,17 +29,28 @@ import org.springframework.scheduling.annotation.Scheduled;
 
 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.rest.server.exceptions.InvalidRequestException;
 
 public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<SearchParameter>implements IFhirResourceDaoSearchParameter<SearchParameter> {
 
 	@Autowired
 	private IFhirSystemDao<Bundle, Meta> mySystemDao;
 	
+	@Override
+	protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
+		super.validateResourceForStorage(theResource, theEntityToSave);
+		
+		if (theResource.getStatus() == null) {
+			throw new InvalidRequestException("Resource.status is missing or invalid: " + theResource.getStatusElement().getValueAsString());
+		}
+	}
+
 	/**
 	 * 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)

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

@@ -0,0 +1,56 @@
+package ca.uhn.fhir.jpa.provider.dstu3;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+
+import org.hl7.fhir.dstu3.model.SearchParameter;
+import org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Test;
+
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+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 {
+		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 (InvalidRequestException e) {
+			assertEquals("", e.getMessage());
+		}
+	}
+
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
+}

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

@@ -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,