Update task resource attributes - PM

.gitignore

@@ -80,4 +80,5 @@ nb-configuration.xml
 ##############################
 .DS_Store
 
-.flattened-pom.xml
+.flattened-pom.xml
+openmrs.log

api/pom.xml

@@ -15,7 +15,7 @@
     <parent>
         <groupId>org.openmrs.module</groupId>
         <artifactId>labonfhir</artifactId>
-        <version>1.4.0-SNAPSHOT</version>
+        <version>1.4.2-SNAPSHOT</version>
     </parent>
 
     <artifactId>labonfhir-api</artifactId>

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

@@ -4,7 +4,6 @@
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
-import java.util.Optional;
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.stream.Collectors;
 
@@ -17,7 +16,6 @@
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.Task;
 import org.openmrs.Encounter;
-import org.openmrs.EncounterProvider;
 import org.openmrs.Obs;
 import org.openmrs.Order;
 import org.openmrs.api.db.DAOException;
@@ -87,28 +85,19 @@ public Task createOrder(Order order) throws OrderCreationException {
 				newReference(order.getUuid(), FhirConstants.SERVICE_REQUEST));
 
 		Reference forReference = newReference(order.getPatient().getUuid(), FhirConstants.PATIENT);
-
-		Reference ownerRef = newReference(config.getLisUserUuid(), FhirConstants.PRACTITIONER);
-
+
 		Reference encounterRef = newReference(order.getEncounter().getUuid(), FhirConstants.ENCOUNTER);
 
-		Optional<EncounterProvider> requesterProvider = order.getEncounter().getActiveEncounterProviders().stream()
-				.findFirst();
+		Reference requesterRef = newReference(order.getEncounter().getLocation().getUuid(), FhirConstants.ORGANIZATION);
 
-		Reference requesterRef = requesterProvider.map(
-				encounterProvider -> newReference(encounterProvider.getUuid(), FhirConstants.PRACTITIONER)).orElse(null);
-
-		Reference locationRef = null;
-		if (order.getEncounter().getLocation() != null) {
-			locationRef = newReference(order.getEncounter().getLocation().getUuid(), FhirConstants.LOCATION);
-		}
+		// Reference locationRef = newReference(order.getEncounter().getLocation().getUuid(), FhirConstants.LOCATION);
 
 		// Create Task Resource for given Order
-		Task newTask = createTask(basedOnRefs, forReference, ownerRef, encounterRef, locationRef ,taskInputs);
+		Task newTask = createTask(basedOnRefs, forReference, null, encounterRef, null,requesterRef ,taskInputs);
 
-		if (order.getEncounter().getActiveEncounterProviders().isEmpty()) {
-			newTask.setRequester(requesterRef);
-		}
+//		if (order.getEncounter().getLocation() != null) {
+//			newTask.setRequester(requesterRef);
+//		}
 
 		// Save the new Task Resource
 		try {
@@ -121,7 +110,7 @@ public Task createOrder(Order order) throws OrderCreationException {
 	}
 
 	private Task createTask(List<Reference> basedOnRefs, Reference forReference, Reference ownerRef,
-			Reference encounterRef, Reference locationRef ,List<Task.ParameterComponent> taskInputs) {
+			Reference encounterRef, Reference locationRef, Reference requesterRef ,List<Task.ParameterComponent> taskInputs) {
 		Task newTask = new Task();
 		newTask.setStatus(Task.TaskStatus.REQUESTED);
 		newTask.setIntent(Task.TaskIntent.ORDER);
@@ -130,6 +119,7 @@ private Task createTask(List<Reference> basedOnRefs, Reference forReference, Ref
 		newTask.setOwner(ownerRef);
 		newTask.setEncounter(encounterRef);
 		newTask.setLocation(locationRef);
+		newTask.setRequester(requesterRef);
 		if (taskInputs != null) {
 			newTask.setInput(taskInputs);
 		}
@@ -160,11 +150,7 @@ public Task createOrder(Encounter encounter) throws OrderCreationException {
 
 		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;
+		Reference requesterRef = newReference(encounter.getLocation().getUuid(), FhirConstants.ORGANIZATION);
 
 		List<Task.ParameterComponent> taskInputs = null;
 		if (config.addObsAsTaskInput()) {
@@ -179,12 +165,20 @@ public Task createOrder(Encounter encounter) throws OrderCreationException {
 		}
 
 		// Create Task Resource for given Order
-		Task newTask = createTask(basedOnRefs, forReference, ownerRef, encounterRef, locationRef ,taskInputs);
-		newTask.setLocation(locationRef);
-
-		if (!encounter.getActiveEncounterProviders().isEmpty()) {
-			newTask.setRequester(requesterRef);
-		}
+		// =========================================
+		// Summary of Payload requirements in terms of location and organization:
+		// Payload coming from OpenMRS should include only the Location and Organization resources corresponding to the MFL-based location that represents the physical spot where a lab order is being collected. This MFL code will then be mapped to the proper IPMS location (in some cases based on the type of test being ordered as well)
+		// The incoming Location should reference the Organization as a managing organization, just like a normal Org/Location pair
+		// For the incoming task resource:
+		// `for` should reference the patient
+		// `requester` should reference the Organization
+		// `owner` and `location` can be left blank
+		// Once the task is processed, owner will reference the mapped IPMS Organization, and location the IPMS location.
+		// Leave the `location ref` and `owner ref` blank. Once the task is processed, owner will reference the mapped Lab Systems Organization, and location the Lab System's location.
+		Task newTask = createTask(basedOnRefs, forReference, null, encounterRef, null, requesterRef, taskInputs);
+		//newTask.setLocation(locationRef);
+
+		//newTask.setRequester(requesterRef);
 
 		// Save the new Task Resource
 		try {

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

@@ -1,6 +1,8 @@
 package org.openmrs.module.labonfhir.api.event;
 
 import javax.jms.Message;
+
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
 
@@ -10,10 +12,16 @@
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.param.TokenAndListParam;
 import ca.uhn.fhir.rest.param.TokenParam;
+import org.hl7.fhir.r4.model.Location;
+import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Resource;
 import org.hl7.fhir.r4.model.Task;
+import org.openmrs.LocationAttribute;
+import org.openmrs.LocationAttributeType;
+import org.openmrs.api.LocationService;
 import org.openmrs.api.context.Daemon;
 import org.openmrs.event.EventListener;
 import org.openmrs.module.DaemonToken;
@@ -31,6 +39,10 @@
 
 public abstract class LabCreationListener implements EventListener {
 
+	private static final String MFL_LOCATION_IDENTIFIER_URI = "http://moh.bw.org/ext/location/identifier/mfl";
+
+	private static final String MFL_LOCATION_ATTRIBUTE_TYPE_UUID = "8a845a89-6aa5-4111-81d3-0af31c45c002";
+
 	private static final Logger log = LoggerFactory.getLogger(EncounterCreationListener.class);
 
 	private DaemonToken daemonToken;
@@ -47,14 +59,17 @@ public abstract class LabCreationListener implements EventListener {
 	private FhirContext ctx;
 
 	@Autowired
-	FhirLocationService fhirLocationService ;
+	FhirLocationService fhirLocationService;
 
 	@Autowired
 	private FhirTaskService fhirTaskService;
 
 	@Autowired
-	private LabOnFhirService labOnFhirService ;
+	private LabOnFhirService labOnFhirService;
 
+	@Autowired
+	private LocationService locationService;
+
 	public DaemonToken getDaemonToken() {
 		return daemonToken;
 	}
@@ -70,8 +85,7 @@ public void onMessage(Message message) {
 		Daemon.runInDaemonThread(() -> {
 			try {
 				processMessage(message);
-			}
-			catch (Exception e) {
+			} catch (Exception e) {
 				log.error("Failed to update the user's last viewed patients property", e);
 			}
 		}, daemonToken);
@@ -87,6 +101,7 @@ public Bundle createLabBundle(Task task) {
 		includes.add(new Include("Task:encounter"));
 		includes.add(new Include("Task:based-on"));
 		includes.add(new Include("Task:location"));
+		includes.add(new Include("Task:requester"));
 
 		IBundleProvider labBundle = fhirTaskService.searchForTasks(new TaskSearchParams(null, null, null, uuid, null, null, includes));
 
@@ -96,10 +111,47 @@ public Bundle createLabBundle(Task task) {
 		if (!task.getLocation().isEmpty()) {
 			labResources.add(fhirLocationService.get(FhirUtils.referenceToId(task.getLocation().getReference()).get()));
 		}
+
+		if (!task.getRequester().isEmpty()) {
+			labResources.add(fhirLocationService.get(FhirUtils.referenceToId(task.getRequester().getReference()).get()));
+		}
+
 		for (IBaseResource r : labResources) {
 			Resource resource = (Resource) r;
+
+			// if resource is location, add MFL Code as location identifier
+			// TODO: Short term:  Make the MFL Location attribute type to be a Global config variable
+			// TODO: Long term: Make the location translator pick and enrich the MFL Code as appropriate
+
 			Bundle.BundleEntryComponent component = transactionBundle.addEntry();
-			component.setResource(resource);
+			if (resource instanceof Location || resource instanceof Organization) {
+				org.openmrs.Location openmrsLocation = locationService.getLocationByUuid(resource.getId());
+				if (openmrsLocation != null) {
+					LocationAttributeType mflLocationAttributeType = locationService.getLocationAttributeTypeByUuid(MFL_LOCATION_ATTRIBUTE_TYPE_UUID);
+					Collection<LocationAttribute> locationAttributeTypes = openmrsLocation.getActiveAttributes();
+					if (!locationAttributeTypes.isEmpty()) {
+						locationAttributeTypes.stream().filter(locationAttribute -> locationAttribute.getAttributeType().equals(mflLocationAttributeType)).findFirst().ifPresent(locationAttribute -> {
+							String mflCode = (String) locationAttribute.getValue();
+
+							Identifier mflIdentifier = new Identifier();
+							mflIdentifier.setSystem(MFL_LOCATION_IDENTIFIER_URI); 
+							mflIdentifier.setValue(mflCode); 
+							if (resource instanceof Organization) {
+								Organization organization = (Organization) resource;
+								organization.addIdentifier(mflIdentifier);
+								component.setResource(organization);
+							} else if (resource instanceof Location) {
+								Location location = (Location) resource;
+								location.addIdentifier(mflIdentifier);
+								component.setResource(location);
+							}
+						});
+					}
+				}
+			} else {
+				component.setResource(resource);	
+			}
+
 			component.getRequest().setUrl(resource.fhirType() + "/" + resource.getIdElement().getIdPart())
 			        .setMethod(Bundle.HTTPVerb.PUT);
 
@@ -113,8 +165,7 @@ protected void sendTask(Task task) {
 				Bundle labBundle = createLabBundle(task);
 				try {
 					client.transaction().withBundle(labBundle).execute();
-				}
-				catch (Exception e) {
+				} catch (Exception e) {
 					saveFailedTask(task.getIdElement().getIdPart(), e.getMessage());
 					log.error("Failed to send Task with UUID " + task.getIdElement().getIdPart(), e);
 				}
@@ -123,7 +174,7 @@ protected void sendTask(Task task) {
 		}
 	}
 
-	private void saveFailedTask(String taskUuid ,String error) {
+	private void saveFailedTask(String taskUuid, String error) {
 		FailedTask failedTask = new FailedTask();
 		failedTask.setError(error);
 		failedTask.setIsSent(false);

api/src/test/java/org/openmrs/module/labonfhir/api/LabOrderHandlerTest.java

@@ -1,17 +1,78 @@
 package org.openmrs.module.labonfhir.api;
 
+import static org.junit.Assert.assertNotNull;
+import static org.mockito.Mockito.when;
+
+import org.hl7.fhir.r4.model.Task;
 import org.junit.Before;
 import org.junit.Test;
+import org.mockito.MockitoAnnotations;
+import org.mockito.Mock;
+import org.openmrs.Encounter;
+import org.openmrs.Location;
+import org.openmrs.Obs;
+import org.openmrs.Order;
+import org.openmrs.Patient;
+import org.openmrs.api.EncounterService;
+import org.openmrs.api.LocationService;
+import org.openmrs.api.ObsService;
+import org.openmrs.api.OrderService;
+import org.openmrs.api.PatientService;
+import org.openmrs.module.labonfhir.api.fhir.OrderCreationException;
 
 public class LabOrderHandlerTest {
+    @Mock
+    private OrderService orderService;
+    @Mock
+    private EncounterService encounterService;
+    @Mock
+    private LocationService locationService;
+    @Mock
+    private PatientService patientService;
+    @Mock
+    private ObsService obsService;
 
+    @Before
+    public void setup() {
+        MockitoAnnotations.initMocks(this);
+    }
 	@Before
 	public void setUp() throws Exception {
 
 	}
 
-	@Test
-	public void createOrder_shouldCreateTaskAndERferenceOrder() {
 
+	@Test
+	public void createOrder_shouldCreateTask() throws OrderCreationException {
+		// Create a mock Order object
+		Order order = new Order();
+		order.setUuid("orderUuid");
+
+		// Create a mock Encounter object
+		Encounter encounter = new Encounter();
+		encounter.setUuid("encounterUuid");
+		encounter.setLocation(new Location());
+		encounter.getLocation().setUuid("locationUuid");
+		encounter.setPatient(new Patient());
+		encounter.getPatient().setUuid("patientUuid");
+
+		// Create a mock Obs object
+		Obs obs = new Obs();
+		obs.setUuid("obsUuid");
+		encounter.getObs().add(obs);
+
+		// Mock the necessary dependencies
+		when(orderService.getOrderByUuid("orderUuid")).thenReturn(order);
+		when(encounterService.getEncounterByUuid("encounterUuid")).thenReturn(encounter);
+		when(locationService.getLocationByUuid("locationUuid")).thenReturn(new Location());
+		when(patientService.getPatientByUuid("patientUuid")).thenReturn(new Patient());
+		when(obsService.getObsByUuid("obsUuid")).thenReturn(new Obs());
+
+		// Call the createOrder method
+		LabOrderHandler labOrderHandler = new LabOrderHandler();
+		Task task = labOrderHandler.createOrder(order);
+
+		// Assert that the task is not null
+		assertNotNull(task);
 	}
-}
+}

omod/pom.xml

@@ -3,7 +3,7 @@
 	<parent>
 		<groupId>org.openmrs.module</groupId>
 		<artifactId>labonfhir</artifactId>
-		<version>1.4.0-SNAPSHOT</version>
+		<version>1.4.2-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>labonfhir-omod</artifactId>