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Merge pull request #2031 from makombe/due-for-pre-art-vl
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KHP3-6851:Due for Pre-ART viral load test flag
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@makombe
makombe authored Oct 30, 2024
2 parents a4bbb50 + 121f80a commit 49411bc
Showing 1 changed file with 148 additions and 1 deletion.
149 changes: 148 additions & 1 deletion ...va/org/openmrs/module/kenyaemr/calculation/library/hiv/NeedsViralLoadTestCalculation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,18 @@

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.joda.time.DateTime;
import org.joda.time.Days;
import org.openmrs.Concept;
import org.openmrs.Encounter;
import org.openmrs.EncounterType;
import org.openmrs.Form;
import org.openmrs.Obs;
import org.openmrs.Order;
import org.openmrs.Patient;
import org.openmrs.Program;
import org.openmrs.api.ConceptService;
import org.openmrs.api.OrderService;
import org.openmrs.api.PatientService;
import org.openmrs.api.context.Context;
import org.openmrs.calculation.patient.PatientCalculationContext;
Expand All @@ -28,11 +36,23 @@
import org.openmrs.module.kenyaemr.calculation.library.hiv.art.LastViralLoadResultCalculation;
import org.openmrs.module.kenyaemr.calculation.library.hiv.art.OnArtCalculation;
import org.openmrs.module.kenyaemr.metadata.HivMetadata;
import org.openmrs.module.kenyaemr.metadata.MchMetadata;
import org.openmrs.module.kenyaemr.util.EmrUtils;
import org.openmrs.module.kenyaemr.util.HtsConstants;
import org.openmrs.module.metadatadeploy.MetadataUtils;
import org.openmrs.parameter.OrderSearchCriteria;
import org.openmrs.ui.framework.SimpleObject;

import liquibase.pro.packaged.b;
import liquibase.pro.packaged.bo;
import liquibase.pro.packaged.d;
import liquibase.pro.packaged.e;

import java.util.Arrays;
import java.util.Calendar;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Set;

Expand All @@ -41,6 +61,14 @@

public class NeedsViralLoadTestCalculation extends AbstractPatientCalculation implements PatientFlagCalculation {
protected static final Log log = LogFactory.getLog(StablePatientsCalculation.class);
String flagMessage = null;
public static final Integer HTS_PMTCT_ANC_ENTRY_POINT_CONCEPT_ID = 160538;
public static final Integer HTS_PMTCT_MAT_ENTRY_POINT_CONCEPT_ID = 160456;
public static final Integer HTS_PMTCT_PNC_ENTRY_POINT_CONCEPT_ID = 1623;
public static final Integer HTSENTRYPOINT_QUESTION_CONCEPT_ID = 160540;




/**
* Needs vl test calculation criteria: New EMR guidelines March 2023
Expand All @@ -54,13 +82,21 @@ public class NeedsViralLoadTestCalculation extends AbstractPatientCalculation im
*/
@Override
public String getFlagMessage() {
return "Due for Viral Load";
return flagMessage;
}

@Override
public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Object> parameterValues, PatientCalculationContext context) {
Program hivProgram = MetadataUtils.existing(Program.class, HivMetadata._Program.HIV);
PatientService patientService = Context.getPatientService();
ConceptService cs = Context.getConceptService();
OrderService orderService = Context.getOrderService();
EncounterType mchEncType = MetadataUtils.existing(EncounterType.class, MchMetadata._EncounterType.MCHCS_CONSULTATION);
Form mchAncForm = MetadataUtils.existing(Form.class, MchMetadata._Form.MCHMS_ANTENATAL_VISIT);
Form mchDeliveryForm = MetadataUtils.existing(Form.class, MchMetadata._Form.MCHMS_DELIVERY);
Form mchPostnatalForm = MetadataUtils.existing(Form.class, MchMetadata._Form.MCHMS_POSTNATAL_VISIT);



Set<Integer> alive = Filters.alive(cohort, context);
Set<Integer> inHivProgram = Filters.inProgram(hivProgram, alive, context);
Expand Down Expand Up @@ -98,6 +134,7 @@ public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Obj
Date artStartDate = EmrCalculationUtils.datetimeResultForPatient(dateInitiatedART, ptId);
Date lastPregStartDate = EmrCalculationUtils.datetimeResultForPatient(pregnancyStartDate, ptId);
Date lastBFStartDate = EmrCalculationUtils.datetimeResultForPatient(breastFeedingStarDate, ptId);


//Check for latest vl and if it exists (vl is only valid if its for the last 12 months)
CalculationResult lastvlresult = lastVlResults.get(ptId);
Expand Down Expand Up @@ -129,10 +166,12 @@ public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Obj
|| (obsPregStatusDate != null && lastVLResultDate != null && obsPregStatusDate.after(lastVLResultDate)) || (obsBFStatusDate != null && lastVLResultDate != null && obsBFStatusDate.after(lastVLResultDate)))) {

needsViralLoadTest = true;
flagMessage = "Due for Viral Load";
}
//After 3 months: All with unsuppressed VL (>200 cps/ml)
else if (lastVlResultValue != null && lastVLResultDate != null && daysSince(lastVLResultDate, context) >= 92 && lastVlResultValue > 200) {
needsViralLoadTest = true;
flagMessage = "Due for Viral Load";
}
//After 3 Months: New positives with no previous VL
else if (artStartDate != null && daysSince(artStartDate, context) >= 92 && lastVLResultDate == null) {
Expand All @@ -144,14 +183,122 @@ else if (artStartDate != null && daysSince(artStartDate, context) >= 92 && lastV
else if (((lastPregStartDate != null && lastVLResultDate != null && lastPregStartDate.before(lastVLResultDate)) || (lastBFStartDate != null && lastVLResultDate != null && lastBFStartDate.before(lastVLResultDate)) || (obsPregStatusDate != null && lastVLResultDate != null && obsPregStatusDate.before(lastVLResultDate)) || (obsBFStatusDate != null && lastVLResultDate != null && obsBFStatusDate.before(lastVLResultDate))
|| patient.getAge() <= 24) && (lastVLResultDate != null && daysSince(lastVLResultDate, context) >= 183 && (lastVlResultLDL != null || (lastVlResultValue != null && lastVlResultValue < 200)))) {
needsViralLoadTest = true;
flagMessage = "Due for Viral Load";
}
//After 12 Months: > 25 years old with suppressed VL or LDL
else if (lastVLResultDate != null && daysSince(lastVLResultDate, context) >= 365 && patient.getAge() >= 25) {
needsViralLoadTest = true;
flagMessage = "Due for Viral Load";
}


ret.put(ptId, new BooleanResult(needsViralLoadTest, this));
}

/*Due for Pre-ART viral load test flag
* Criteria: In MCH program, Not on art and no previous vl test/Results,confirmed positive while in MCH
*
*
*/
if(activeInMCH.contains(ptId)) {
Encounter lastHtsInitialEnc = EmrUtils.lastEncounter(patient, HtsConstants.htsEncType, HtsConstants.htsInitialForm);
Encounter lastHtsRetestEnc = EmrUtils.lastEncounter(patient, HtsConstants.htsEncType, HtsConstants.htsRetestForm);
Encounter lastAncEnc = EmrUtils.lastEncounter(patient, mchEncType, mchAncForm);
Encounter lastMchDeliveryEnc = EmrUtils.lastEncounter(patient, mchEncType, mchDeliveryForm);
Encounter lastMchPostnatalEnc = EmrUtils.lastEncounter(patient, mchEncType, mchPostnatalForm);
Concept htsFinalTestQuestion = cs.getConcept(HtsConstants.HTS_FINAL_TEST_CONCEPT_ID);
Concept htsPositiveResult = cs.getConcept(HtsConstants.HTS_POSITIVE_RESULT_CONCEPT_ID);
Concept htsEntryPointQuestion = cs.getConcept(HTSENTRYPOINT_QUESTION_CONCEPT_ID);
Concept htsPmtctAncEntryPoint = cs.getConcept(HTS_PMTCT_ANC_ENTRY_POINT_CONCEPT_ID);
Concept htsPmtctMatEntryPoint = cs.getConcept(HTS_PMTCT_MAT_ENTRY_POINT_CONCEPT_ID);
Concept htsPmtctPncEntryPoint = cs.getConcept(HTS_PMTCT_PNC_ENTRY_POINT_CONCEPT_ID);
Concept dateOfDelivery = cs.getConcept(Dictionary.DATE_OF_CONFINEMENT); //Though named date of confinement, same concept used for delivery date
Encounter lastHtsEnc = null;
Date dateOfDeliveryValue = null;
Date dateTestedPositiveAtHts = null;
List<Concept> vlOrderConcepts = Arrays.asList(cs.getConceptByUuid(Dictionary.HIV_VIRAL_LOAD), cs.getConceptByUuid(Dictionary.HIV_VIRAL_LOAD_QUALITATIVE));
OrderSearchCriteria OrderSearchCriteria = new OrderSearchCriteria( patient, null, vlOrderConcepts, null, null, null,
null, null, false, null, null, null, null, true, true, false, false);
List<Order> vlOrders = orderService.getOrders(OrderSearchCriteria);

if (lastHtsInitialEnc != null && lastHtsRetestEnc == null) {
lastHtsEnc = lastHtsInitialEnc;
} else if (lastHtsInitialEnc == null && lastHtsRetestEnc != null) {
lastHtsEnc = lastHtsRetestEnc;
} else if (lastHtsInitialEnc != null && lastHtsRetestEnc != null) {
if (lastHtsInitialEnc.getEncounterDatetime().after(lastHtsRetestEnc.getEncounterDatetime())) {
lastHtsEnc = lastHtsInitialEnc;
} else {
lastHtsEnc = lastHtsRetestEnc;
}
}
boolean isConfirmedPositiveAtAnc = lastAncEnc != null ? EmrUtils.encounterThatPassCodedAnswer(lastAncEnc, htsFinalTestQuestion, htsPositiveResult) : false;
boolean isConfirmedPositiveAtPostnatal = lastMchPostnatalEnc != null ? EmrUtils.encounterThatPassCodedAnswer(lastMchPostnatalEnc, htsFinalTestQuestion, htsPositiveResult) : false;
boolean isConfirmedPositiveAtDelivery = lastMchDeliveryEnc != null ? EmrUtils.encounterThatPassCodedAnswer(lastMchDeliveryEnc, htsFinalTestQuestion, htsPositiveResult) : false;
boolean testedPositiveWithin24MonthsInPostnatal = false;

if(lastMchPostnatalEnc != null) {

Date dateTestedPositivePnc = null;
for (Obs obs : lastMchPostnatalEnc.getObs()) {
if(obs.getConcept().equals(dateOfDelivery)) {
dateOfDeliveryValue = obs.getValueDate();
} else if(obs.getConcept().equals(htsFinalTestQuestion) && obs.getValueCoded().equals(htsPositiveResult)) {
dateTestedPositivePnc = obs.getObsDatetime();
}
}
if(dateOfDeliveryValue != null && dateTestedPositivePnc != null) {
testedPositiveWithin24MonthsInPostnatal = testedPositiveWithin24MonthsInPnc(dateOfDeliveryValue, dateTestedPositivePnc);
}
}

if ( vlOrders.size() == 0 && artStartDate == null &&
(isConfirmedPositiveAtAnc || (isConfirmedPositiveAtPostnatal && testedPositiveWithin24MonthsInPostnatal) || isConfirmedPositiveAtDelivery)) {
needsViralLoadTest = true;
flagMessage = "Due for Pre-ART Viral Load";
}

if(lastHtsEnc != null) {
boolean isPositiveTestResult = lastHtsEnc != null ? EmrUtils.encounterThatPassCodedAnswer(lastHtsEnc, htsFinalTestQuestion, htsPositiveResult) : false;
if(isPositiveTestResult) {
dateTestedPositiveAtHts = lastHtsEnc.getEncounterDatetime();
}
if(isPositiveTestResult && vlOrders.size() == 0 && artStartDate == null) {
for (Obs obs : lastHtsEnc.getObs()) {
if(obs.getConcept().equals(htsEntryPointQuestion) && (obs.getValueCoded().equals(htsPmtctAncEntryPoint) ||
obs.getValueCoded().equals(htsPmtctMatEntryPoint))) {
needsViralLoadTest = true;
flagMessage = "Due for Pre-ART Viral Load";
}
}
}
}
// check if confirmed positive using hts form and still within 24 months at postnatal
if(dateTestedPositiveAtHts != null && dateOfDeliveryValue != null && dateTestedPositiveAtHts.after(dateOfDeliveryValue) && vlOrders.size() == 0 && artStartDate == null) {
testedPositiveWithin24MonthsInPostnatal = testedPositiveWithin24MonthsInPnc(dateOfDeliveryValue, dateTestedPositiveAtHts);
if(testedPositiveWithin24MonthsInPostnatal) {
needsViralLoadTest = true;
flagMessage = "Due for Pre-ART Viral Load";
}
}

ret.put(ptId, new BooleanResult(needsViralLoadTest, this));
}
}
return ret;
}
private boolean testedPositiveWithin24MonthsInPnc(Date deliveryDate ,Date dateTestedPositive) {
boolean isTestedPositiveWithin24Months = false;
Calendar startCalendar = Calendar.getInstance();
startCalendar.setTime(deliveryDate);
Calendar endCalendar = Calendar.getInstance();
endCalendar.setTime(dateTestedPositive);
int yearDiff = endCalendar.get(Calendar.YEAR) - startCalendar.get(Calendar.YEAR);
int monthDiff = yearDiff * 12 + endCalendar.get(Calendar.MONTH) - startCalendar.get(Calendar.MONTH);

if (monthDiff <= 24) {
isTestedPositiveWithin24Months = true;
}
return isTestedPositiveWithin24Months;
}
}

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