Merge pull request #18 from openmrs/feat/crProvider

(feat) Implement Search API and consolidate the CR Patient Resource provider
openmrs · Sep 23, 2024 · f065f1d · f065f1d
2 parents 08a10e2 + f3ef268
commit f065f1d
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Showing 11 changed files with 1,017 additions and 100 deletions.
diff --git a/api/src/main/java/org/openmrs/module/clientregistry/ClientRegistryConfig.java b/api/src/main/java/org/openmrs/module/clientregistry/ClientRegistryConfig.java
@@ -1,10 +1,9 @@
 /**
- * This Source Code Form is subject to the terms of the Mozilla Public License,
- * v. 2.0. If a copy of the MPL was not distributed with this file, You can
- * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
- * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
- * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
- * graphic logo is a trademark of OpenMRS Inc.
+ * This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of
+ * the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ * OpenMRS is also distributed under the terms of the Healthcare Disclaimer located at
+ * http://openmrs.org/license. Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the
+ * OpenMRS graphic logo is a trademark of OpenMRS Inc.
  */
 package org.openmrs.module.clientregistry;
 
@@ -28,16 +27,16 @@ public class ClientRegistryConfig {
 	@Qualifier("adminService")
 	AdministrationService administrationService;
 
-	@Value("${CLIENTREGISTRY_SERVERURL}")
+	@Value("${CLIENTREGISTRY_SERVERURL:}")
 	private String serverUrl;
 
-	@Value("${CLIENTREGISTRY_USERNAME}")
+	@Value("${CLIENTREGISTRY_USERNAME:}")
 	private String username;
 
-	@Value("${CLIENTREGISTRY_PASSWORD}")
+	@Value("${CLIENTREGISTRY_PASSWORD:}")
 	private String password;
 
-	@Value("${CLIENTREGISTRY_IDENTIFIERROOT}")
+	@Value("${CLIENTREGISTRY_IDENTIFIERROOT:}")
 	private String identifierRoot;
 
 	public boolean clientRegistryConnectionEnabled() {

diff --git a/api/src/main/java/org/openmrs/module/clientregistry/ClientRegistryConstants.java b/api/src/main/java/org/openmrs/module/clientregistry/ClientRegistryConstants.java
@@ -21,4 +21,13 @@ public class ClientRegistryConstants {
 	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 CR_FHIR_OPERATION = "$cr";
+
+	public static final String CR_FHIR_SEARCH_OPERATION = "$cr-search";
+
+	public static final String CR_FHIR_UPDATE_OPERATION = "$cr-update";
+
+	public static final String CR_FHIR_DELETE_OPERATION = "$cr-delete";
+
 }
diff --git a/api/src/main/java/org/openmrs/module/clientregistry/api/CRPatientService.java b/api/src/main/java/org/openmrs/module/clientregistry/api/CRPatientService.java
@@ -2,12 +2,54 @@
 
 import org.hl7.fhir.r4.model.Patient;
 import org.openmrs.module.fhir2.api.search.param.PatientSearchParams;
-
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import java.util.List;
 
 public interface CRPatientService {
 
-	List<Patient> getCRPatients(String sourceIdentifier, String sourceIdentifierSystem, List<String> extraTargetSystems);
+	/**
+	 * Queries patient by ID
+	 */
+	Patient getPatientById(String id);
+
+	/**
+	 * Queries patients through a PIXm manager using native IDs.
+	 * 
+	 * @param sourceIdentifier the source identifier of the patient
+	 * @param sourceIdentifierSystem the system of the source identifier
+	 * @param extraTargetSystems additional target systems
+	 * @return a bundle containing patients that match the specified identifiers
+	 */
+	IBundleProvider getPatientsByPIX(String sourceIdentifier, String sourceIdentifierSystem, List<String> extraTargetSystems);
+
+	/**
+	 * Searches for patients, including fuzzy search.
+	 * 
+	 * @param patientSearchParams the parameters for searching patients
+	 * @return a bundle containing patients that match the search criteria
+	 */
+	IBundleProvider searchPatients(PatientSearchParams patientSearchParams);
+
+	/**
+	 * Creates a patient record
+	 * 
+	 * @param patient the patient to create
+	 * @return the created patient
+	 */
+	Patient createPatient(Patient patient);
+
+	/**
+	 * Updates a patient record.
+	 * 
+	 * @param patient the patient to update
+	 * @return the updated patient
+	 */
+	Patient updatePatient(Patient patient);
 
-	List<Patient> searchCRForPatients(PatientSearchParams patientSearchParams);
+	/**
+	 * Purges a patient record from the registry.
+	 * 
+	 * @param patient the patient to purge
+	 */
+	void purgePatient(Patient patient);
 }
diff --git a/api/src/main/java/org/openmrs/module/clientregistry/api/impl/FhirCRPatientServiceImpl.java b/api/src/main/java/org/openmrs/module/clientregistry/api/impl/FhirCRPatientServiceImpl.java
@@ -1,24 +1,26 @@
 package org.openmrs.module.clientregistry.api.impl;
 
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.gclient.ICriterion;
 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.apache.commons.lang3.StringUtils;
 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.api.search.CRSearchBundleProvider;
+import org.openmrs.module.clientregistry.api.search.PatientSearchCriteriaBuilder;
 import org.openmrs.module.clientregistry.providers.FhirCRConstants;
 import org.openmrs.module.fhir2.FhirConstants;
+import org.openmrs.module.fhir2.api.FhirGlobalPropertyService;
 import org.openmrs.module.fhir2.api.search.param.PatientSearchParams;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import org.springframework.beans.factory.annotation.Qualifier;
-
 import java.util.Collections;
 import java.util.List;
 import java.util.Objects;
@@ -31,58 +33,86 @@ public class FhirCRPatientServiceImpl implements CRPatientService {
 	@Qualifier("clientRegistryFhirClient")
 	private IGenericClient fhirClient;
 
-	/**
-	 * 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.
-	 */
+	@Autowired
+	private PatientSearchCriteriaBuilder criteriaBuilder;
+
+	@Autowired
+	private FhirGlobalPropertyService globalPropertyService;
+
+	@Override
+	public Patient getPatientById(String id) {
+		if (StringUtils.isBlank(id)) {
+			return null;
+		}
+		return fhirClient.read().resource(Patient.class).withId(id).execute();
+	}
+
 	@Override
-	public List<Patient> getCRPatients(String sourceIdentifier, String sourceIdentifierSystem, List<String> targetSystems) {
+	public IBundleProvider getPatientsByPIX(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));
-
+		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)));
+			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());
-
+		List<String> crIdentifiers = crMatchingParams.getParameter().stream().filter(param -> Objects.equals(param.getName(), "targetId"))
+				.map(param -> ((Reference) param.getValue()).getReference()).collect(Collectors.toList());
+
 		if (crIdentifiers.isEmpty()) {
-			return Collections.emptyList();
+			return new CRSearchBundleProvider(Collections.emptyList(), globalPropertyService);
 		}
-
-		// 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);
+		Bundle patientBundle = fhirClient.search().forResource(Patient.class)
+		        .where(new StringClientParam(Patient.SP_RES_ID).matches().values(crIdentifiers)).returnBundle(Bundle.class)
+		        .execute();
+
+		return new CRSearchBundleProvider(parseCRPatientSearchResults(patientBundle), globalPropertyService);
+
+	}
+
+	@Override
+	public IBundleProvider searchPatients(PatientSearchParams patientSearchParams) {
+		List<ICriterion<?>> criterions = criteriaBuilder.buildCriteria(patientSearchParams);
+		IQuery<IBaseBundle> query = fhirClient.search().forResource(Patient.class);
+
+		for (int i = 0; i < criterions.size(); i++) {
+			ICriterion<?> criterion = criterions.get(i);
+			if (i == 0) {
+				query.where(criterion);
+			} else {
+				query.and(criterion);
+			}
+		}
+		Bundle patientBundle = query.returnBundle(Bundle.class).execute();
+		return new CRSearchBundleProvider(parseCRPatientSearchResults(patientBundle), globalPropertyService);
+	}
+
+	@Override
+	public Patient createPatient(Patient patient) {
+		return (Patient) fhirClient.create().resource(patient).execute().getResource();
 	}
 
 	@Override
-	public List<Patient> searchCRForPatients(PatientSearchParams patientSearchParams) {
-		return null;
+	public Patient updatePatient(Patient patient) {
+		return (Patient) fhirClient.update().resource(patient).execute().getResource();
+	}
+
+	@Override
+	public void purgePatient(Patient patient) {
+		fhirClient.delete().resource(patient).execute();
 	}
 
 	/**
 	 * 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());
-    }
+		return patientBundle.getEntry().stream().filter(entry -> entry.getResource().hasType(FhirConstants.PATIENT))
+		        .map(entry -> (Patient) entry.getResource()).collect(Collectors.toList());
+	}
 }
diff --git a/api/src/main/java/org/openmrs/module/clientregistry/api/search/CRSearchBundleProvider.java b/api/src/main/java/org/openmrs/module/clientregistry/api/search/CRSearchBundleProvider.java
@@ -0,0 +1,27 @@
+package org.openmrs.module.clientregistry.api.search;
+
+import java.io.Serializable;
+import java.util.List;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.openmrs.module.fhir2.FhirConstants;
+import org.openmrs.module.fhir2.api.FhirGlobalPropertyService;
+import ca.uhn.fhir.rest.server.SimpleBundleProvider;
+
+public class CRSearchBundleProvider extends SimpleBundleProvider implements Serializable {
+
+	private final FhirGlobalPropertyService globalPropertyService;
+
+	public CRSearchBundleProvider(List<? extends IBaseResource> patientList, FhirGlobalPropertyService globalPropertyService) {
+		super(patientList);
+		this.globalPropertyService = globalPropertyService;
+	}
+
+	@Override
+	public Integer preferredPageSize() {
+		if (size() == null) {
+			setSize(globalPropertyService.getGlobalProperty(FhirConstants.OPENMRS_FHIR_DEFAULT_PAGE_SIZE, 10));
+		}
+		return size();
+	}
+
+}