FM2-531 : Add Location Resource to lab bundle (#27)

* add Location to lab bundle

* fix parsing uuid

* add openelis id system

* update fhir system on restart

* save or update identifier system

api/src/main/java/org/openmrs/module/labonfhir/LabOnFhirActivator.java

@@ -10,9 +10,17 @@
 package org.openmrs.module.labonfhir;
 
 import lombok.SneakyThrows;
+
+import java.util.Optional;
+
+import org.openmrs.PatientIdentifier;
+import org.openmrs.PatientIdentifierType;
+import org.openmrs.api.PatientService;
 import org.openmrs.module.BaseModuleActivator;
 import org.openmrs.module.DaemonToken;
 import org.openmrs.module.DaemonTokenAware;
+import org.openmrs.module.fhir2.api.FhirPatientIdentifierSystemService;
+import org.openmrs.module.fhir2.model.FhirPatientIdentifierSystem;
 import org.openmrs.module.labonfhir.api.OpenElisManager;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -24,51 +32,77 @@
 
 @Component
 public class LabOnFhirActivator extends BaseModuleActivator implements ApplicationContextAware, DaemonTokenAware {
-
+	
 	private static final Logger log = LoggerFactory.getLogger(LabOnFhirActivator.class);
-
+	
 	private static ApplicationContext applicationContext;
-
+	
 	private static DaemonToken daemonToken;
-
+	
 	@Autowired
 	private LabOnFhirConfig config;
-
+	
 	@Autowired
 	private OpenElisManager openElisManager;
-
+
+	@Autowired
+	PatientService patientService;
+
+	@Autowired
+	FhirPatientIdentifierSystemService fhirPatientIdentifierSystemService;
+
 	@SneakyThrows
 	@Override
 	public void started() {
 		applicationContext.getAutowireCapableBeanFactory().autowireBean(this);
-
+		
 		openElisManager.setDaemonToken(daemonToken);
-
+		
 		// subscribe to encounter creation events
 		if (config.isOpenElisEnabled()) {
 			openElisManager.enableOpenElisConnector();
 		}
-
+		createFhirPatientIdentierSystem();
+
 		log.info("Lab on FHIR Module Started!");
-
+		
 	}
-
+	
 	@Override
 	public void stopped() {
 		if (openElisManager != null) {
 			openElisManager.disableOpenElisConnector();
 		}
-
+		
 		log.info("Lab on FHIR Module Shut Down!");
 	}
-
+	
 	@Override
 	public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
 		this.applicationContext = applicationContext;
 	}
-
+	
 	@Override
 	public void setDaemonToken(DaemonToken token) {
 		this.daemonToken = token;
 	}
+
+	private void createFhirPatientIdentierSystem() {
+		PatientIdentifierType pidType = patientService
+				.getPatientIdentifierTypeByUuid(config.getPatientIentifierUuid().trim());
+
+		Optional<FhirPatientIdentifierSystem> existingIdSystem = fhirPatientIdentifierSystemService
+				.getFhirPatientIdentifierSystem(pidType);
+		if (existingIdSystem.isPresent()) {
+			existingIdSystem.get().setPatientIdentifierType(pidType);
+			existingIdSystem.get().setUrl(config.getLisIentifierSystemUrl().trim());
+			fhirPatientIdentifierSystemService.saveFhirPatientIdentifierSystem(existingIdSystem.get());
+		} else {
+			FhirPatientIdentifierSystem idSystem = new FhirPatientIdentifierSystem();
+			idSystem.setName("OpenLIS ID System");
+			idSystem.setPatientIdentifierType(pidType);
+			idSystem.setUrl(config.getLisIentifierSystemUrl().trim());
+			fhirPatientIdentifierSystemService.saveFhirPatientIdentifierSystem(idSystem);
+		}
+	}
 }

api/src/main/java/org/openmrs/module/labonfhir/LabOnFhirConfig.java

@@ -56,6 +56,10 @@ public class LabOnFhirConfig implements ApplicationContextAware {
 
 	public static final String GP_PASSWORD = "labonfhir.password";
 
+	public static final String GP_PATIENT_IDENTIFIER_UUID = "labonfhir.openmrsPatientIdentifier.uuid";
+
+	public static final String GP_LIS_IDENTIFIER_SYSTEM_URL = "labonfhir.openElisIdentifierSystem.url";
+
 	public enum AuthType{
 		SSL,
 		BASIC
@@ -124,6 +128,14 @@ public String getOpenElisPassword() {
 		return administrationService.getGlobalProperty(GP_PASSWORD);
 	}
 
+	public String getPatientIentifierUuid() {
+		return administrationService.getGlobalProperty(GP_PATIENT_IDENTIFIER_UUID ,"05a29f94-c0ed-11e2-94be-8c13b969e334");
+	}
+
+	public String getLisIentifierSystemUrl() {
+		return administrationService.getGlobalProperty(GP_LIS_IDENTIFIER_SYSTEM_URL ,"http://openelis-global.org/pat_nationalId");
+	}
+
 	public AuthType getAuthType() {
 		String authTypeGp = administrationService.getGlobalProperty(GP_AUTH_TYPE);
 		switch (authTypeGp.toUpperCase()) {

api/src/main/java/org/openmrs/module/labonfhir/api/OpenElisFhirOrderHandler.java

@@ -50,6 +50,8 @@ public Task createOrder(Encounter encounter) throws OrderCreationException {
 
 		Reference encounterRef = newReference(encounter.getUuid(), FhirConstants.ENCOUNTER);
 
+		Reference locationRef = newReference(encounter.getLocation().getUuid(), FhirConstants.LOCATION);
+
 		Optional<EncounterProvider> requesterProvider = encounter.getActiveEncounterProviders().stream().findFirst();
 
 		Reference requesterRef = requesterProvider.isPresent() ? newReference(requesterProvider.get().getUuid(), FhirConstants.PRACTITIONER) : null;
@@ -62,6 +64,7 @@ public Task createOrder(Encounter encounter) throws OrderCreationException {
 		newTask.setFor(forReference);
 		newTask.setOwner(ownerRef);
 		newTask.setEncounter(encounterRef);
+		newTask.setLocation(locationRef);
 
 		if(!encounter.getActiveEncounterProviders().isEmpty()){
 			newTask.setRequester(requesterRef);

api/src/main/java/org/openmrs/module/labonfhir/api/event/EncounterCreationListener.java

@@ -18,7 +18,9 @@
 import org.openmrs.Encounter;
 import org.openmrs.api.APIException;
 import org.openmrs.api.EncounterService;
+import org.openmrs.module.fhir2.api.FhirLocationService;
 import org.openmrs.module.fhir2.api.FhirTaskService;
+import org.openmrs.module.fhir2.api.util.FhirUtils;
 import org.openmrs.api.context.Daemon;
 import org.openmrs.event.EventListener;
 import org.openmrs.module.DaemonToken;
@@ -65,6 +67,9 @@ public void setDaemonToken(DaemonToken daemonToken) {
 
 	@Autowired
 	private FhirTaskService fhirTaskService;
+
+	@Autowired
+	FhirLocationService fhirLocationService ;
 
 	@Autowired
 	@Qualifier("fhirR4")
@@ -144,11 +149,13 @@ private Bundle createLabBundle(Task task) {
 		includes.add(new Include("Task:based-on"));
 
 		IBundleProvider labBundle = fhirTaskService.searchForTasks(null, null, null, uuid, null, null, includes);
-		labBundle.getAllResources();
 
 		Bundle transactionBundle = new Bundle();
 		transactionBundle.setType(Bundle.BundleType.TRANSACTION);
 		List<IBaseResource> labResources = labBundle.getAllResources();
+		if (!task.getLocation().isEmpty()) {
+			labResources.add(fhirLocationService.get(FhirUtils.referenceToId(task.getLocation().getReference()).get()));
+		}
 		for (IBaseResource r : labResources) {
 			Resource resource = (Resource) r;
 			Bundle.BundleEntryComponent component = transactionBundle.addEntry();

omod/src/main/resources/config.xml

@@ -100,4 +100,15 @@
 		<description>Password for HTTP Basic Auth with the LIS</description>
 		<defaultValue>password</defaultValue>
 	</globalProperty>
+	<globalProperty>
+		<property>@[email protected]</property>
+		<description>Patient Identifier used to generate the FHIR Identifier System</description>
+		<defaultValue>05a29f94-c0ed-11e2-94be-8c13b969e334</defaultValue>
+	</globalProperty>
+
+	<globalProperty>
+		<property>@[email protected]</property>
+		<description>OpenElis Identifier System url</description>
+		<defaultValue>http://openelis-global.org/pat_nationalId</defaultValue>
+	</globalProperty>
 </module>

pom.xml

@@ -225,8 +225,8 @@
     </profile>
   </profiles>
   <properties>
-    <revision>1.2.0</revision>
-    <fhir2Version>1.4.0</fhir2Version>
+    <revision>1.2.1</revision>
+    <fhir2Version>1.6.0</fhir2Version>
     <maven.compiler.source>1.8</maven.compiler.source>
     <maven.compiler.target>1.8</maven.compiler.target>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>