fTTP BF fix, added support for lab values, reworked FHIR store clients

fTTP BF resolution was missing the source/ prefix for the pseudonym.
Adds support for lab values with profile
https://www.medizininformatik-initiative.de/fhir/core/modul-labor/StructureDefinition/ObservationLab
Uses the loinc code in the update condition for lab values as discussed
in #4.
Adds an initial FHIR store implementation for the fhir-bridge.

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

@@ -21,6 +21,8 @@ public interface ConstantsDataTransfer
 	String NAMING_SYSTEM_NUM_CODEX_CRR_PSEUDONYM = "http://www.netzwerk-universitaetsmedizin.de/sid/crr-pseudonym";
 	String NAMING_SYSTEM_NUM_CODEX_BLOOM_FILTER = "http://www.netzwerk-universitaetsmedizin.de/sid/bloom-filter";
 
+	String RFC_4122_SYSTEM = "urn:ietf:rfc:4122";
+
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER = "http://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/data-transfer";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PATIENT = "patient";
 	String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PSEUDONYM = "pseudonym";

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

@@ -22,6 +22,8 @@
 
 import ca.uhn.fhir.context.FhirContext;
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer;
+import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.fhir.FhirClient;
+import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.fhir.FhirClientBuilder;
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.domain.DateWithPrecision;
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.variables.PatientReference;
 import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.variables.PatientReferenceList;
@@ -39,19 +41,23 @@ public class FhirClientFactory
 	private final Path searchBundleOverride;
 	private final String localIdentifierValue;
 
+	private final FhirClientBuilder builder;
+
 	public FhirClientFactory(HapiFhirClientFactory hapiClientFactory, FhirContext fhirContext,
-			Path searchBundleOverride, String localIdentifierValue)
+			Path searchBundleOverride, String localIdentifierValue, FhirClientBuilder builder)
 	{
 		this.hapiClientFactory = hapiClientFactory;
 		this.fhirContext = fhirContext;
 		this.searchBundleOverride = searchBundleOverride;
 		this.localIdentifierValue = localIdentifierValue;
+
+		this.builder = builder;
 	}
 
 	public FhirClient getFhirClient()
 	{
 		if (hapiClientFactory.isConfigured())
-			return new FhirClientImpl(hapiClientFactory, fhirContext, searchBundleOverride);
+			return builder.build(fhirContext, hapiClientFactory, searchBundleOverride);
 		else
 			return createFhirClientStub();
 	}

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

@@ -172,7 +172,7 @@ public Optional<String> getDicPseudonym(String bloomFilter)
 					.withParameters(createParametersForBfWorkflow(bloomFilter)).accept(Constants.CT_FHIR_XML_NEW)
 					.encoded(EncodingEnum.XML).execute();
 
-			return getPseudonym(parameters);
+			return getPseudonym(parameters).map(p -> fttpTarget + "/" + p);
 		}
 		catch (Exception e)
 		{

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

@@ -47,7 +47,6 @@ public class HapiFhirClientFactory
 	private final String basicAuthUsername;
 	private final String basicAuthPassword;
 	private final String bearerToken;
-	private final boolean supportsIdentifierReferenceSearch;
 
 	private final ApacheRestfulClientFactory clientFactory;
 
@@ -62,10 +61,9 @@ public class HapiFhirClientFactory
 	 *            may be <code>null</code>
 	 * @param bearerToken
 	 *            may be <code>null</code>
-	 * @param supportsIdentifierReferenceSearch
 	 */
 	public HapiFhirClientFactory(FhirContext fhirContext, String serverBase, String basicAuthUsername,
-			String basicAuthPassword, String bearerToken, boolean supportsIdentifierReferenceSearch)
+			String basicAuthPassword, String bearerToken)
 	{
 		if (fhirContext != null)
 			this.fhirContext = fhirContext;
@@ -76,7 +74,6 @@ public HapiFhirClientFactory(FhirContext fhirContext, String serverBase, String
 		this.basicAuthUsername = basicAuthUsername;
 		this.basicAuthPassword = basicAuthPassword;
 		this.bearerToken = bearerToken;
-		this.supportsIdentifierReferenceSearch = supportsIdentifierReferenceSearch;
 
 		if (isConfigured())
 		{
@@ -87,11 +84,6 @@ public HapiFhirClientFactory(FhirContext fhirContext, String serverBase, String
 			clientFactory = null;
 	}
 
-	public boolean supportsIdentifierReferenceSearch()
-	{
-		return supportsIdentifierReferenceSearch;
-	}
-
 	protected boolean isConfigured()
 	{
 		return serverBase != null && !serverBase.isEmpty();

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

@@ -0,0 +1,55 @@
+package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client;
+
+import java.util.function.BiConsumer;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.hl7.fhir.r4.model.OperationOutcome;
+import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
+import org.slf4j.Logger;
+
+public class OutcomeLogger
+{
+	private final Logger logger;
+
+	public OutcomeLogger(Logger logger)
+	{
+		this.logger = logger;
+	}
+
+	public void logOutcome(OperationOutcome outcome)
+	{
+		outcome.getIssue().forEach(issue ->
+		{
+			String display = issue.getCode() == null ? null : issue.getCode().getDisplay();
+			String details = issue.getDetails() == null ? null : issue.getDetails().getText();
+			String diagnostics = issue.getDiagnostics();
+
+			String message = Stream.of(display, details, diagnostics).filter(s -> s != null && !s.isBlank())
+					.collect(Collectors.joining(" "));
+
+			getLoggerForSeverity(issue.getSeverity(), logger).accept("Issue: {}", message);
+		});
+	}
+
+	private BiConsumer<String, Object> getLoggerForSeverity(IssueSeverity severity, Logger logger)
+	{
+		if (severity != null)
+		{
+			switch (severity)
+			{
+				case ERROR:
+				case FATAL:
+					return logger::error;
+				case WARNING:
+					return logger::warn;
+				case NULL:
+				case INFORMATION:
+				default:
+					return logger::info;
+			}
+		}
+
+		return logger::info;
+	}
+}