add support for Support FHIR Pagination when Pulling results

api/src/main/java/org/openmrs/module/labonfhir/api/dao/LabOnFhirDao.java

@@ -3,9 +3,11 @@
 import java.util.List;
 
 import org.hibernate.criterion.Restrictions;
+import org.openmrs.api.APIException;
 import org.openmrs.api.db.hibernate.DbSession;
 import org.openmrs.api.db.hibernate.DbSessionFactory;
 import org.openmrs.module.labonfhir.api.model.FailedTask;
+import org.openmrs.module.labonfhir.api.model.TaskRequest;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 
@@ -35,5 +37,17 @@ public List<FailedTask> getAllFailedTasks(Boolean isSent) {
             return getSession().createCriteria(FailedTask.class).list();
         }
     }
+
+
+    public TaskRequest saveOrUpdateTaskRequest(TaskRequest taskRequest) throws APIException {
+        getSession().saveOrUpdate(taskRequest);
+        return taskRequest;
+    }
+
+    public TaskRequest getLastTaskRequest() throws APIException {
+        String hql = "FROM TaskRequest tr WHERE tr.requestDate = (SELECT MAX(t.requestDate) FROM TaskRequest t)";
+        return (TaskRequest)getSession().createQuery(hql).uniqueResult();   
+    }
+
 
 }

api/src/main/java/org/openmrs/module/labonfhir/api/model/FailedTask.java

@@ -31,6 +31,7 @@ public Integer getId() {
     }
     @Override
     public void setId(Integer id) {
+        this.id = id;
     }
 
     public String getError() {

api/src/main/java/org/openmrs/module/labonfhir/api/model/TaskRequest.java

@@ -0,0 +1,42 @@
+package org.openmrs.module.labonfhir.api.model;
+
+import java.util.Date;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
+import javax.persistence.Table;
+
+import org.openmrs.BaseOpenmrsData;
+
+@Entity
+@Table(name = "task_request")
+public class TaskRequest extends BaseOpenmrsData {
+
+    @Id
+    @GeneratedValue
+    @Column(name = "id")
+    private Integer id;
+
+    @Column(name = "request_date")
+    private Date requestDate;
+
+    @Override
+    public Integer getId() {
+        return id;
+    }
+
+    @Override
+    public void setId(Integer id) {
+        this.id = id;
+    }
+
+    public Date getRequestDate() {
+        return requestDate;
+    }
+
+    public void setRequestDate(Date requestDate) {
+        this.requestDate = requestDate;
+    }
+}

api/src/main/java/org/openmrs/module/labonfhir/api/scheduler/FetchTaskUpdates.java

@@ -3,16 +3,20 @@
 import static org.apache.commons.lang3.exception.ExceptionUtils.getStackTrace;
 
 import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.gclient.TokenClientParam;
+import ca.uhn.fhir.rest.param.DateRangeParam;
 import lombok.AccessLevel;
 import lombok.Setter;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.hibernate.SessionFactory;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.DiagnosticReport;
@@ -28,13 +32,16 @@
 import org.openmrs.module.fhir2.api.dao.FhirObservationDao;
 import org.openmrs.module.fhir2.api.translators.ObservationReferenceTranslator;
 import org.openmrs.module.labonfhir.LabOnFhirConfig;
+import org.openmrs.module.labonfhir.api.model.TaskRequest;
+import org.openmrs.module.labonfhir.api.service.LabOnFhirService;
 import org.openmrs.scheduler.tasks.AbstractTask;
 import org.springframework.beans.BeansException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.ApplicationContextAware;
 import org.springframework.stereotype.Component;
+import java.text.SimpleDateFormat;
 
 @Component
 @Setter(AccessLevel.PACKAGE)
@@ -72,29 +79,63 @@ public class FetchTaskUpdates extends AbstractTask implements ApplicationContext
 	@Qualifier("sessionFactory")
 	SessionFactory sessionFactory;
 
+	@Autowired
+    private LabOnFhirService labOnFhirService;
+
 	@Override
 	public void execute() {
-
+		
 		try {
 			applicationContext.getAutowireCapableBeanFactory().autowireBean(this);
-		} catch (Exception e) {
+		}
+		catch (Exception e) {
 			// return;
 		}
-
+		
 		if (!config.isLisEnabled()) {
 			return;
 		}
-
+		
 		try {
+			SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
+			Date newDate = new Date();
+			Calendar calendar = Calendar.getInstance();
+			calendar.setTime(newDate);
+			calendar.add(Calendar.YEAR, -5);
+			Date fiveYearsAgo = calendar.getTime();
+
+			TaskRequest lastRequest = labOnFhirService.getLastTaskRequest();
+			String lastRequstDate = dateFormat.format(fiveYearsAgo);
+			if (lastRequest != null) {
+				lastRequstDate = dateFormat.format(lastRequest.getRequestDate());
+			}
+
+			String currentTime = dateFormat.format(newDate);
+			DateRangeParam lastUpdated = new DateRangeParam().setLowerBound(lastRequstDate).setUpperBound(currentTime);
+
 			// Get List of Tasks that belong to this instance and update them
-			updateTasksInBundle(client.search().forResource(Task.class)
-					.where(Task.IDENTIFIER.hasSystemWithAnyCode(FhirConstants.OPENMRS_FHIR_EXT_TASK_IDENTIFIER))
-					.where(Task.STATUS.exactly().code(TaskStatus.COMPLETED.toCode())).returnBundle(Bundle.class)
-					.execute());
-		} catch (Exception e) {
+			Bundle taskBundle = client.search().forResource(Task.class)
+			        .where(Task.IDENTIFIER.hasSystemWithAnyCode(FhirConstants.OPENMRS_FHIR_EXT_TASK_IDENTIFIER))
+			        .where(Task.STATUS.exactly().code(TaskStatus.COMPLETED.toCode())).lastUpdated(lastUpdated)
+			        .returnBundle(Bundle.class).execute();
+
+			List<Bundle> taskBundles = new ArrayList<>();
+			taskBundles.add(taskBundle);
+			//Support FHIR Server Pagination
+			while (taskBundle.getLink(IBaseBundle.LINK_NEXT) != null) {
+				taskBundle = client.loadPage().next(taskBundle).execute();
+				taskBundles.add(taskBundle);
+			}
+			updateTasksInBundle(taskBundles);
+
+			TaskRequest request = new TaskRequest();
+			request.setRequestDate(newDate);
+			labOnFhirService.saveOrUpdateTaskRequest(request);
+		}
+		catch (Exception e) {
 			log.error("ERROR executing FetchTaskUpdates : " + e.toString() + getStackTrace(e));
 		}
-
+		
 		super.startExecuting();
 	}
 
@@ -105,35 +146,36 @@ public void shutdown() {
 		this.stopExecuting();
 	}
 
-	private void updateTasksInBundle(Bundle taskBundle) {
-
-		for (Iterator tasks = taskBundle.getEntry().iterator(); tasks.hasNext();) {
-			String openmrsTaskUuid = null;
-
-			try {
-				// Read incoming LIS Task
-				Task openelisTask = (Task) ((Bundle.BundleEntryComponent) tasks.next()).getResource();
-				openmrsTaskUuid = openelisTask.getIdentifierFirstRep().getValue();
-
-				// Find original openmrs task using Identifier
-				Task openmrsTask = taskService.get(openmrsTaskUuid);
-
-				// Only update if matching OpenMRS Task found
-				if (openmrsTask != null) {
-					// Handle status
-					openmrsTask.setStatus(openelisTask.getStatus());
-
-					Boolean taskOutPutUpdated = false;
-					if (openelisTask.hasOutput()) {
-						// openmrsTask.setOutput(openelisTask.getOutput());
-						taskOutPutUpdated = updateOutput(openelisTask.getOutput(), openmrsTask);
-					}
-					if (taskOutPutUpdated) {
-						taskService.update(openmrsTaskUuid, openmrsTask);
+	private void updateTasksInBundle(List<Bundle> taskBundles) {
+		for (Bundle bundle : taskBundles) {
+			for (Iterator tasks = bundle.getEntry().iterator(); tasks.hasNext();) {
+				String openmrsTaskUuid = null;
+				
+				try {
+					// Read incoming LIS Task
+					Task openelisTask = (Task) ((Bundle.BundleEntryComponent) tasks.next()).getResource();
+					openmrsTaskUuid = openelisTask.getIdentifierFirstRep().getValue();
+					// Find original openmrs task using Identifier
+					Task openmrsTask = taskService.get(openmrsTaskUuid);
+					
+					// Only update if matching OpenMRS Task found
+					if (openmrsTask != null) {
+						// Handle status
+						openmrsTask.setStatus(openelisTask.getStatus());
+						
+						Boolean taskOutPutUpdated = false;
+						if (openelisTask.hasOutput()) {
+							// openmrsTask.setOutput(openelisTask.getOutput());
+							taskOutPutUpdated = updateOutput(openelisTask.getOutput(), openmrsTask);
+						}
+						if (taskOutPutUpdated) {
+							taskService.update(openmrsTaskUuid, openmrsTask);
+						}
 					}
 				}
-			} catch (Exception e) {
-				log.error("Could not save task " + openmrsTaskUuid + ":" + e.toString() + getStackTrace(e));
+				catch (Exception e) {
+					log.error("Could not save task " + openmrsTaskUuid + ":" + e.toString() + getStackTrace(e));
+				}
 			}
 		}
 	}

api/src/main/java/org/openmrs/module/labonfhir/api/service/LabOnFhirService.java

@@ -2,6 +2,7 @@
 
 import org.openmrs.api.OpenmrsService;
 import org.openmrs.module.labonfhir.api.model.FailedTask;
+import org.openmrs.module.labonfhir.api.model.TaskRequest;
 
 import java.util.List;
 import org.openmrs.api.APIException;
@@ -40,5 +41,23 @@ public interface LabOnFhirService extends OpenmrsService{
 	@Transactional
 	List<FailedTask> getAllFailedTasks(Boolean isSent) throws APIException;
 
-
+	/**
+	 * Saves an TaskRequest
+	 * 
+	 * @param taskRequest
+	 * @return TaskRequest
+	 * @throws APIException
+	 */
+	@Transactional
+	TaskRequest saveOrUpdateTaskRequest(TaskRequest taskRequest) throws APIException;
+
+
+	/**
+	 * Returns the Last Task Request
+
+	 * @throws APIException
+	 */
+	@Transactional(readOnly = true)
+	TaskRequest getLastTaskRequest() throws APIException;
+
 }

api/src/main/java/org/openmrs/module/labonfhir/api/service/impl/LabOnFhirServiceImpl.java

@@ -5,6 +5,7 @@
 import org.openmrs.api.APIException;
 import org.openmrs.module.labonfhir.api.dao.LabOnFhirDao;
 import org.openmrs.module.labonfhir.api.model.FailedTask;
+import org.openmrs.module.labonfhir.api.model.TaskRequest;
 import org.openmrs.module.labonfhir.api.service.LabOnFhirService;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -43,5 +44,15 @@ public void onStartup() {
     public void onShutdown() {
 
     }
+
+    @Override
+    public TaskRequest getLastTaskRequest() throws APIException {
+       return  dao.getLastTaskRequest();
+    }
+
+    @Override
+    public TaskRequest saveOrUpdateTaskRequest(TaskRequest taskRequest) throws APIException {
+        return dao.saveOrUpdateTaskRequest(taskRequest);
+    }
 
 }

api/src/main/resources/liquibase.xml

@@ -86,6 +86,31 @@
             <column name="uuid" value="ae35121c-41e6-46f1-b2a2-0d9d2fa63e74" />
         </insert>
     </changeSet>
+     <changeSet id="create-task-request-table-2023-08-24" author="mozzymutesa" dbms="mysql">
+		<preConditions onFail="MARK_RAN">
+			<not><tableExists tableName="task_request"/></not>
+		</preConditions>
+		<comment>
+			Creating the task_request table
+		</comment>
+		<createTable tableName="task_request">
+			<column name="id" type="int" autoIncrement="true">
+				<constraints primaryKey="true" nullable="false"/>
+			</column>
+            <column name="request_date" type="DATETIME"/>
+            <column name="uuid" type="char(38)">
+				<constraints nullable="false" unique="true"></constraints>
+			</column>
+            <column name="date_voided" type="DATETIME"/>
+            <column name="date_changed" type="DATETIME"/>
+            <column name="date_created" type="DATETIME"/>
+            <column name="void_reason" type="varchar(255)" />
+            <column name="changed_by" type="int" />
+            <column name="voided_by" type="int" />
+            <column name="creator" type="int" />
+            <column defaultValueBoolean="false" name="voided" type="BOOLEAN"/>
+		</createTable>
+    </changeSet> 
 </databaseChangeLog>