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Merge pull request #1682 from jecihjoy/openmrs-2.6.x-upgrade
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Openmrs 2.6.x upgrade
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@makombe
makombe authored Oct 3, 2023
2 parents 12a8f68 + 47a7cc5 commit 1d3bee0
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Showing 37 changed files with 2,572 additions and 517 deletions.
19 changes: 10 additions & 9 deletions ...src/main/java/org/openmrs/module/kenyaemr/advice/SyncHFEAppointmentsWithBahmniModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -221,7 +221,6 @@ private void processEditHivFollowupEncounter(Encounter enc) throws Throwable {
appointmentServiceDefinition.setAppointmentServiceId(appointmentServiceDefinitionService.getAppointmentServiceByUuid(DRUG_REFILL_SERVICE).getId());

Appointment editedFollowUpAppointment = appointmentsService.getAppointmentByUuid(enc.getUuid());

Appointment refillAppointment = new Appointment();
Date refillStartDateTime = DateUtil.convertToDate(dateFormat.format(o.getValueDatetime()).concat("T07:00:00.0Z"), DateUtil.DateFormatType.UTC);
Date refillEndDateTime = DateUtil.convertToDate(dateFormat.format(o.getValueDatetime()).concat("T20:00:00.0Z"), DateUtil.DateFormatType.UTC);
Expand All @@ -234,10 +233,11 @@ private void processEditHivFollowupEncounter(Encounter enc) throws Throwable {
refillAppointment.setProvider(EmrUtils.getProvider(Context.getAuthenticatedUser()));
refillAppointment.setAppointmentKind(AppointmentKind.Scheduled);
Appointment app = appointmentsService.validateAndSave(refillAppointment);

editedFollowUpAppointment.setRelatedAppointment(app);
Appointment app2 = appointmentsService.validateAndSave(editedFollowUpAppointment);


if (editedFollowUpAppointment != null) {
editedFollowUpAppointment.setRelatedAppointment(app);
Appointment app2 = appointmentsService.validateAndSave(editedFollowUpAppointment);
}
}

}
Expand Down Expand Up @@ -277,7 +277,7 @@ private void processCreateHivFollowupEncounter(Encounter enc) throws Throwable {
refillApptDate = o.getValueDatetime();
}

if(appointmentReason != null && appointmentReason == 160523 || appointmentReason != null && appointmentReason == 160521 ) {
if((appointmentReason != null && appointmentReason == 160523) || (appointmentReason != null && appointmentReason == 160521) ) {
AppointmentServiceDefinition appointmentServiceDefinition = new AppointmentServiceDefinition();

// create HIV followup appointment
Expand Down Expand Up @@ -316,8 +316,10 @@ private void processCreateHivFollowupEncounter(Encounter enc) throws Throwable {
refillAppointment.setAppointmentKind(AppointmentKind.Scheduled);
Appointment app = appointmentsService.validateAndSave(refillAppointment);

currentFollowUpAppointment.setRelatedAppointment(app);
Appointment app2 = appointmentsService.validateAndSave(currentFollowUpAppointment);
if (currentFollowUpAppointment != null ) {
currentFollowUpAppointment.setRelatedAppointment(app);
Appointment app2 = appointmentsService.validateAndSave(currentFollowUpAppointment);
}
}

} else if ( appointmentReason != null && appointmentReason == 1283) {
Expand Down Expand Up @@ -369,7 +371,6 @@ private void processProgramEncounter(Encounter enc) throws Throwable {

if(editAppointment != null) {
//edit MCH or PREP or TB or KP appointment

Date nextApptStartDateTime = DateUtil.convertToDate(dateFormat.format(o.getValueDatetime()).concat("T07:00:00.0Z"), DateUtil.DateFormatType.UTC);
Date nextApptEndDateTime = DateUtil.convertToDate(dateFormat.format(o.getValueDatetime()).concat("T20:00:00.0Z"), DateUtil.DateFormatType.UTC);
editAppointment.setStartDateTime(nextApptStartDateTime);
Expand Down
279 changes: 279 additions & 0 deletions ...nmrs/module/kenyaemr/calculation/library/hiv/LastestVLTakenWithinIntervalCalculation.java
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10 changes: 8 additions & 2 deletions ...java/org/openmrs/module/kenyaemr/calculation/library/tb/NeedsTbSputumTestCalculation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@
import org.openmrs.Concept;
import org.openmrs.Obs;
import org.openmrs.Program;
import org.openmrs.api.ConceptService;
import org.openmrs.api.context.Context;
import org.openmrs.calculation.patient.PatientCalculationContext;
import org.openmrs.calculation.result.CalculationResultMap;
import org.openmrs.module.kenyacore.calculation.AbstractPatientCalculation;
Expand Down Expand Up @@ -60,13 +62,15 @@ public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Obj
// Get all patients who are alive and in TB program
Set<Integer> alive = Filters.alive(cohort, context);
Set<Integer> inTbProgram = Filters.inProgram(tbProgram, alive, context);
ConceptService cs = Context.getConceptService();

// Get concepts
Concept tbsuspect = Dictionary.getConcept(Dictionary.DISEASE_SUSPECTED);
Concept pulmonaryTb = Dictionary.getConcept(Dictionary.PULMONARY_TB);
Concept smearPositive = Dictionary.getConcept(Dictionary.POSITIVE);
Concept NEGATIVE = Dictionary.getConcept(Dictionary.NEGATIVE);
Concept SPUTUM_FOR_ACID_FAST_BACILLI = Dictionary.getConcept(Dictionary.SPUTUM_FOR_ACID_FAST_BACILLI);
Concept geneXpertConcept = cs.getConcept(162202);

// check if there is any observation recorded per the tuberculosis disease status
CalculationResultMap lastObsTbDiseaseStatus = Calculations.lastObs(Dictionary.getConcept(Dictionary.TUBERCULOSIS_DISEASE_STATUS), cohort, context);
Expand All @@ -81,6 +85,7 @@ public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Obj

// get the date when Tb treatment was started, the patient should be in tb program to have this date
CalculationResultMap tbStartTreatmentDate = Calculations.lastObs(Dictionary.getConcept(Dictionary.TUBERCULOSIS_DRUG_TREATMENT_START_DATE), cohort, context);
CalculationResultMap lastGeneXpertConcept = Calculations.lastObs(geneXpertConcept, alive, context);

CalculationResultMap ret = new CalculationResultMap();
for (Integer ptId : cohort) {
Expand All @@ -91,10 +96,11 @@ public CalculationResultMap evaluate(Collection<Integer> cohort, Map<String, Obj
Date treatmentStartDate = EmrCalculationUtils.datetimeObsResultForPatient(tbStartTreatmentDate, ptId);
Obs lastObsTbDiseaseResults = EmrCalculationUtils.obsResultForPatient(lastObsTbDiseaseStatus, ptId);
Obs lastSputumResultsObs = EmrCalculationUtils.obsResultForPatient(lastSputumResults, ptId);

Obs lastGeneXpertObs = EmrCalculationUtils.obsResultForPatient(lastGeneXpertConcept, ptId);
//
// check if a patient is alive
if (alive.contains(ptId)) {
if ((lastObsTbDiseaseResults != null) && (lastObsTbDiseaseResults.getValueCoded().equals(tbsuspect)) && lastSputumResultsObs == null && !(inTbProgram.contains(ptId))) {
if ((lastObsTbDiseaseResults != null) && (lastObsTbDiseaseResults.getValueCoded().equals(tbsuspect)) && lastSputumResultsObs == null && !(inTbProgram.contains(ptId)) && lastGeneXpertObs ==null) {
needsSputum = true;
}
else if(inTbProgram.contains(ptId) && diseaseClassification != null && tbResults != null && (diseaseClassification.getValueCoded().equals(pulmonaryTb)) && (tbResults.getValueCoded().equals(smearPositive)) && treatmentStartDate != null) {
Expand Down
10 changes: 10 additions & 0 deletions .../openmrs/module/kenyaemr/reporting/builder/common/ActivePatientSnapshotReportBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,8 @@
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.ETLRefillDateDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.ETLStabilityDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.HeightAtArtDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.MedicalCoverDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.MedicalCoverStatusDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.NCDDateDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.NCDStatusDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.NCDsDataDefinition;
Expand Down Expand Up @@ -187,6 +189,12 @@ protected PatientDataSetDefinition activePatientsDataSetDefinition(String datase
BloodPressureDataDefinition bloodPressureDataDefinition = new BloodPressureDataDefinition();
bloodPressureDataDefinition.addParameter(new Parameter("endDate", "End Date", Date.class));
bloodPressureDataDefinition.addParameter(new Parameter("startDate", "Start Date", Date.class));
MedicalCoverDataDefinition medicalCoverDataDefinition = new MedicalCoverDataDefinition();
medicalCoverDataDefinition.addParameter(new Parameter("endDate", "End Date", Date.class));
medicalCoverDataDefinition.addParameter(new Parameter("startDate", "Start Date", Date.class));
MedicalCoverStatusDataDefinition medicalCoverStatusDataDefinition = new MedicalCoverStatusDataDefinition();
medicalCoverStatusDataDefinition.addParameter(new Parameter("endDate", "End Date", Date.class));
medicalCoverStatusDataDefinition.addParameter(new Parameter("startDate", "Start Date", Date.class));


DataConverter formatter = new ObjectFormatter("{familyName}, {givenName}");
Expand Down Expand Up @@ -238,6 +246,8 @@ protected PatientDataSetDefinition activePatientsDataSetDefinition(String datase
dsd.addColumn("NCDs Onset Date", ncdDateDataDefinition, "endDate=${endDate}");
dsd.addColumn("NCDs status", ncdStatusDataDefinition, "endDate=${endDate}");
dsd.addColumn("AHD Client", new CalculationDataDefinition("AHD Client", new PatientsWithAdvancedHivDiseaseCalculation()), "", new BooleanResultsConverter());
dsd.addColumn("Medical cover", medicalCoverDataDefinition, "endDate=${endDate}");
dsd.addColumn("Medical cover status", medicalCoverStatusDataDefinition, "endDate=${endDate}");


return dsd;
Expand Down
33 changes: 20 additions & 13 deletions ...enmrs/module/kenyaemr/reporting/builder/hiv/CCCDefaulterTracingRegisterReportBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,16 +23,9 @@
import org.openmrs.module.kenyaemr.reporting.calculation.converter.RDQACalculationResultConverter;
import org.openmrs.module.kenyaemr.reporting.cohort.definition.CCCDefaulterTracingRegisterCohortDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.MissedAppointmentReasonsConverter;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.HIVTestOneDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.ETLLastVisitDateDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.art.ETLNextAppointmentDateDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.defaulterTracing.FinalOutcomeDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.defaulterTracing.ProviderCommentsDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.defaulterTracing.ReasonForMissedAppointmentDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.defaulterTracing.ReturnToCareDateDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.defaulterTracing.HonouredAppointmentDateDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.defaulterTracing.TracingNumberDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.defaulterTracing.TracingOutcomeDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.defaulterTracing.TracingTypeDataDefinition;
import org.openmrs.module.kenyaemr.reporting.data.converter.definition.defaulterTracing.*;
import org.openmrs.module.metadatadeploy.MetadataUtils;
import org.openmrs.module.reporting.common.SortCriteria;
import org.openmrs.module.reporting.data.DataDefinition;
Expand Down Expand Up @@ -105,6 +98,21 @@ protected DataSetDefinition datasetColumns() {
providerDataDefinition.setSingleProvider(true);
PersonAttributeType phoneNumber = MetadataUtils.existing(PersonAttributeType.class, CommonMetadata._PersonAttributeType.TELEPHONE_CONTACT);

String dateParams = "startDate=${startDate},endDate=${endDate}";

DateMissedAppointmentBeforeTracingDataDefinition dateMissedAppointment = new DateMissedAppointmentBeforeTracingDataDefinition();
dateMissedAppointment.addParameter(new Parameter("startDate", "Start Date", Date.class));
dateMissedAppointment.addParameter(new Parameter("endDate", "End Date", Date.class));

HonouredAppointmentDateDataDefinition dateHonouredAppointment = new HonouredAppointmentDateDataDefinition();
dateHonouredAppointment.addParameter(new Parameter("startDate", "Start Date", Date.class));
dateHonouredAppointment.addParameter(new Parameter("endDate", "End Date", Date.class));

LastVisitDateBeforeMissedAppointmentDataDefinition lastVisitBeforeMissedApp = new LastVisitDateBeforeMissedAppointmentDataDefinition();
lastVisitBeforeMissedApp.addParameter(new Parameter("startDate", "Start Date", Date.class));
lastVisitBeforeMissedApp.addParameter(new Parameter("endDate", "End Date", Date.class));


dsd.addColumn("Name", nameDef, "");
dsd.addColumn("id", new PatientIdDataDefinition(), "");
dsd.addColumn("Date of Birth", new BirthdateDataDefinition(), "", new BirthdateConverter(DATE_FORMAT));
Expand All @@ -118,16 +126,15 @@ protected DataSetDefinition datasetColumns() {
dsd.addColumn("Outcome", new TracingOutcomeDataDefinition(),"");
dsd.addColumn("Tracing attempt No", new TracingNumberDataDefinition(),"");
dsd.addColumn("Final Outcome", new FinalOutcomeDataDefinition(),"");
dsd.addColumn("Last Visit Date", new ETLLastVisitDateDataDefinition(),"", new DateConverter(DATE_FORMAT));
dsd.addColumn("Last Appointment Date", new ETLNextAppointmentDateDataDefinition(), "", new DateConverter(DATE_FORMAT));
dsd.addColumn("Last Visit Date", lastVisitBeforeMissedApp,dateParams, new DateConverter(DATE_FORMAT));
dsd.addColumn("Last Appointment Date", dateMissedAppointment, dateParams, new DateConverter(DATE_FORMAT));
dsd.addColumn("Reason for missed appointment", new ReasonForMissedAppointmentDataDefinition(),"", new MissedAppointmentReasonsConverter());
dsd.addColumn("Date promised to come", new ReturnToCareDateDataDefinition(),"", new DateConverter(DATE_FORMAT));
dsd.addColumn("Honoured appointment date", new HonouredAppointmentDateDataDefinition(),"", new DateConverter(DATE_FORMAT));
dsd.addColumn("Honoured appointment date", dateHonouredAppointment,dateParams, new DateConverter(DATE_FORMAT));
dsd.addColumn("Comments", new ProviderCommentsDataDefinition(),"");
dsd.addColumn("Provider", providerDataDefinition,"", new EncounterProviderConverter());



CCCDefaulterTracingRegisterCohortDefinition cd = new CCCDefaulterTracingRegisterCohortDefinition();
cd.addParameter(new Parameter("startDate", "Start Date", Date.class));
cd.addParameter(new Parameter("endDate", "End Date", Date.class));
Expand Down
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