implements #29 switch from logical reference to chained parameters

Implements a workaround feature, that can be disable replacing
"patient:identifer" with "patient.identifier" before performing searches
against the fhir-bridge.

Author: hhund

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/HapiFhirClientFactory.java

@@ -53,6 +53,7 @@ public class HapiFhirClientFactory
 	private final String bearerToken;
 
 	private final boolean hapiClientVerbose;
+	private final boolean useChainedParameterNotLogicalReference;
 
 	private final ApacheRestfulClientFactory clientFactory;
 
@@ -73,10 +74,14 @@ public class HapiFhirClientFactory
 	 *            >= -1, -1: system default, 0: infinity, >0: timeout in ms
 	 * @param connectionRequestTimeout
 	 *            >= -1, -1: system default, 0: infinity, >0: timeout in ms
+	 * @param hapiClientVerbose
+	 *            <code>true</code> for verbose logging
+	 * @param useChainedParameterNotLogicalReference
+	 *            <code>true</code> to enable modifying the search parameters during data storage
 	 */
 	public HapiFhirClientFactory(FhirContext fhirContext, String serverBase, String basicAuthUsername,
 			String basicAuthPassword, String bearerToken, int connectTimeout, int socketTimeout,
-			int connectionRequestTimeout, boolean hapiClientVerbose)
+			int connectionRequestTimeout, boolean hapiClientVerbose, boolean useChainedParameterNotLogicalReference)
 	{
 		if (fhirContext != null)
 			this.fhirContext = fhirContext;
@@ -89,6 +94,7 @@ public HapiFhirClientFactory(FhirContext fhirContext, String serverBase, String
 		this.bearerToken = bearerToken;
 
 		this.hapiClientVerbose = hapiClientVerbose;
+		this.useChainedParameterNotLogicalReference = useChainedParameterNotLogicalReference;
 
 		if (isConfigured())
 		{
@@ -504,4 +510,9 @@ private void configureLoggingInterceptor(IGenericClient client)
 			client.registerInterceptor(loggingInterceptor);
 		}
 	}
+
+	public boolean shouldUseChainedParameterNotLogicalReference()
+	{
+		return useChainedParameterNotLogicalReference;
+	}
 }

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/FhirBridgeClient.java

@@ -30,8 +30,6 @@ public class FhirBridgeClient extends AbstractComplexFhirClient
 	private static final Logger logger = LoggerFactory.getLogger(FhirBridgeClient.class);
 	private static final OutcomeLogger outcomeLogger = new OutcomeLogger(logger);
 
-	public static final String RFC_4122_SYSTEM = "urn:ietf:rfc:4122";
-
 	/**
 	 * @param fhirContext
 	 *            not <code>null</code>
@@ -209,32 +207,35 @@ private void createOrUpdateEntry(int index, BundleEntryComponent entry, Patient
 
 	private Optional<Resource> findResourceInLocalFhirStore(String url, Class<? extends Resource> resourceType)
 	{
+		if (clientFactory.shouldUseChainedParameterNotLogicalReference())
+			url = url.replace("patient:identifier", "patient.identifier");
+
 		try
 		{
-			Bundle patientBundle = clientFactory.getFhirStoreClient().search().byUrl(url).sort()
+			Bundle resultBundle = clientFactory.getFhirStoreClient().search().byUrl(url).sort()
 					.descending("_lastUpdated").count(1).returnBundle(Bundle.class).execute();
 
 			if (logger.isDebugEnabled())
 				logger.debug("{} search-bundle result: {}", resourceType.getAnnotation(ResourceDef.class).name(),
-						fhirContext.newJsonParser().encodeResourceToString(patientBundle));
+						fhirContext.newJsonParser().encodeResourceToString(resultBundle));
 
-			if (patientBundle.getTotal() > 0)
+			if (resultBundle.getTotal() > 0)
 			{
-				if (patientBundle.getTotal() > 1)
+				if (resultBundle.getTotal() > 1)
 					logger.warn("FHIR store has more than one Resource with url {}, using last updated", url);
 
-				if (patientBundle.getEntryFirstRep().hasResource()
-						&& resourceType.isInstance(patientBundle.getEntryFirstRep().getResource()))
-					return Optional.of((Patient) patientBundle.getEntryFirstRep().getResource());
+				if (resultBundle.getEntryFirstRep().hasResource()
+						&& resourceType.isInstance(resultBundle.getEntryFirstRep().getResource()))
+					return Optional.of(resultBundle.getEntryFirstRep().getResource());
 				else
 				{
 					logger.warn("Error while search for Resource with url {}, bundle has no {} resource", url,
 							resourceType.getAnnotation(ResourceDef.class).name());
 
-					if (patientBundle.getEntryFirstRep().getResponse().hasOutcome()
-							&& patientBundle.getEntryFirstRep().getResponse().getOutcome() instanceof OperationOutcome)
+					if (resultBundle.getEntryFirstRep().getResponse().hasOutcome()
+							&& resultBundle.getEntryFirstRep().getResponse().getOutcome() instanceof OperationOutcome)
 						outcomeLogger.logOutcome(
-								(OperationOutcome) patientBundle.getEntryFirstRep().getResponse().getOutcome());
+								(OperationOutcome) resultBundle.getEntryFirstRep().getResponse().getOutcome());
 
 					return Optional.empty();
 				}

codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/TransferDataConfig.java

@@ -93,6 +93,9 @@ public class TransferDataConfig
 	@Value("${de.netzwerk_universitaetsmedizin.codex.fhir.client:de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.fhir.FhirBridgeClient}")
 	private String fhirStoreClientClass;
 
+	@Value("${de.netzwerk_universitaetsmedizin.codex.fhir.useChainedParameterNotLogicalReference:true}")
+	private boolean fhirStoreUseChainedParameterNotLogicalReference;
+
 	@Value("${de.netzwerk_universitaetsmedizin.codex.fhir.searchBundleOverride:#{null}}")
 	private String fhirStoreSearchBundleOverride;
 
@@ -176,7 +179,8 @@ public HapiFhirClientFactory hapiFhirClientFactory()
 	{
 		return new HapiFhirClientFactory(fhirContext, fhirStoreBaseUrl, fhirStoreUsername, fhirStorePassword,
 				fhirStoreBearerToken, fhirStoreConnectTimeout, fhirStoreSocketTimeout,
-				fhirStoreConnectionRequestTimeout, fhirStoreHapiClientVerbose);
+				fhirStoreConnectionRequestTimeout, fhirStoreHapiClientVerbose,
+				fhirStoreUseChainedParameterNotLogicalReference);
 	}
 
 	@Bean