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U4X-738: VL Program Data improvisions #178

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merged 5 commits into from
Oct 16, 2024
Merged

U4X-738: VL Program Data improvisions #178

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ab5aaed
adjusted logging of failed fields in the vl program data
dbaluku Jul 10, 2024
09c600e
Merge branch 'master' of https://github.com/METS-Programme/openmrs-mo…
dbaluku Aug 12, 2024
3330be9
Merge branch 'master' of https://github.com/METS-Programme/openmrs-mo…
dbaluku Aug 12, 2024
9a4dc96
Merge branch 'master' of https://github.com/METS-Programme/openmrs-mo…
dbaluku Oct 4, 2024
160a993
improvised on vl indicators that lead to failure of syncing to cphl e…
dbaluku Oct 15, 2024
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2 changes: 2 additions & 0 deletions api/src/main/java/org/openmrs/module/ugandaemrsync/api/UgandaEMRSyncService.java
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Expand Up @@ -483,5 +483,7 @@ public Encounter addVLToEncounter(String vlQualitative, String vlQuantitative, S
public List<SyncFhirResource> getSyncFHIRResourceBySyncFhirProfile(SyncFhirProfile syncFhirProfile, String synceDateFrom, String synceDateTo);

public List<SyncTask> searchSyncTask(SyncTaskType syncTaskType,Integer statusCode,Date fromDate, Date toDate);

public void deleteSyncTask(String syncTask, SyncTaskType syncTaskType);
}

7 changes: 7 additions & 0 deletions api/src/main/java/org/openmrs/module/ugandaemrsync/api/dao/UgandaEMRSyncDao.java
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Expand Up @@ -10,11 +10,14 @@
package org.openmrs.module.ugandaemrsync.api.dao;

import org.hibernate.Criteria;
import org.hibernate.Query;
import org.hibernate.SQLQuery;
import org.hibernate.Transaction;
import org.hibernate.criterion.Order;
import org.hibernate.criterion.Restrictions;
import org.hibernate.type.StringType;
import org.openmrs.Patient;
import org.openmrs.api.context.Context;
import org.openmrs.api.db.hibernate.DbSession;
import org.openmrs.api.db.hibernate.DbSessionFactory;
import org.openmrs.module.ugandaemrsync.model.SyncTask;
Expand Down Expand Up @@ -471,4 +474,8 @@ public List<SyncTask> searchSyncTask(SyncTaskType syncTaskType, Integer statusCo
}
return criteria.list();
}

public void deleteUnSuccessfulSyncTasks(String syncTask, SyncTaskType syncTaskType) {
Context.getAdministrationService().executeSQL(String.format("delete from sync_task where status_code != %s and sync_task = '%s' and sync_task_type= %s",200,syncTask,syncTaskType.getSyncTaskTypeId()),false);
}
}
5 changes: 5 additions & 0 deletions api/src/main/java/org/openmrs/module/ugandaemrsync/api/impl/UgandaEMRSyncServiceImpl.java
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Expand Up @@ -1172,5 +1172,10 @@ public List<SyncTask> getSyncTasksByType(SyncTaskType syncTaskType) {
public List<SyncTask> searchSyncTask(SyncTaskType syncTaskType,Integer statusCode,Date fromDate, Date toDate) {
return dao.searchSyncTask( syncTaskType, statusCode, fromDate, toDate);
}

@Override
public void deleteSyncTask(String syncTask, SyncTaskType syncTaskType) {
dao.deleteUnSuccessfulSyncTasks(syncTask,syncTaskType);
}
}

5 changes: 5 additions & 0 deletions api/src/main/java/org/openmrs/module/ugandaemrsync/server/SyncConstant.java
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Expand Up @@ -503,5 +503,10 @@ public class SyncConstant {
public static List<String> VL_SYNC_TASK_COLUMNS = Arrays.asList("sync_task_id", "sync_task_type", "sync_task", "status", "status_code", "sent_to_url", "require_action", "action_completed", "date_sent", "creator", "date_created", "changed_by", "date_changed", "voided", "date_voided", "voided_by ", "void_reason", "uuid");

public static final String Latest_obs_of_Person = "SELECT %s from obs where person_id=%s and concept_id=%s and obs_datetime <= '%s' and voided= 0 ORDER BY obs_datetime DESC LIMIT 1";
public static final String Latest_drug_order_of_person = "SELECT o.concept_id FROM orders o\n" +
" INNER JOIN order_type ot ON o.order_type_id = ot.order_type_id\n" +
" INNER JOIN drug_order d_o ON o.order_id = d_o.order_id\n" +
"where ot.uuid='131168f4-15f5-102d-96e4-000c29c2a5d7' and o.voided=0 and patient_id=%s and DATE(date_activated) <='%s'" +
" and o.concept_id in (SELECT answer_concept from concept_answer where concept_id=90315) ORDER BY date_activated DESC LIMIT 1\n";
public static final String ALIS_SYNC_TASK_TYPE_UUID = "d4a3ebbb-e793-4e56-867c-0cf998e51f56";
}
196 changes: 144 additions & 52 deletions ...a/org/openmrs/module/ugandaemrsync/tasks/SendViralLoadProgramDataToCentralServerTask.java
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Expand Up @@ -19,23 +19,12 @@

import java.io.IOException;
import java.text.ParseException;
import java.time.LocalDate;
import java.time.ZoneId;
import java.util.*;
import java.util.stream.Collectors;

import static org.openmrs.module.ugandaemrsync.server.SyncConstant.VIRAL_LOAD_SYNC_TYPE_UUID;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.VL_PROGRAM_DATA_SYNC_TYPE_UUID;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.VL_SEND_PROGRAM_DATA_FHIR_JSON_STRING;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.PATIENT_IDENTIFIER_TYPE;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.OPENMRS_IDENTIFIER_TYPE_UUID;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.ANC_IDENTIFIER_TYPE_UUID;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.NATIONAL_ID_IDENTIFIER_TYPE_UUID;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.PNC_IDENTIFIER_TYPE_UUID;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.Latest_obs_of_Person;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.firstLineBody;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.secondLineBody;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.thirdLineBody;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.VIRAL_LOAD_ORDERS_QUERY;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.REGIMEN_LINE_QUERY;
import static org.openmrs.module.ugandaemrsync.server.SyncConstant.*;

/**
* Posts Viral load PROGRAM data to the central server
Expand Down Expand Up @@ -79,6 +68,7 @@ public void execute() {
String json = dataOutput.get("json");
String empty_fields = dataOutput.get("empty_fields");
String patientARTno = dataOutput.get("patient");
ugandaEMRSyncService.deleteSyncTask(order.getAccessionNumber(),syncTaskType);
Map map = ugandaEMRHttpURLConnection.sendPostBy(syncTaskType.getUrl(), syncTaskType.getUrlUserName(), syncTaskType.getUrlPassword(), "", json, false);
if (map != null) {
SyncTask newSyncTask = new SyncTask();
Expand Down Expand Up @@ -109,6 +99,7 @@ public Map<String, String> generateVLProgramDataFHIRBody(TestOrder testOrder, St
Map<String, String> jsonMap = new HashMap<>();
UgandaEMRSyncService ugandaEMRSyncService = new UgandaEMRSyncServiceImpl();
String filledJsonFile = "";
String empty_fields="";
if (testOrder != null) {
AdministrationService administrationService = Context.getAdministrationService();

Expand All @@ -125,17 +116,22 @@ public Map<String, String> generateVLProgramDataFHIRBody(TestOrder testOrder, St
String sampleID = testOrder.getAccessionNumber();
String gender = patient.getGender();
List current_regimenList = administrationService.executeSQL(String.format(Latest_obs_of_Person,"value_coded", patientId,90315,date_activated),true);
List current_regimen_orders_List = administrationService.executeSQL(String.format(Latest_drug_order_of_person, patientId,date_activated),true);

String empty_fields="";
String current_regimen="";
int regimen_code=0;
if(current_regimenList.size() > 0) {
ArrayList regimenList = (ArrayList) current_regimenList.get(0);
regimen_code = Integer.parseInt(regimenList.get(0).toString());
current_regimen = Context.getConceptService().getConcept(regimen_code).getName().getName();
}else if (current_regimen_orders_List.size()>0){
ArrayList regimenList = (ArrayList) current_regimen_orders_List.get(0);
regimen_code = Integer.parseInt(regimenList.get(0).toString());

current_regimen = Context.getConceptService().getConcept(regimen_code).getName().getName();
}
if(current_regimen.isEmpty())
empty_fields += empty_fields+", current regimen";
empty_fields += ", current regimen";

List obs_dsdmList = administrationService.executeSQL(String.format(Latest_obs_of_Person,"value_coded", patientId,165143,date_activated),true);

Expand All @@ -146,29 +142,29 @@ public Map<String, String> generateVLProgramDataFHIRBody(TestOrder testOrder, St
int dsdm_code = Integer.parseInt(myList.get(0).toString());


if(dsdm_code==165138){
if(dsdm_code==165138){
dsdm = "FBIM";
dsdm_hie_code = "734163000_01";
}
else if (dsdm_code==165140) {
}
else if (dsdm_code==165140) {
dsdm = "FBG";
dsdm_hie_code = "734163000_02";
}
else if(dsdm_code==165139){
else if(dsdm_code==165139){
dsdm = "FTDR";
dsdm_hie_code = "734163000_03";
}
else if (dsdm_code==165142) {
else if (dsdm_code==165142) {
dsdm = "CDDP";
dsdm_hie_code = "734163000_04";
}
else if(dsdm_code==165141){
else if(dsdm_code==165141){
dsdm = "CCLAD";
dsdm_hie_code = "734163000_05";
}
}
if(dsdm_hie_code.isEmpty())
empty_fields += empty_fields+", dsdm";
dsdm_hie_code="734163000_01";

List obs_adherenceList = administrationService.executeSQL(String.format(Latest_obs_of_Person,"value_coded", patientId,90221,date_activated),true);
String adherence="";
Expand All @@ -189,9 +185,12 @@ else if(dsdm_code==165141){
}
}
if(adherence_hie_code.isEmpty())
empty_fields += empty_fields+", adherence";
empty_fields += ", adherence";

List current_regimen_start_date = administrationService.executeSQL(String.format("SELECT TIMESTAMPDIFF(MONTH, obs_datetime,'%s') from obs where person_id=%s and concept_id=90315 and voided=0 and value_coded = %s ORDER BY obs_datetime ASC LIMIT 1",date_activated.toString(),patientId,regimen_code),true);
List current_regimen_start_date_by_orders = administrationService.executeSQL(String.format("SELECT TIMESTAMPDIFF(MONTH, date_activated,'%s') from orders o INNER JOIN order_type ot ON o.order_type_id = ot.order_type_id\n" +
"\t INNER JOIN drug_order d_o ON o.order_id = d_o.order_id\n" +
"\t where ot.uuid='131168f4-15f5-102d-96e4-000c29c2a5d7' and patient_id= %s and o.voided=0 and o.concept_id = %s ORDER BY date_activated ASC LIMIT 1",date_activated.toString(),patientId,regimen_code),true);

String duration_string="";
String duration_string_hie_code="";
Expand All @@ -218,9 +217,32 @@ else if( duration < 6) {
duration_string="< 6months";
duration_string_hie_code = "261773006_01";
}
} else if (current_regimen_start_date_by_orders.size()>0) {
ArrayList myList = (ArrayList) current_regimen_start_date_by_orders.get(0);
int duration= Integer.parseInt(myList.get(0).toString());
if(duration >=60) {
duration_string=">5yrs";
duration_string_hie_code = "261773006_05";
}
else if(duration >=24 && duration < 60 ) {
duration_string="2 -< 5yrs";
duration_string_hie_code = "261773006_04";
}
else if(duration >=12 && duration < 24 ) {
duration_string="1 - 2yrs";
duration_string_hie_code = "261773006_03";
}
else if(duration >=6 && duration < 12) {
duration_string="6 months - < 1yr";
duration_string_hie_code = "261773006_02";
}
else if( duration < 6) {
duration_string="< 6months";
duration_string_hie_code = "261773006_01";
}
}
if(duration_string_hie_code.isEmpty())
empty_fields += empty_fields+", duration on art";
if (duration_string_hie_code.isEmpty())
empty_fields += ", duration on art";

List obs_pregnantList = administrationService.executeSQL(String.format(Latest_obs_of_Person,"value_coded", patientId,90041,date_activated),true);

Expand Down Expand Up @@ -264,39 +286,46 @@ else if( duration < 6) {
}

if(artStartDate==null)
empty_fields += empty_fields+", ART Start Date";
empty_fields += ", ART Start Date";

List obs_indication_for_VL = administrationService.executeSQL(String.format(Latest_obs_of_Person,"value_coded", patientId,168689,date_activated),true);

String vl_indication_hie_code ="";
int vl_indicator_code=0;
if(obs_indication_for_VL.size()>0) {
ArrayList myList = (ArrayList) obs_indication_for_VL.get(0);
int vl_indicator_code = Integer.parseInt(myList.get(0).toString());

if(vl_indicator_code==168683){ // 6 months after ART initiation
vl_indication_hie_code = "315124004_01";
}
else if (vl_indicator_code==168684) { //12 months after ART initiation
vl_indication_hie_code = "315124004_02";
}
else if(vl_indicator_code==168688){ //Routine
vl_indication_hie_code = "315124004_03";
}
else if (vl_indicator_code==168687) { //Repeat (after IAC)
vl_indication_hie_code = "315124004_04";
}
else if(vl_indicator_code==168685){ //Suspected treatment failure
vl_indication_hie_code = "315124004_05";
}
else if (vl_indicator_code==166508) { //1st ANC visit
vl_indication_hie_code = "315124004_06";
vl_indicator_code = Integer.parseInt(myList.get(0).toString());

vl_indication_hie_code = getVl_indication_hie_code(vl_indicator_code);
}
if(vl_indication_hie_code.isEmpty()){
// do manual fill of vl indication warning : this is a hack
List last_vl = administrationService.executeSQL(String.format(Latest_obs_of_Person,"DATE(value_datetime)", patientId,163023,date_activated),true);
if(pregnant){
vl_indicator_code= 166508;
}else if(artStartDate!=null && isSixToSevenMonthsAgo(artStartDate,date_activated)){
vl_indicator_code=168683;
}else if( artStartDate!=null &&isTwelveToThirteenMonthsAgo(artStartDate,date_activated)){
vl_indicator_code = 168684;
}else if(last_vl.size()>0){
ArrayList myList = (ArrayList) last_vl.get(0);
Date last_vl_date = Context.getService(UgandaEMRSyncService.class).convertStringToDate(myList.get(0).toString(),"","yyyy-MM-dd");

if(patient.getAge() <= 15 && last_vl_date!=null && isSixToSevenMonthsAgo(last_vl_date,date_activated)){
vl_indicator_code=168688 ;
}else if(patient.getAge() >15 && last_vl_date!=null && isTwelveToThirteenMonthsAgo(last_vl_date,date_activated)){
vl_indicator_code=168688 ;
}else{
vl_indicator_code=168688 ;
}
}else{
vl_indicator_code=168688 ;
}
else if(vl_indicator_code==168686){ //Special Considerations
vl_indication_hie_code = "315124004_07";
vl_indication_hie_code = getVl_indication_hie_code(vl_indicator_code);
if(vl_indication_hie_code.isEmpty()){
empty_fields += " Indication for viral load";
}
}
if(vl_indication_hie_code.isEmpty())
empty_fields += empty_fields+", indication for vl";

List obs_WHOList = administrationService.executeSQL(String.format(Latest_obs_of_Person,"value_coded", patientId,90203,date_activated),true);

Expand Down Expand Up @@ -354,7 +383,7 @@ else if(vl_indicator_code==168686){ //Special Considerations
}
}
if(who_hie_code.isEmpty())
empty_fields += empty_fields+", who code";
empty_fields += ", who code";

String regimenline = getRegimenLineOfPatient(patient);
String coded_regimen_line ="";
Expand All @@ -366,7 +395,7 @@ else if(vl_indicator_code==168686){ //Special Considerations
coded_regimen_line=thirdLineBody;
}
if(coded_regimen_line.isEmpty())
empty_fields += empty_fields+", regimen_line";
coded_regimen_line= firstLineBody;

jsonMap.put("empty_fields",empty_fields);
jsonMap.put("patient",patientARTNO);
Expand All @@ -377,6 +406,34 @@ else if(vl_indicator_code==168686){ //Special Considerations
return jsonMap;
}

private static String getVl_indication_hie_code(int vl_indicator_code) {

String vl_indication_hie_code ="";

if(vl_indicator_code ==168683){ // 6 months after ART initiation
vl_indication_hie_code = "315124004_01";
}
else if (vl_indicator_code ==168684) { //12 months after ART initiation
vl_indication_hie_code = "315124004_02";
}
else if(vl_indicator_code ==168688){ //Routine
vl_indication_hie_code = "315124004_03";
}
else if (vl_indicator_code ==168687) { //Repeat (after IAC)
vl_indication_hie_code = "315124004_04";
}
else if(vl_indicator_code ==168685){ //Suspected treatment failure
vl_indication_hie_code = "315124004_05";
}
else if (vl_indicator_code ==166508) { //1st ANC visit
vl_indication_hie_code = "315124004_06";
}
else if(vl_indicator_code ==168686){ //Special Considerations
vl_indication_hie_code = "315124004_07";
}
return vl_indication_hie_code;
}


public List<Order> getOrders() throws IOException, ParseException {
OrderService orderService = Context.getOrderService();
Expand Down Expand Up @@ -419,4 +476,39 @@ private String getRegimenLineOfPatient(Patient patient){
}


public boolean isSixToSevenMonthsAgo(Date date,Date dateActivated) {
// Convert Date to LocalDate
LocalDate inputDate = date.toInstant().atZone(ZoneId.systemDefault()).toLocalDate();

// Get current date
LocalDate activeDate = dateActivated.toInstant().atZone(ZoneId.systemDefault()).toLocalDate();

// Calculate the date 6 and 7 months ago
LocalDate sixMonthsAgo = activeDate.minusMonths(6);
LocalDate sevenMonthsAgo = activeDate.minusMonths(7);

// Check if the input date is between 6 and 7 months ago
return (inputDate.isBefore(sevenMonthsAgo) || inputDate.isEqual(sevenMonthsAgo)) &&
(inputDate.isAfter(sixMonthsAgo) || inputDate.isEqual(sixMonthsAgo));
}

public boolean isTwelveToThirteenMonthsAgo(Date date,Date dateActivated) {
LocalDate inputDate = date.toInstant().atZone(ZoneId.systemDefault()).toLocalDate();
LocalDate activeDate = dateActivated.toInstant().atZone(ZoneId.systemDefault()).toLocalDate();

LocalDate twelveMonthsAgo = activeDate.minusMonths(11);
LocalDate thirteenMonthsAgo = activeDate.minusMonths(13);

return (inputDate.isBefore(thirteenMonthsAgo) || inputDate.isEqual(thirteenMonthsAgo)) &&
(inputDate.isAfter(twelveMonthsAgo) || inputDate.isEqual(twelveMonthsAgo));
}

public boolean is12MonthsAfter(Date date,Date dateActivated) {
LocalDate inputDate = date.toInstant().atZone(ZoneId.systemDefault()).toLocalDate();
LocalDate activeDate = dateActivated.toInstant().atZone(ZoneId.systemDefault()).toLocalDate();

LocalDate thirteenMonthsAgo = activeDate.minusMonths(13);

return (inputDate.isAfter(thirteenMonthsAgo) );
}
}
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