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Refactor code to replace component annotations with xml configurations #48

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Refactor code to replace component annotations with xml configurations #48

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fd3a55a
chore: Update Maven repository URLs in pom.xml
moshonk May 12, 2024
16c4e52
[maven-release-plugin] prepare release 1.4.0
moshonk May 12, 2024
83a8f08
chore: Update labonfhir version to 1.4.0-SNAPSHOT
moshonk May 12, 2024
3f2e4d7
chore: Update .gitignore to include openmrs.log
moshonk May 12, 2024
b7f446e
chore: Update Maven repository URLs in pom.xml
moshonk May 12, 2024
af9dc6d
[maven-release-plugin] prepare release 1.4.1
moshonk May 12, 2024
1a1e117
[maven-release-plugin] prepare for next development iteration
moshonk May 12, 2024
1c1518e
chore: Add MFL Code as location identifier in LabCreationListener
moshonk May 14, 2024
e597f18
Refactor code to replace component annotations with xml configurations
moshonk Aug 23, 2024
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3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -80,4 +80,5 @@ nb-configuration.xml
##############################
.DS_Store

.flattened-pom.xml
.flattened-pom.xml
openmrs.log
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);
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3 changes: 1 addition & 2 deletions api/src/main/java/org/openmrs/module/labonfhir/LabOnFhirConfig.java
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Expand Up @@ -28,9 +28,8 @@
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 {

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3 changes: 1 addition & 2 deletions api/src/main/java/org/openmrs/module/labonfhir/api/LabOrderHandler.java
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Expand Up @@ -27,9 +27,8 @@
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
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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);
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1 change: 0 additions & 1 deletion api/src/main/java/org/openmrs/module/labonfhir/api/event/EncounterCreationListener.java
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Expand Up @@ -16,7 +16,6 @@
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;

@Component("labEncounterListener")
public class EncounterCreationListener extends LabCreationListener {
private static final Logger log = LoggerFactory.getLogger(OrderCreationListener.class);
@Autowired
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54 changes: 47 additions & 7 deletions api/src/main/java/org/openmrs/module/labonfhir/api/event/LabCreationListener.java
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@@ -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;

Expand All @@ -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.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;
Expand All @@ -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;
Expand All @@ -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;
}
Expand All @@ -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);
Expand All @@ -96,8 +110,35 @@ public Bundle createLabBundle(Task task) {
if (!task.getLocation().isEmpty()) {
labResources.add(fhirLocationService.get(FhirUtils.referenceToId(task.getLocation().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 enrich the MFL Code as appropriate

if (resource instanceof Location) {
Location location = (Location) resource;
if (location != null) {
org.openmrs.Location openmrsLocation = locationService.getLocationByUuid(location.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);
location.addIdentifier(mflIdentifier);
});
}
}
}
}

Bundle.BundleEntryComponent component = transactionBundle.addEntry();
component.setResource(resource);
component.getRequest().setUrl(resource.fhirType() + "/" + resource.getIdElement().getIdPart())
Expand All @@ -113,8 +154,7 @@ 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);
}
Expand All @@ -123,7 +163,7 @@ 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);
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2 changes: 0 additions & 2 deletions api/src/main/java/org/openmrs/module/labonfhir/api/event/OrderCreationListener.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("labOrderListener")
public class OrderCreationListener extends LabCreationListener {

private static final Logger log = LoggerFactory.getLogger(OrderCreationListener.class);
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1 change: 0 additions & 1 deletion api/src/main/java/org/openmrs/module/labonfhir/api/scheduler/FetchTaskUpdates.java
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Expand Up @@ -49,7 +49,6 @@

import java.text.SimpleDateFormat;

@Component
@Setter(AccessLevel.PACKAGE)
public class FetchTaskUpdates extends AbstractTask implements ApplicationContextAware {

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3 changes: 0 additions & 3 deletions api/src/main/java/org/openmrs/module/labonfhir/api/scheduler/RetryFailedTasks.java
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Expand Up @@ -16,12 +16,9 @@
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.stereotype.Component;

import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.api.IGenericClient;

@Component
public class RetryFailedTasks extends AbstractTask implements ApplicationContextAware {
private static Log log = LogFactory.getLog(RetryFailedTasks.class);

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11 changes: 9 additions & 2 deletions api/src/main/resources/moduleApplicationContext.xml
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Expand Up @@ -10,8 +10,15 @@
http://www.springframework.org/schema/context
http://www.springframework.org/schema/context/spring-context-3.0.xsd">

<context:component-scan base-package="org.openmrs.module.labonfhir"/>

<bean id="labEncounterListener" class="org.openmrs.module.labonfhir.api.event.EncounterCreationListener"></bean>
<bean id="labOrderListener" class="org.openmrs.module.labonfhir.api.event.OrderCreationListener"></bean>
<bean id="labOnFhirActivator" class="org.openmrs.module.labonfhir.LabOnFhirActivator"></bean>
<bean id="fetchTaskUpdates" class="org.openmrs.module.labonfhir.api.scheduler.FetchTaskUpdates"></bean>
<bean id="retryFailedTasks" class="org.openmrs.module.labonfhir.api.scheduler.RetryFailedTasks"></bean>
<bean id ="labOrderManager" class="org.openmrs.module.labonfhir.api.LabOrderManager"></bean>
<bean id="labOrderHandler" class="org.openmrs.module.labonfhir.api.LabOrderHandler"></bean>
<bean id="labOnFhirConfig" class="org.openmrs.module.labonfhir.LabOnFhirConfig"></bean>

<bean parent="openmrsEventListeners">
<property name="globalPropertyListeners">
<list merge="true">
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44 changes: 30 additions & 14 deletions pom.xml
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Expand Up @@ -19,10 +19,10 @@
<url>https://wiki.openmrs.org/x/FQ4z</url>

<scm>
<connection>scm:git:git@github.com:openmrs/openmrs-module-labonfhir.git</connection>
<developerConnection>scm:git:git@github.com:openmrs/openmrs-module-labonfhir.git</developerConnection>
<url>https://github.com/openmrs/openmrs-module-labonfhir/</url>
<tag>HEAD</tag>
<connection>scm:git:git@bitbucket.org:botswana-emrs/openmrs-module-labonfhir.git</connection>
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@moshonk do we need this change here??

<developerConnection>scm:git:git@bitbucket.org:botswana-emrs/openmrs-module-labonfhir.git</developerConnection>
<url>https://bitbucket.org/botswana-emrs/openmrs-module-labonfhir</url>
<tag>1.4.0</tag>
</scm>

<developers>
Expand Down Expand Up @@ -201,6 +201,11 @@
</build>

<repositories>
<repository>
<id>repsy</id>
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do we need this repository here ??

<name>Maven Repository on Repsy</name>
<url>https://repo.repsy.io/mvn/intellisoftdev/default</url>
</repository>
<repository>
<id>openmrs-repo</id>
<name>OpenMRS Nexus Repository</name>
Expand Down Expand Up @@ -229,18 +234,16 @@
<id>github-packages</id>
<distributionManagement>
<!-- Deploy to Github Packages -->
<repository>
<id>github-packages</id>
<name>Github Maven Repo</name>
<url>https://maven.pkg.github.com/openmrs/openmrs-module-labonfhir</url>
<uniqueVersion>false</uniqueVersion>
</repository>
<snapshotRepository>
<id>github-packages</id>
<name>Github Maven Repo</name>
<url>https://maven.pkg.github.com/openmrs/openmrs-module-labonfhir</url>
<uniqueVersion>true</uniqueVersion>
<id>repsy</id>
<name>My Private Maven Repository on Repsy</name>
<url>https://repo.repsy.io/mvn/intellisoftdev/default</url>
</snapshotRepository>
<repository>
<id>repsy</id>
<name>My Private Maven Repository on Repsy</name>
<url>https://repo.repsy.io/mvn/intellisoftdev/default</url>
</repository>
</distributionManagement>
</profile>
</profiles>
Expand All @@ -254,4 +257,17 @@
<openmrsPlatformVersion>2.3.1</openmrsPlatformVersion>
<hapifhirVersion>4.2.0</hapifhirVersion>
</properties>
<distributionManagement>
<!-- Deploy to Github Packages -->
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@moshonk This is already deployed to OpenMRS Artifactory

<snapshotRepository>
<id>repsy</id>
<name>My Private Maven Repository on Repsy</name>
<url>https://repo.repsy.io/mvn/intellisoftdev/default</url>
</snapshotRepository>
<repository>
<id>repsy</id>
<name>My Private Maven Repository on Repsy</name>
<url>https://repo.repsy.io/mvn/intellisoftdev/default</url>
</repository>
</distributionManagement>
</project>
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