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Feat: #46

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f23c239
Feat:
moshonk Jun 14, 2024
4342ccd
feat: Update FhirConfig to set socket timeout for FHIR client
moshonk Jul 1, 2024
784ae5f
chore: Add lab encounter and order creation listeners beans instead o…
moshonk Jul 1, 2024
559b07a
chore: Refactor LabOrderHandler to include location and requester ref…
moshonk Jul 1, 2024
7432527
Refactor code to replace component annotations with xml configurations
moshonk Aug 23, 2024
6a236e1
chore: Add global property for lab ordering site concept UUID
moshonk Sep 1, 2024
25357bc
Added the functionality to include ordering site in the lab order pay…
moshonk Sep 1, 2024
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2 changes: 2 additions & 0 deletions api/src/main/java/org/openmrs/module/labonfhir/FhirConfig.java
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Expand Up @@ -37,6 +37,8 @@ public IGenericClient getFhirClient() throws Exception {
configureFhirHttpClient(client);
}

fhirContext.getRestfulClientFactory().setSocketTimeout(config.getFhirClientTimeout());

IGenericClient fhirClient = fhirContext.newRestfulGenericClient(config.getLisUrl());
if (config.getAuthType().equals(AuthType.BASIC)) {
BasicAuthInterceptor authInterceptor = new BasicAuthInterceptor(config.getLisUserName(),
Expand Down
2 changes: 0 additions & 2 deletions api/src/main/java/org/openmrs/module/labonfhir/LabOnFhirActivator.java
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Expand Up @@ -27,9 +27,7 @@
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.stereotype.Component;

@Component
public class LabOnFhirActivator extends BaseModuleActivator implements ApplicationContextAware, DaemonTokenAware {

private static final Logger log = LoggerFactory.getLogger(LabOnFhirActivator.class);
Expand Down
16 changes: 14 additions & 2 deletions api/src/main/java/org/openmrs/module/labonfhir/LabOnFhirConfig.java
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Expand Up @@ -28,12 +28,12 @@
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.context.annotation.Configuration;
import org.springframework.stereotype.Component;

@Component
@Configuration
public class LabOnFhirConfig implements ApplicationContextAware {

private static final String LAB_ORDERING_SITE_CONCEPT_UUID = "labonfhir.labOrderLocationConceptUuid";

public static final String GP_LIS_URL = "labonfhir.lisUrl";

public static final String GP_LIS_USER_UUID = "labonfhir.lisUserUuid";
Expand Down Expand Up @@ -68,6 +68,8 @@ public class LabOnFhirConfig implements ApplicationContextAware {

public static final String GP_FILTER_ORDER_BY_TEST_UUIDS = "labonfhir.filterOrderBytestUuids";

public static final String GP_FHIR_CLIENT_TIMEOUT = "labonfhir.clientTimeout";

public enum AuthType{
SSL,
BASIC
Expand Down Expand Up @@ -231,4 +233,14 @@ private KeyStore loadKeystore(String filePath) {
public void setApplicationContext(ApplicationContext applicationContext) throws BeansException {
this.applicationContext = applicationContext;
}

public int getFhirClientTimeout() {
String fhirClientTimeout = administrationService.getGlobalProperty(GP_FHIR_CLIENT_TIMEOUT, "180000");
return Integer.valueOf(fhirClientTimeout);
}

public Object getLabOrderingSiteConceptUuid() {
String labOrderingSiteConceptUuid = administrationService.getGlobalProperty(LAB_ORDERING_SITE_CONCEPT_UUID);
return labOrderingSiteConceptUuid;
}
}
69 changes: 44 additions & 25 deletions api/src/main/java/org/openmrs/module/labonfhir/api/LabOrderHandler.java
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Expand Up @@ -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;

Expand All @@ -27,9 +26,7 @@
import org.openmrs.module.labonfhir.LabOnFhirConfig;
import org.openmrs.module.labonfhir.api.fhir.OrderCreationException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;

@Component
public class LabOrderHandler {

@Autowired
Expand Down Expand Up @@ -88,22 +85,22 @@ public Task createOrder(Order order) throws OrderCreationException {

Reference forReference = newReference(order.getPatient().getUuid(), FhirConstants.PATIENT);

Reference ownerRef = newReference(config.getLisUserUuid(), FhirConstants.PRACTITIONER);
// Reference ownerRef = newReference(config.getLisUserUuid(), FhirConstants.PRACTITIONER);
Reference ownerRef = newReference(order.getEncounter().getLocation().getUuid(), FhirConstants.ORGANIZATION);

Reference encounterRef = newReference(order.getEncounter().getUuid(), FhirConstants.ENCOUNTER);

Optional<EncounterProvider> requesterProvider = order.getEncounter().getActiveEncounterProviders().stream()
.findFirst();
Reference locationRef = getLocatonRef(order.getEncounter());

Reference requesterRef = requesterProvider.map(
encounterProvider -> newReference(encounterProvider.getUuid(), FhirConstants.PRACTITIONER)).orElse(null);
Reference requesterRef = getRequesterRef(order.getEncounter());

//if (order.getEncounter().getLocation() != null) {
// requesterRef = newReference(order.getEncounter().getLocation().getUuid(), FhirConstants.ORGANIZATION);
// locationRef = newReference(order.getEncounter().getLocation().getUuid(), FhirConstants.LOCATION);
//}

// Create Task Resource for given Order
Task newTask = createTask(basedOnRefs, forReference, ownerRef, encounterRef ,taskInputs);

if (order.getEncounter().getActiveEncounterProviders().isEmpty()) {
newTask.setRequester(requesterRef);
}
Task newTask = createTask(basedOnRefs, forReference, ownerRef, encounterRef, locationRef,requesterRef ,taskInputs);

// Save the new Task Resource
try {
Expand All @@ -116,14 +113,16 @@ public Task createOrder(Order order) throws OrderCreationException {
}

private Task createTask(List<Reference> basedOnRefs, Reference forReference, Reference ownerRef,
Reference encounterRef ,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);
newTask.setBasedOn(basedOnRefs);
newTask.setFor(forReference);
newTask.setOwner(ownerRef);
newTask.setEncounter(encounterRef);
newTask.setRequester(requesterRef);
newTask.setLocation(locationRef);
if (taskInputs != null) {
newTask.setInput(taskInputs);
}
Expand All @@ -148,17 +147,19 @@ public Task createOrder(Encounter encounter) throws OrderCreationException {

Reference forReference = newReference(encounter.getPatient().getUuid(), FhirConstants.PATIENT);

Reference ownerRef = newReference(config.getLisUserUuid(), FhirConstants.PRACTITIONER);
// Reference ownerRef = newReference(config.getLisUserUuid(), FhirConstants.PRACTITIONER);

Reference encounterRef = newReference(encounter.getUuid(), FhirConstants.ENCOUNTER);

Reference locationRef = newReference(encounter.getLocation().getUuid(), FhirConstants.LOCATION);
// get ordering site location from the encounter obs
Reference locationRef = getLocatonRef(encounter);

Optional<EncounterProvider> requesterProvider = encounter.getActiveEncounterProviders().stream().findFirst();
// Reference locationRef = newReference(encounter.getLocation().getUuid(), FhirConstants.LOCATION);

Reference requesterRef = requesterProvider.isPresent() ?
newReference(requesterProvider.get().getUuid(), FhirConstants.PRACTITIONER) :
null;
// Optional<EncounterProvider> requesterProvider = encounter.getActiveEncounterProviders().stream().findFirst();
Reference requesterRef = getRequesterRef(encounter);

Reference ownerRef = newReference(encounter.getLocation().getUuid(), FhirConstants.ORGANIZATION);

List<Task.ParameterComponent> taskInputs = null;
if (config.addObsAsTaskInput()) {
Expand All @@ -173,12 +174,9 @@ public Task createOrder(Encounter encounter) throws OrderCreationException {
}

// Create Task Resource for given Order
Task newTask = createTask(basedOnRefs, forReference, ownerRef, encounterRef ,taskInputs);
Task newTask = createTask(basedOnRefs, forReference, ownerRef, encounterRef,locationRef, requesterRef, taskInputs);
newTask.setLocation(locationRef);

if (!encounter.getActiveEncounterProviders().isEmpty()) {
newTask.setRequester(requesterRef);
}
newTask.setRequester(requesterRef);

// Save the new Task Resource
try {
Expand All @@ -194,4 +192,25 @@ private Reference newReference(String uuid, String type) {
return new Reference().setReference(type + "/" + uuid).setType(type);
}

private Reference getLocatonRef(Encounter encounter) {
final AtomicReference<Reference> locationRef = new AtomicReference<>(null);
encounter.getAllObs().stream().filter(obs -> obs.getConcept().getUuid().equals(config.getLabOrderingSiteConceptUuid()))
.findFirst().ifPresent(obs -> {
locationRef.set(newReference(obs.getValueText(), FhirConstants.LOCATION));
});
return locationRef.get();
}

private Reference getRequesterRef(Encounter encounter) {
EncounterProvider requesterProvider = encounter.getActiveEncounterProviders().stream()
.findFirst().orElse(null);
Reference requesterRef = null; // Initialize the variable with null
if (requesterProvider != null) {
requesterRef = newReference(requesterProvider.getProvider().getUuid(), FhirConstants.PRACTITIONER);
}

return requesterRef;
}


}
2 changes: 0 additions & 2 deletions api/src/main/java/org/openmrs/module/labonfhir/api/LabOrderManager.java
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Expand Up @@ -15,9 +15,7 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;

@Component
public class LabOrderManager implements GlobalPropertyListener {

private static final Logger log = LoggerFactory.getLogger(LabOrderManager.class);
Expand Down
75 changes: 72 additions & 3 deletions api/src/main/java/org/openmrs/module/labonfhir/api/event/LabCreationListener.java
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@@ -1,6 +1,7 @@
package org.openmrs.module.labonfhir.api.event;

import javax.jms.Message;

import java.util.HashSet;
import java.util.List;

Expand All @@ -10,13 +11,20 @@
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.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Reference;
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;
import org.openmrs.module.fhir2.FhirConstants;
import org.openmrs.module.fhir2.api.FhirLocationService;
import org.openmrs.module.fhir2.api.FhirTaskService;
import org.openmrs.module.fhir2.api.util.FhirUtils;
Expand All @@ -27,12 +35,17 @@
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;

import org.openmrs.module.fhir2.api.search.param.TaskSearchParams;

public abstract class LabCreationListener implements EventListener {

private static final Logger log = LoggerFactory.getLogger(EncounterCreationListener.class);

protected static final String MFL_LOCATION_IDENTIFIER_URI = "http://moh.bw.org/ext/location/identifier/mfl-code";

protected static final String MFL_LOCATION_ATTRIBUTE_TYPE_UUID = "8a845a89-6aa5-4111-81d3-0af31c45c002";

private DaemonToken daemonToken;

@Autowired
Expand All @@ -55,6 +68,9 @@ public abstract class LabCreationListener implements EventListener {
@Autowired
private LabOnFhirService labOnFhirService ;

@Autowired
private LocationService locationService;

public DaemonToken getDaemonToken() {
return daemonToken;
}
Expand Down Expand Up @@ -86,15 +102,17 @@ public Bundle createLabBundle(Task task) {
includes.add(new Include("Task:owner"));
includes.add(new Include("Task:encounter"));
includes.add(new Include("Task:based-on"));
includes.add(new Include("Task:location"));
includes.add(new Include("Task:practitioner"));


IBundleProvider labBundle = fhirTaskService.searchForTasks(new TaskSearchParams(null, null, null, uuid, null, null, includes));

Bundle transactionBundle = new Bundle();
transactionBundle.setType(Bundle.BundleType.TRANSACTION);
List<IBaseResource> labResources = labBundle.getAllResources();
if (!task.getLocation().isEmpty() && config.getLabUpdateTriggerObject().equals("Encounter")) {
labResources.add(fhirLocationService.get(FhirUtils.referenceToId(task.getLocation().getReference()).get()));
}
updateMflCodeToLocationAndOrganizationResourceBundle(task, labResources);

for (IBaseResource r : labResources) {
Resource resource = (Resource) r;
Bundle.BundleEntryComponent component = transactionBundle.addEntry();
Expand All @@ -106,6 +124,57 @@ public Bundle createLabBundle(Task task) {
return transactionBundle;
}

protected void updateMflCodeToLocationAndOrganizationResourceBundle(Task task, List<IBaseResource> labResources) {
if (task.getOwner() != null) {
String mflCode = getMflCode(task.getOwner().getReference(), FhirConstants.ORGANIZATION);
if (mflCode != null) {
Identifier mflIdentifier = new Identifier()
.setSystem(MFL_LOCATION_IDENTIFIER_URI)
.setValue(mflCode);
Reference ownerRef = new Reference();
ownerRef.setIdentifier(mflIdentifier);
ownerRef.setType(FhirConstants.ORGANIZATION);
task.setOwner(ownerRef);
}

}

if (task.getLocation() != null) {
String mflCode = getMflCode(task.getLocation().getReference(), FhirConstants.LOCATION);
if (mflCode != null) {
Identifier mflIdentifier = new Identifier()
.setSystem(MFL_LOCATION_IDENTIFIER_URI)
.setValue(mflCode);
Reference locationRef = new Reference();
locationRef.setIdentifier(mflIdentifier);
locationRef.setType(FhirConstants.LOCATION);
task.setLocation(locationRef);
}
}
labResources.removeIf(r->r.getIdElement().getValue().equals(task.getIdElement().getValue()));
labResources.add(task);
}

private String getMflCode(String reference, String referencePath) {
String locationReferenceId = FhirUtils.referenceToId(reference).orElse(null);
String mflCode = null;
if (locationReferenceId != null) {
String locationUuid = locationReferenceId.replace(referencePath + "/", "");
org.openmrs.Location openmrsLocation = locationService.getLocationByUuid(locationUuid);
if (openmrsLocation != null) {
LocationAttributeType mflLocationAttributeType = locationService.getLocationAttributeTypeByUuid(MFL_LOCATION_ATTRIBUTE_TYPE_UUID);
LocationAttribute mflLocationAttribute = openmrsLocation.getActiveAttributes().stream()
.filter(locationAttribute -> locationAttribute.getAttributeType().equals(mflLocationAttributeType))
.findFirst()
.orElse(null);
if (mflLocationAttribute != null) {
mflCode = (String) mflLocationAttribute.getValue();
}
}
}
return mflCode;
}

protected void sendTask(Task task) {
if (task != null) {
if (config.getActivateFhirPush()) {
Expand Down
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