Openmrs 2.6.x upgrade

api/src/main/java/org/openmrs/module/kenyaemr/advice/SyncHFEAppointmentsWithBahmniModule.java

@@ -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);
@@ -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);
+                }
             }
 
         }
@@ -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
@@ -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) {
@@ -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);

api/src/main/java/org/openmrs/module/kenyaemr/calculation/library/tb/NeedsTbSputumTestCalculation.java

@@ -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;
@@ -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);
@@ -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) {
@@ -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) {

api/src/main/java/org/openmrs/module/kenyaemr/reporting/builder/common/ActivePatientSnapshotReportBuilder.java

@@ -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;
@@ -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}");
@@ -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;

api/src/main/java/org/openmrs/module/kenyaemr/reporting/builder/hiv/CCCDefaulterTracingRegisterReportBuilder.java

@@ -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;
@@ -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));
@@ -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));