Merge pull request #11 from openmrs/HIE-2-pixm

[HIE-2] Skeleton code for client registry search flow

api/src/main/java/org/openmrs/module/clientregistry/ClientRegistryConfig.java

@@ -10,6 +10,7 @@
 
 import org.apache.commons.lang.StringUtils;
 import org.openmrs.api.AdministrationService;
+import org.openmrs.module.clientregistry.providers.FhirCRConstants;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
@@ -46,7 +47,21 @@ public boolean clientRegistryConnectionEnabled() {
 	public String getClientRegistryServerUrl() {
 		return serverUrl;
 	}
-
+
+	public String getClientRegistryGetPatientEndpoint() {
+		String globalPropPatientEndpoint = administrationService
+		        .getGlobalProperty(ClientRegistryConstants.GP_FHIR_CLIENT_REGISTRY_GET_PATIENT_ENDPOINT);
+
+		// default to Patient/$ihe-pix if patient endpoint is not defined in config
+		return (globalPropPatientEndpoint == null || globalPropPatientEndpoint.isEmpty()) ? String.format("Patient/%s",
+		    FhirCRConstants.IHE_PIX_OPERATION) : globalPropPatientEndpoint;
+	}
+
+	public String getClientRegistryDefaultPatientIdentifierSystem() {
+		return administrationService
+		        .getGlobalProperty(ClientRegistryConstants.GP_CLIENT_REGISTRY_DEFAULT_PATIENT_IDENTIFIER_SYSTEM);
+	}
+
 	public String getClientRegistryUserName() {
 		return username;
 	}
@@ -58,4 +73,8 @@ public String getClientRegistryPassword() {
 	public String getClientRegistryIdentifierRoot() {
 		return identifierRoot;
 	}
+
+	public String getClientRegistryTransactionMethod() {
+		return administrationService.getGlobalProperty(ClientRegistryConstants.GP_CLIENT_REGISTRY_TRANSACTION_METHOD);
+	}
 }

api/src/main/java/org/openmrs/module/clientregistry/ClientRegistryConstants.java

@@ -2,14 +2,20 @@
 
 public class ClientRegistryConstants {
 
-	public static final String GP_CLIENT_REGISTRY_SERVER_URL = "clientregistry.serverUrl";
+	public static final String GP_CLIENT_REGISTRY_SERVER_URL = "clientregistry.clientRegistryServerUrl";
+
+	public static final String GP_FHIR_CLIENT_REGISTRY_GET_PATIENT_ENDPOINT = "clientregistry.fhirGetPatientEndpoint";
+
+	public static final String GP_CLIENT_REGISTRY_DEFAULT_PATIENT_IDENTIFIER_SYSTEM = "clientregistry.defaultPatientIdentifierSystem";
 
 	public static final String GP_CLIENT_REGISTRY_USER_NAME = "clientregistry.username";
 
 	public static final String GP_CLIENT_REGISTRY_PASSWORD = "clientregistry.password";
 
 	public static final String GP_CLIENT_REGISTRY_IDENTIFIER_ROOT = "clientregistry.identifierRoot";
 
+	public static final String GP_CLIENT_REGISTRY_TRANSACTION_METHOD = "clientregistry.transactionMethod";
+
 	public static final String UPDATE_MESSAGE_DESTINATION = "topic://UPDATED:org.openmrs.Patient";
 
 	public static final String CLIENT_REGISTRY_INTERNAL_ID_SYSTEM = "http://clientregistry.org/openmrs";

api/src/main/java/org/openmrs/module/clientregistry/ClientRegistryTransactionType.java

@@ -0,0 +1,6 @@
+package org.openmrs.module.clientregistry;
+
+public enum ClientRegistryTransactionType {
+	FHIR,
+	HL7
+}

api/src/main/java/org/openmrs/module/clientregistry/api/CRPatientService.java

@@ -0,0 +1,13 @@
+package org.openmrs.module.clientregistry.api;
+
+import org.hl7.fhir.r4.model.Patient;
+import org.openmrs.module.fhir2.api.search.param.PatientSearchParams;
+
+import java.util.List;
+
+public interface CRPatientService {
+
+	List<Patient> getCRPatients(String sourceIdentifier, String sourceIdentifierSystem, List<String> extraTargetSystems);
+
+	List<Patient> searchCRForPatients(PatientSearchParams patientSearchParams);
+}

api/src/main/java/org/openmrs/module/clientregistry/api/ClientRegistryManager.java

@@ -10,8 +10,11 @@
 import org.openmrs.api.GlobalPropertyListener;
 import org.openmrs.event.Event;
 import org.openmrs.module.DaemonToken;
+import org.openmrs.module.clientregistry.ClientRegistryConfig;
 import org.openmrs.module.clientregistry.ClientRegistryConstants;
+import org.openmrs.module.clientregistry.ClientRegistryTransactionType;
 import org.openmrs.module.clientregistry.api.event.PatientCreateUpdateListener;
+import org.openmrs.module.clientregistry.api.impl.FhirCRPatientServiceImpl;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
@@ -27,6 +30,12 @@ public class ClientRegistryManager implements GlobalPropertyListener {
 	@Autowired
 	private PatientCreateUpdateListener patientListener;
 
+	@Autowired
+	private FhirCRPatientServiceImpl fhirPatientService;
+
+	@Autowired
+	private ClientRegistryConfig clientRegistryConfig;
+
 	public void setDaemonToken(DaemonToken daemonToken) {
 		this.daemonToken = daemonToken;
 	}
@@ -82,4 +91,30 @@ public void disableClientRegistry() {
 
 		isRunning.set(false);
 	}
+
+	/**
+	 * Determine the appropriate PatientService class based off of the client registry transaction
+	 * type configuration
+	 * 
+	 * @return PatientService class corresponding to the appropriate transaction type supported by
+	 *         the client registry
+	 * @throws IllegalArgumentException if defined transaction type is unsupported
+	 */
+	public CRPatientService getPatientService() throws IllegalArgumentException {
+		try {
+			String transactionMethodGlobalProperty = clientRegistryConfig.getClientRegistryTransactionMethod().toUpperCase();
+
+			switch (ClientRegistryTransactionType.valueOf(transactionMethodGlobalProperty)) {
+				case FHIR:
+					return fhirPatientService;
+				case HL7:
+					throw new IllegalArgumentException("HL7 transaction type is currently unsupported");
+			}
+		}
+		catch (Exception ignored) {
+
+		}
+
+		throw new IllegalArgumentException("Unsupported transaction type");
+	}
 }

api/src/main/java/org/openmrs/module/clientregistry/api/event/PatientCreateUpdateListener.java

@@ -5,6 +5,7 @@
 import javax.jms.Message;
 
 import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -20,6 +21,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.stereotype.Component;
+import ca.uhn.fhir.parser.DataFormatException;
 
 @Component
 public class PatientCreateUpdateListener implements EventListener {
@@ -98,7 +100,18 @@ private void processMessage(Message message) throws JMSException {
 			if (mapMessage.getJMSDestination().toString().equals(ClientRegistryConstants.UPDATE_MESSAGE_DESTINATION)) {
 				client.update().resource(patient).execute();
 			} else {
-				client.create().resource(patient).execute();
+				try {
+					client.create().resource(patient).execute();
+				}
+				catch (FhirClientConnectionException e) {
+					Throwable cause = e.getCause();
+					if (cause instanceof DataFormatException) {
+						// just warn if the CR responds with unsupported data format
+						log.warn(e.getMessage());
+					} else {
+						throw e;
+					}
+				}
 			}
 		}
 	}

api/src/main/java/org/openmrs/module/clientregistry/api/impl/FhirCRPatientServiceImpl.java

@@ -0,0 +1,89 @@
+package org.openmrs.module.clientregistry.api.impl;
+
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.gclient.IOperationUntypedWithInputAndPartialOutput;
+import ca.uhn.fhir.rest.gclient.IQuery;
+import ca.uhn.fhir.rest.gclient.StringClientParam;
+import ca.uhn.fhir.rest.param.StringOrListParam;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.UriOrListParam;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.r4.model.*;
+import org.openmrs.module.clientregistry.ClientRegistryConfig;
+import org.openmrs.module.clientregistry.api.CRPatientService;
+import org.openmrs.module.clientregistry.providers.FhirCRConstants;
+import org.openmrs.module.fhir2.FhirConstants;
+import org.openmrs.module.fhir2.api.search.param.PatientSearchParams;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
+
+@Component
+public class FhirCRPatientServiceImpl implements CRPatientService {
+
+	@Autowired
+	private IGenericClient fhirClient;
+
+	@Autowired
+	private ClientRegistryConfig config;
+
+	/**
+	 * Get patient identifiers from an external client registry's $ihe-pix implementation. Use the
+	 * returned identifiers to then request a matching Patient bundle from the client registry.
+	 */
+	@Override
+	public List<Patient> getCRPatients(String sourceIdentifier, String sourceIdentifierSystem, List<String> targetSystems) {
+		// construct request to external FHIR $ihe-pix endpoint
+		IOperationUntypedWithInputAndPartialOutput<Parameters> identifiersRequest = fhirClient
+				.operation()
+				.onType(FhirConstants.PATIENT)
+				.named(FhirCRConstants.IHE_PIX_OPERATION)
+				.withSearchParameter(Parameters.class, FhirCRConstants.SOURCE_IDENTIFIER, new TokenParam(sourceIdentifierSystem, sourceIdentifier));
+
+		if (!targetSystems.isEmpty()) {
+			identifiersRequest.andSearchParameter(FhirCRConstants.TARGET_SYSTEM, new StringParam(String.join(",", targetSystems)));
+		}
+
+		Parameters crMatchingParams = identifiersRequest.useHttpGet().execute();
+		List<String> crIdentifiers = crMatchingParams.getParameter().stream()
+				.filter(param -> Objects.equals(param.getName(), "targetId"))
+				.map(param -> param.getValue().toString())
+				.collect(Collectors.toList());
+
+		if (crIdentifiers.isEmpty()) {
+			return Collections.emptyList();
+		}
+
+		// construct and send request to external client registry
+		Bundle patientBundle = fhirClient
+				.search()
+				.forResource(Patient.class)
+				.where(new StringClientParam(Patient.SP_RES_ID).matches().values(crIdentifiers))
+				.returnBundle(Bundle.class)
+				.execute();
+
+		return parseCRPatientSearchResults(patientBundle);
+	}
+
+	@Override
+	public List<Patient> searchCRForPatients(PatientSearchParams patientSearchParams) {
+		return null;
+	}
+
+	/**
+	 * Filter and parse out fhir patients from Client Registry Patient Search results
+	 */
+	private List<Patient> parseCRPatientSearchResults(Bundle patientBundle) {
+        return patientBundle
+                .getEntry()
+                .stream()
+                .filter(entry -> entry.hasType(FhirConstants.PATIENT))
+                .map(entry -> (Patient) entry.getResource())
+				.collect(Collectors.toList());
+    }
+}

api/src/main/java/org/openmrs/module/clientregistry/providers/FhirCRConstants.java

@@ -0,0 +1,27 @@
+package org.openmrs.module.clientregistry.providers;
+
+import ca.uhn.fhir.model.api.annotation.SearchParamDefinition;
+import ca.uhn.fhir.rest.gclient.StringClientParam;
+import ca.uhn.fhir.rest.gclient.TokenClientParam;
+import ca.uhn.fhir.rest.gclient.UriClientParam;
+import ca.uhn.fhir.rest.param.StringOrListParam;
+
+public class FhirCRConstants {
+
+	public static final String IHE_PIX_OPERATION = "$ihe-pix";
+
+	@SearchParamDefinition(name = "sourceIdentifier", path = "Patient.sourceIdentifier", description = "A patient identifier used to find cross-matching identifiers in client registry", type = "token")
+	public static final String SOURCE_IDENTIFIER = "sourceIdentifier";
+
+	public static final TokenClientParam SOURCE_IDENTIFIER_PARAM = new TokenClientParam("sourceIdentifier");
+
+	@SearchParamDefinition(name = "targetSystem", path = "Patient.targetSystem", description = "Assigning Authorities for the Patient Identifier Domains from which the returned identifiers shall be selected", type = "token")
+	public static final String TARGET_SYSTEM = "targetSystem";
+
+	public static final UriClientParam TARGET_SYSTEM_PARAM = new UriClientParam("targetSystem");
+
+	@SearchParamDefinition(name = "_format", path = "Patient.targetSystem", description = "Assigning Authorities for the Patient Identifier Domains from which the returned identifiers shall be selected", type = "token")
+	public static final String _FORMAT = "_FORMAT";
+
+	public static final StringClientParam _FORMAT_PARAM = new StringClientParam("_format");
+}

api/src/main/java/org/openmrs/module/clientregistry/providers/r4/FhirCRPatientResourceProvider.java

@@ -0,0 +1,99 @@
+package org.openmrs.module.clientregistry.providers.r4;
+
+import ca.uhn.fhir.model.valueset.BundleTypeEnum;
+import ca.uhn.fhir.rest.annotation.Search;
+import ca.uhn.fhir.rest.param.StringParam;
+import ca.uhn.fhir.rest.param.StringOrListParam;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.IResourceProvider;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import lombok.Setter;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Patient;
+import ca.uhn.fhir.rest.annotation.Operation;
+import ca.uhn.fhir.rest.annotation.OperationParam;
+import org.openmrs.module.clientregistry.ClientRegistryConfig;
+import org.openmrs.module.clientregistry.api.ClientRegistryManager;
+import org.openmrs.module.clientregistry.providers.FhirCRConstants;
+import org.openmrs.module.fhir2.api.annotations.R4Provider;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.Objects;
+import java.util.stream.Collectors;
+
+import static lombok.AccessLevel.PACKAGE;
+
+@Component("crPatientFhirR4ResourceProvider")
+@R4Provider
+@Setter(PACKAGE)
+public class FhirCRPatientResourceProvider implements IResourceProvider {
+
+	@Autowired
+	private ClientRegistryManager clientRegistryManager;
+
+	@Autowired
+	private ClientRegistryConfig config;
+
+	@Override
+	public Class<? extends IBaseResource> getResourceType() {
+		return Patient.class;
+	}
+
+	/**
+	 * FHIR endpoint to get Patient references from external client registry Example request: GET
+	 * [fhirbase
+	 * ]/Patient/$ihe-pix?sourceIdentifier={sourceSystem|}1234[&targetSystem=system1,system2]
+	 * 
+	 * @param sourceIdentifierParam patient identifier token. If source system is included in token,
+	 *            we will use it to override the module defined source system.
+	 * @param targetSystemsParam (optional) Patient assigning authorities (ie systems) from which
+	 *            the returned identifiers shall be selected
+	 * @return List of matching FHIR patients returned by the client registry
+	 */
+	@Operation(name = FhirCRConstants.IHE_PIX_OPERATION, idempotent=true, type = Patient.class, bundleType = BundleTypeEnum.SEARCHSET)
+	public List<Patient> getCRPatientById(
+			@OperationParam(name = FhirCRConstants.SOURCE_IDENTIFIER) TokenParam sourceIdentifierParam,
+	        @OperationParam(name = FhirCRConstants.TARGET_SYSTEM) StringOrListParam targetSystemsParam
+	) {
+
+		if (sourceIdentifierParam == null || sourceIdentifierParam.getValue() == null) {
+			throw new InvalidRequestException("sourceIdentifier must be specified");
+		}
+
+		List<String> targetSystems = targetSystemsParam == null
+				? Collections.emptyList()
+				: targetSystemsParam.getValuesAsQueryTokens().stream().filter(Objects::nonNull).map(StringParam::getValue).collect(Collectors.toList());
+
+		// If no sourceSystem provided, use config defined default
+		boolean userDefinedSourceSystem = sourceIdentifierParam.getSystem() != null && !sourceIdentifierParam.getSystem().isEmpty();
+		String sourceIdentifierSystem = userDefinedSourceSystem
+				? sourceIdentifierParam.getSystem()
+				: config.getClientRegistryDefaultPatientIdentifierSystem();
+
+		if (sourceIdentifierSystem == null || sourceIdentifierSystem.isEmpty()) {
+			throw new InvalidRequestException("ClientRegistry module does not have a default source system assigned " +
+					"via the defaultPatientIdentifierSystem property. Source system must be provided as a token in " +
+					"the sourceIdentifier request param");
+		}
+
+		List<Patient> patients = clientRegistryManager.getPatientService().getCRPatients(
+				sourceIdentifierParam.getValue(), sourceIdentifierSystem, targetSystems
+		);
+
+		if (patients.isEmpty()) {
+			throw new ResourceNotFoundException("No Client Registry patients found.");
+		}
+
+		return patients;
+	}
+
+	@Search
+	public List<Patient> searchClientRegistryPatients() {
+		throw new NotImplementedOperationException("search client registry is not yet implemented");
+	}
+}