MEPTS-179 Routine fixes, base cohort and gender filter removal (#108)

* Fetch the entire list of the lactation map as oppossed to the last obs

* Include the equal boundaries to the second criteria for the routine

* Include equality bounds to the criteria 1 routine

* Including the Observations between the dates in the criteria 3 of routine

* Merged with the work done here Mepts 213 pregnant breast feeding queries

* Exclude 1 day from te six months boundary for criteria 1

* Attach bounadries to the viral load comapred to repoerting period and lower limit

* Adding 1 day to the lower boundaries of the viral load results and suppression

* Remove the boundaries on the 15 months date in criteria 2 routine

* Revert the removal of boundaries in the fifteen months criteria for routine

* We don't exclude restart treatment anymore

api/src/main/java/org/openmrs/module/eptsreports/reporting/calculation/pvls/BreastfeedingDateCalculation.java

@@ -66,7 +66,7 @@ public CalculationResultMap evaluate(
             cohort,
             Arrays.asList(location),
             Arrays.asList(yes),
-            TimeQualifier.LAST,
+            TimeQualifier.ANY,
             null,
             context);
 
@@ -129,7 +129,8 @@ private Date getResultantDate(
 
       ListResult patientResult = (ListResult) patientStateMap.get(pId);
 
-      Obs lactattingObs = EptsCalculationUtils.resultForPatient(lactatingMap, pId);
+      ListResult lactatingResults = (ListResult) lactatingMap.get(pId);
+      List<Obs> lactatingObs = EptsCalculationUtils.extractResultValues(lactatingResults);
       Obs criteriaHivObs = EptsCalculationUtils.resultForPatient(criteriaHivStartMap, pId);
       ListResult deliveryDateResult = (ListResult) deliveryDateMap.get(pId);
       List<Obs> deliveryDateObsList = EptsCalculationUtils.extractResultValues(deliveryDateResult);
@@ -138,7 +139,7 @@ private Date getResultantDate(
       // get a list of all eligible dates
       List<Date> allEligibleDates =
           Arrays.asList(
-              this.isLactating(lastVlDate, lactattingObs),
+              this.isLactating(lastVlDate, lactatingObs),
               this.hasHIVStartDate(lastVlDate, criteriaHivObs),
               this.hasDeliveryDate(lastVlDate, deliveryDateObsList),
               this.isInBreastFeedingInProgram(lastVlDate, patientStateList));
@@ -172,12 +173,14 @@ private Date hasDeliveryDate(Date lastVlDate, List<Obs> deliveryDateObsList) {
     return deliveryDate;
   }
 
-  private Date isLactating(Date lastVlDate, Obs lactantObs) {
+  private Date isLactating(Date lastVlDate, List<Obs> lactantObsList) {
     Date lactatingDate = null;
-    if (lactantObs != null
-        && this.isInBreastFeedingViralLoadRange(
-            lastVlDate, lactantObs.getEncounter().getEncounterDatetime())) {
-      lactatingDate = lactantObs.getEncounter().getEncounterDatetime();
+    for (Obs lactantObs : lactantObsList) {
+      if (lactantObs.getObsDatetime() != null
+          && this.isInBreastFeedingViralLoadRange(
+              lastVlDate, lactantObs.getEncounter().getEncounterDatetime())) {
+        lactatingDate = lactantObs.getEncounter().getEncounterDatetime();
+      }
     }
     return lactatingDate;
   }

api/src/main/java/org/openmrs/module/eptsreports/reporting/calculation/pvls/RoutineCalculation.java

@@ -34,6 +34,8 @@
 import org.openmrs.module.eptsreports.reporting.calculation.generic.InitialArtStartDateCalculation;
 import org.openmrs.module.eptsreports.reporting.utils.EptsCalculationUtils;
 import org.openmrs.module.eptsreports.reporting.utils.EptsReportConstants.PatientsOnRoutineEnum;
+import org.openmrs.module.reporting.common.DateUtil;
+import org.openmrs.module.reporting.common.DurationUnit;
 import org.openmrs.module.reporting.common.TimeQualifier;
 import org.springframework.stereotype.Component;
 
@@ -164,8 +166,8 @@ private boolean isOnRoutine(
         && lastVlObs.getObsDatetime() != null
         && criteria != null
         && onArtForMoreThan3Months.contains(pId)
-        && lastVlObs.getObsDatetime().after(latestVlLowerDateLimit)
-        && lastVlObs.getObsDatetime().before(onOrBefore)) {
+        && lastVlObs.getObsDatetime().compareTo(latestVlLowerDateLimit) >= 0
+        && lastVlObs.getObsDatetime().compareTo(onOrBefore) <= 0) {
 
       // get all the VL results for each patient from enrollment
       ListResult vlObsResultFromEndOfReportingPeriod =
@@ -268,8 +270,8 @@ private boolean isOnRoutineCriteria2(
           && allVls.getValueNumeric() != null
           && allVls.getValueNumeric() < 1000) {
         if (criteria.equals(PatientsOnRoutineEnum.ADULTCHILDREN)
-            && allVls.getObsDatetime().compareTo(twelveMonths) < 0
-            && allVls.getObsDatetime().compareTo(fifteenMonths) > 0) {
+            && allVls.getObsDatetime().compareTo(twelveMonths) <= 0
+            && allVls.getObsDatetime().compareTo(fifteenMonths) >= 0) {
           return true;
         } else if (criteria.equals(PatientsOnRoutineEnum.BREASTFEEDINGPREGNANT)
             && allVls.getObsDatetime().before(lastViralLoadDate)) {
@@ -292,15 +294,15 @@ private boolean isOnRoutineCriteria1(
       Date nineMonths = EptsCalculationUtils.addMonths(artInitiationDate, 9);
 
       boolean withinAdultLimits =
-          lastViralLoadDate.compareTo(sixMonths) > 0
+          lastViralLoadDate.compareTo(sixMonths) >= 0
               && lastViralLoadDate.compareTo(nineMonths) <= 0;
       boolean withinBreastfeedingLimits =
-          lastViralLoadDate.compareTo(threeMonths) > 0
+          lastViralLoadDate.compareTo(threeMonths) >= 0
               && lastViralLoadDate.compareTo(sixMonths) <= 0;
-
+      Date sixMonthsLess1Day = DateUtil.adjustDate(sixMonths, -1, DurationUnit.DAYS);
       if (criteria.equals(PatientsOnRoutineEnum.ADULTCHILDREN) && withinAdultLimits) {
         return !EptsCalculationUtils.anyObsBetween(
-            allViralLoadForPatient, artInitiationDate, sixMonths);
+            allViralLoadForPatient, artInitiationDate, sixMonthsLess1Day);
       } else if (criteria.equals(PatientsOnRoutineEnum.BREASTFEEDINGPREGNANT)
           && withinBreastfeedingLimits) {
         return !EptsCalculationUtils.anyObsBetween(
@@ -316,8 +318,8 @@ private List<Obs> getViralLoadForPatientTakenWithin12Months(
     // populate viralLoadForPatientTakenWithin12Months with obs which fall within the 12month window
     for (Obs obs : vLoadList) {
       if (obs != null
-          && obs.getObsDatetime().after(latestVlLowerDateLimit)
-          && obs.getObsDatetime().before(onOrBefore)) {
+          && obs.getObsDatetime().compareTo(latestVlLowerDateLimit) >= 0
+          && obs.getObsDatetime().compareTo(onOrBefore) <= 0) {
         viralLoadForPatientTakenWithin12Months.add(obs);
       }
     }

api/src/main/java/org/openmrs/module/eptsreports/reporting/library/cohorts/TxNewCohortQueries.java

@@ -157,7 +157,6 @@ public CohortDefinition getTxNewBreastfeedingComposition() {
         EptsReportUtils.map(
             getPatientsWhoGaveBirthWithinReportingPeriod(),
             "startDate=${onOrAfter},endDate=${onOrBefore},location=${location}"));
-    cd.addSearch("FEMININO", EptsReportUtils.map(genderCohorts.femaleCohort(), ""));
     cd.addSearch(
         "LACTANTE",
         EptsReportUtils.map(
@@ -169,8 +168,7 @@ public CohortDefinition getTxNewBreastfeedingComposition() {
                 Arrays.asList(commonMetadata.getYesConcept())),
             "onOrAfter=${onOrAfter},onOrBefore=${onOrBefore},locationList=${location}"));
 
-    String compositionString =
-        "(DATAPARTO OR INICIOLACTANTE OR LACTANTEPROGRAMA OR LACTANTE) AND FEMININO";
+    String compositionString = "(DATAPARTO OR INICIOLACTANTE OR LACTANTEPROGRAMA OR LACTANTE)";
 
     cd.setCompositionString(compositionString);
     return cd;
@@ -197,16 +195,11 @@ public CohortDefinition getTxNewCompositionCohort(String cohortName) {
         Mapped.map(
             hivCohortQueries.getPatientsTransferredFromOtherHealthFacility(),
             "onOrAfter=${onOrAfter},onOrBefore=${onOrBefore},location=${location}");
-    Mapped<CohortDefinition> restartedTreatment =
-        Mapped.map(
-            hivCohortQueries.getPatientsWhoRestartedTreatment(),
-            "onOrAfter=${onOrAfter},onOrBefore=${onOrBefore},locationList=${location}");
 
     txNewComposition.getSearches().put("startedART", startedART);
     txNewComposition.getSearches().put("transferredIn", transferredIn);
-    txNewComposition.getSearches().put("restartedTreatment", restartedTreatment);
 
-    txNewComposition.setCompositionString("startedART NOT (transferredIn OR restartedTreatment)");
+    txNewComposition.setCompositionString("startedART NOT transferredIn");
     return txNewComposition;
   }
 }

api/src/main/java/org/openmrs/module/eptsreports/reporting/library/queries/PregnantQueries.java

@@ -37,7 +37,7 @@ public static String getPregnantWhileOnArt(
         + adultInitailEncounter
         + ","
         + adultSegEncounter
-        + ") and e.encounter_datetime between :startDate and :endDate and e.location_id=:location and pe.gender='F'"
+        + ") and e.encounter_datetime between :startDate and :endDate and e.location_id=:location "
         + " union"
         + " Select p.patient_id"
         + " from patient p"
@@ -51,7 +51,7 @@ public static String getPregnantWhileOnArt(
         + adultInitailEncounter
         + ","
         + adultSegEncounter
-        + ") and e.encounter_datetime between :startDate and :endDate and e.location_id=:location and pe.gender='F' "
+        + ") and e.encounter_datetime between :startDate and :endDate and e.location_id=:location "
         + " union"
         + " Select p.patient_id"
         + " from patient p"
@@ -65,12 +65,12 @@ public static String getPregnantWhileOnArt(
         + adultInitailEncounter
         + ","
         + adultSegEncounter
-        + ") and e.encounter_datetime between :startDate and :endDate and e.location_id=:location and pe.gender='F'"
+        + ") and e.encounter_datetime between :startDate and :endDate and e.location_id=:location "
         + " union"
         + " select pp.patient_id from patient_program pp"
         + " inner join person pe on pp.patient_id=pe.person_id"
         + " where pp.program_id="
         + etvProgram
-        + " and pp.voided=0 and pp.date_enrolled between :startDate and :endDate and pp.location_id=:location and pe.gender='F'";
+        + " and pp.voided=0 and pp.date_enrolled between :startDate and :endDate and pp.location_id=:location ";
   }
 }

api/src/main/java/org/openmrs/module/eptsreports/reporting/library/queries/ViralLoadQueries.java

@@ -38,7 +38,7 @@ public static String getPatientsWithViralLoadSuppression(
         + " AND  o.concept_id="
         + vlConceptQuestion
         + " AND o.value_numeric IS NOT NULL AND"
-        + " e.encounter_datetime BETWEEN date_add(:endDate, interval -12 MONTH) and :endDate AND"
+        + " e.encounter_datetime BETWEEN date_add(date_add(:endDate, interval -12 MONTH), interval 1 day) AND :endDate AND"
         + " e.location_id=:location GROUP BY p.patient_id"
         + ") ultima_carga"
         + " INNER JOIN obs ON obs.person_id=ultima_carga.patient_id AND obs.obs_datetime="
@@ -69,7 +69,7 @@ public static String getPatientsHavingViralLoadInLast12Months(
         + ") AND o.concept_id="
         + vlConceptQuestion
         + " AND o.value_numeric IS NOT NULL AND"
-        + " e.encounter_datetime BETWEEN date_add(:endDate, interval -12 MONTH) AND :endDate AND"
+        + " e.encounter_datetime BETWEEN date_add(date_add(:endDate, interval -12 MONTH), interval 1 day) AND :endDate AND"
         + " e.location_id=:location";
   }
 }

api/src/main/java/org/openmrs/module/eptsreports/reporting/utils/EptsCalculationUtils.java

@@ -385,8 +385,8 @@ public static boolean dateBetween(Date startDate, Date endDate, Date dateInQuest
   public static boolean anyObsBetween(List<Obs> vlObsList, Date startDate, Date endDate) {
     for (Obs obs : vlObsList) {
       if (obs.getObsDatetime() != null
-          && obs.getObsDatetime().after(startDate)
-          && obs.getObsDatetime().before(endDate)) {
+          && obs.getObsDatetime().compareTo(startDate) >= 0
+          && obs.getObsDatetime().compareTo(endDate) <= 0) {
         return true;
       }
     }