Update Referring ServiceRequest with Accession Number

src/main/java/org/openelisglobal/dataexchange/fhir/service/FhirPersistanceService.java

@@ -40,6 +40,8 @@ Bundle createUpdateFhirResourcesInFhirStore(List<FhirOperations> fhirOperationsL
 
     Optional<Task> getTaskBasedOnServiceRequest(String referringId);
 
+    Optional<ServiceRequest> getServiceRequestByReferingId(String referringId);
+
     Optional<Task> getTaskBasedOnTask(String taskId);
 
     Bundle createUpdateFhirResourcesInFhirStore(Map<String, Resource> createResources,

src/main/java/org/openelisglobal/dataexchange/fhir/service/FhirPersistanceServiceImpl.java

@@ -354,6 +354,40 @@ public Optional<Task> getTaskBasedOnServiceRequest(String referringId) {
         return Optional.empty();
     }
 
+    @Override
+    public Optional<ServiceRequest> getServiceRequestByReferingId(String referringId) {
+        ServiceRequest serviceRequest = null;
+        Bundle bundle = localFhirClient.search()//
+                .forResource(ServiceRequest.class)//
+                .returnBundle(Bundle.class)//
+                .where(ServiceRequest.IDENTIFIER.exactly().identifier(referringId))//
+                .execute();
+        if (bundle.hasEntry()) {
+            serviceRequest = (ServiceRequest) bundle.getEntryFirstRep().getResource();
+        }
+        if (serviceRequest == null) {
+            LogEvent.logDebug(this.getClass().getName(), "", "no service request with identifier " + referringId);
+            for (String remotePath : fhirConfig.getRemoteStorePaths()) {
+
+                bundle = localFhirClient.search()//
+                        .forResource(ServiceRequest.class)//
+                        .returnBundle(Bundle.class)//
+                        .where(ServiceRequest.IDENTIFIER.exactly().systemAndIdentifier(remotePath, referringId))//
+                        .execute();
+                if (bundle.hasEntry()) {
+                    serviceRequest = (ServiceRequest) bundle.getEntryFirstRep().getResource();
+                }
+            }
+        }
+        if (serviceRequest == null) {
+            LogEvent.logDebug(this.getClass().getName(), "",
+                "no service request with identifier " + referringId + " with configured systems");
+        } else {
+            return Optional.of(serviceRequest);
+        }
+        return Optional.empty();
+    }
+
     @Override
     public Optional<Task> getTaskBasedOnTask(String taskId) {
         Bundle bundle = localFhirClient.search()//

src/main/java/org/openelisglobal/dataexchange/fhir/service/FhirTransformServiceImpl.java

@@ -380,6 +380,12 @@ public void transformPersistOrderEntryFhirObjects(SamplePatientUpdateData update
 			this.addToOperations(fhirOperations, tempIdGenerator, referringTask.get());
 		}
 
+		Optional<ServiceRequest> referingServiceRequest = getReferringServiceRequestForSample(updateData.getSample());
+		if (referingServiceRequest.isPresent()) {
+			updateReferringServiceRequestWithSampleInfo(updateData.getSample(), referingServiceRequest.get());
+			this.addToOperations(fhirOperations, tempIdGenerator, referingServiceRequest.get());
+		}
+
 		// patient
 		org.hl7.fhir.r4.model.Patient patient = transformToFhirPatient(patientInfo.getPatientPK());
 		this.addToOperations(fhirOperations, tempIdGenerator, patient);
@@ -428,6 +434,11 @@ private void updateReferringTaskWithTaskInfo(Task referringTask, Task task) {
 		}
 	}
 
+	private void updateReferringServiceRequestWithSampleInfo(Sample sample, ServiceRequest serviceRequest) {
+		serviceRequest.setRequisition(
+		    this.createIdentifier(fhirConfig.getOeFhirSystem() + "/samp_labNo", sample.getAccessionNumber()));
+	}
+
 	private Optional<Task> getReferringTaskForSample(Sample sample) {
 		List<ElectronicOrder> eOrders = electronicOrderService.getElectronicOrdersByExternalId(sample.getReferringId());
 		if (eOrders.size() > 0 && ElectronicOrderType.FHIR.equals(eOrders.get(0).getType())) {
@@ -436,6 +447,14 @@ private Optional<Task> getReferringTaskForSample(Sample sample) {
 		return Optional.empty();
 	}
 
+	private Optional<ServiceRequest> getReferringServiceRequestForSample(Sample sample) {
+		List<ElectronicOrder> eOrders = electronicOrderService.getElectronicOrdersByExternalId(sample.getReferringId());
+		if (eOrders.size() > 0 && ElectronicOrderType.FHIR.equals(eOrders.get(0).getType())) {
+			return fhirPersistanceService.getServiceRequestByReferingId(sample.getReferringId());
+		}
+		return Optional.empty();
+	}
+
 	private Practitioner transformProviderToPractitioner(String providerId) {
 		return transformProviderToPractitioner(providerService.get(providerId));
 	}

src/main/resources/application.properties

@@ -1,31 +1,46 @@
+#Faclity FHIR server
 #org.openelisglobal.facilitylist.fhirstore = https://hub.openelisci.org:5000/gofr/exemple4
 #org.openelisglobal.facilitylist.authurl= https://hub.openelisci.org:5000/gofr/token
 #org.openelisglobal.facilitylist.username= [email protected]
 #org.openelisglobal.facilitylist.password= gofr
 #org.openelisglobal.facilitylist.auth= token
 facilitylist.schedule.fixedRate=864000000
-spring.liquibase.contexts=ci_general,ci_recency_testing,ci_TB
 
-#org.openelisglobal.remote.source.uri=https://hub.openelisci.org:5000/fhir/ 
-##org.openelisglobal.remote.source.identifier=Organization/0c0488e7-81e3-4f29-a22f-f73cf5ef5c20 
-#org.openelisglobal.fhir.subscriber=https://hub.openelisci.org:5000/fhir/ 
+#Liquibase Profile
+#spring.liquibase.contexts=
 
 
-org.openelisglobal.server.uri=https://oe.openelis.org:8443/OpenELIS-Global/fhir/
-org.openelisglobal.datasubscriber.uri=https://datasubscriber.openelis.org:8443/subscription/fhirResourceGroup/
-org.openelisglobal.fhirstore.uri=http://localhost:8081/fhir/
+#Local FHIR server
+#org.openelisglobal.server.uri=https://oe.openelis.org:8443/OpenELIS-Global/fhir/
+#org.openelisglobal.datasubscriber.uri=https://datasubscriber.openelis.org:8443/subscription/fhirResourceGroup/
+#org.openelisglobal.fhirstore.uri=http://localhost:8081/fhir/
 
-org.openelisglobal.remote.source.identifier=Practitioner/738185ba-eac9-11e5-8f4d-e06995eac916
-org.openelisglobal.remote.source.uri=http://185.218.126.190:5001/fhir/
-org.openelisglobal.remote.source.updateStatus=false
-org.openelisglobal.task.useBasedOn=true
-org.openelisglobal.fhirstore.username=openelis
-org.openelisglobal.fhirstore.password=Openelis123!
-org.openelisglobal.fhir.subscriber.allowHTTP=true
+# Remote FHIR server/Consolidated Server
+#org.openelisglobal.remote.source.uri=http://185.218.126.190:5001/fhir/
+#org.openelisglobal.remote.source.identifier=Practitioner/738185ba-eac9-11e5-8f4d-e06995eac916
+#org.openelisglobal.remote.source.updateStatus=false
+#org.openelisglobal.task.useBasedOn=true
+#org.openelisglobal.fhirstore.username=openelis
+#org.openelisglobal.fhirstore.password=Openelis123!
+#org.openelisglobal.fhir.subscriber.allowHTTP=true
 
-org.openelisglobal.fhir.subscriber=http://185.218.126.190:5001/fhir/
+#org.openelisglobal.fhir.subscriber=http://185.218.126.190:5001/fhir/
+#org.openelisglobal.fhir.subscriber.resources=Task,Patient,ServiceRequest,DiagnosticReport,Observation,Specimen,Practitioner,Encounter
 
-org.openelisglobal.fhir.subscriber.resources=Task,Patient,ServiceRequest,DiagnosticReport,Observation,Specimen,Practitioner,Encounter
+#provider FHIR server
+#org.openelisglobal.providerlist.fhirstore=http://localhost:8081/fhir/
+#org.openelisglobal.requester.identifier=Practitioner/f9badd80-ab76-11e2-9e96-0800200c9a66
+#org.openelisglobal.requester.lastName=Dr. Mauritius
+#org.openelisglobal.requester.firstName=Felix
+#org.openelisglobal.requester.phone=230 5123 1234
 
-spring.jpa.show-sql=true
-spring.jpa.properties.hibernate.format_sql=true
+#Hibernate Config 
+#spring.jpa.show-sql=true
+#spring.jpa.properties.hibernate.format_sql=true
+
+# SSL Config
+#server.ssl.key-store = file:/ssl/lf.keystore
+#server.ssl.key-store-password = testtest
+#server.ssl.key-password = testtest
+#server.ssl.trust-store=file:/ssl/lf.truststore
+#server.ssl.trust-store-password=testtest