Mepts 263 (#125)

* E1: Number of active patients in ART at the end of current month who performed Viral Load Test (Annual Notification)

* Added the functionality to exclude the patients who had a VL with the year of reporting for E1

* Adding a generic way to easly pull the common indicators of E1 E2 and E3

* Initial work for the E2 indicators

* Add the E2 indicator and it required definitions

* Adding E3 indicators and its definitions

* Added the F1 indicator

* Added F2 indicator definitions

* Initial work on the F3 indicators

* Finish work on the section F of the report

* Proper mapping of end date so that it can be picked in a claculation

* Fix the exclusion criteria so that those outside should be included in our indicators

* Replacing the for each loop to iterators

* Proper calulation of the date required as start date

* Change from using reporting ORM to native sql

* Proper parameter mappings and proper nagations

* Preparing to start converting ExcludeCriteriaForEandFCalculation into sql equivalent

* Initial work on the exclusion for E1

* Complete change of the calculation for exclusion criteria for E and F done

* Replacing java code for the start date exclution criteria with sql

* General code clean up

* MEPTS-263: updated comment blocks for E-F sections in master card resumo report to match indicator names in the specs

* Combine union of the E2 exclusion into one query

* Using the visit date as encounter date as oppossed to end date for F2 exclusion

* Fix the F2 and F3 exclusion criteria to base on visit date as end date as oppossed to when we were applying the end of reporting period

* Proper E1 exclusion end date set based on the lab results date as oppossed to the end of reporting period

* E2 exclusion done including the date from the encounter date as oppossed to the end of reporting period

* Include the lab visit date for the criteria 3 exclusion instead of using reporting end period

* Fix for Total 0-14 bringing in some case +15

* Fix B.4 where not calculating correctly for total +15

* Fix B.7, B.8,B.10 and B.12 where the references to excel file where wrong, where all pointing to female desagregation

api/src/main/java/org/openmrs/module/eptsreports/reporting/library/datasets/resumo/ResumoMensalDataSetDefinition.java

@@ -60,6 +60,7 @@ public ResumoMensalDataSetDefinition(
 
   public DataSetDefinition constructResumoMensalDataset() {
     CohortIndicatorDataSetDefinition dsd = new CohortIndicatorDataSetDefinition();
+    String mappings = "startDate=${startDate},endDate=${endDate},location=${location}";
     dsd.setName("Resumo Mensal Data set B");
     dsd.addParameters(getParameters());
 
@@ -410,6 +411,91 @@ public DataSetDefinition constructResumoMensalDataset() {
         getPatientsWhoInitiatedPreTarvDuringCurrentMonthAndDiagnosedForActiveTB(),
         "");
 
+    // E1 indicators
+
+    addRow(
+        dsd,
+        "E1",
+        "Annual Notification",
+        map(
+            eptsGeneralIndicator.getIndicator(
+                "E1",
+                map(
+                    resumoMensalCohortQueries
+                        .getNumberOfActivePatientsInArtAtEndOfCurrentMonthWithVlPerformed(),
+                    mappings)),
+            mappings),
+        resumoMensalAandBdisaggregations.disAggForE());
+    // E2
+    addRow(
+        dsd,
+        "E2",
+        "Annual Notification",
+        map(
+            eptsGeneralIndicator.getIndicator(
+                "E2",
+                map(
+                    resumoMensalCohortQueries
+                        .getNumberOfActivePatientsInArtAtTheEndOfTheCurrentMonthHavingVlTestResults(),
+                    mappings)),
+            mappings),
+        resumoMensalAandBdisaggregations.disAggForE());
+
+    // E3
+    addRow(
+        dsd,
+        "E3",
+        "Annual Notification",
+        map(
+            eptsGeneralIndicator.getIndicator(
+                "E3",
+                map(
+                    resumoMensalCohortQueries
+                        .getActivePatientsOnArtWhoRecievedVldSuppressionResults(),
+                    mappings)),
+            mappings),
+        resumoMensalAandBdisaggregations.disAggForE());
+
+    // F1
+    dsd.addColumn(
+        "F1",
+        "Number of patients who had clinical appointment during the reporting month",
+        map(
+            eptsGeneralIndicator.getIndicator(
+                "F1",
+                map(
+                    resumoMensalCohortQueries
+                        .getNumberOfPatientsWhoHadClinicalAppointmentDuringTheReportingMonth(),
+                    mappings)),
+            mappings),
+        "");
+    // F2
+    dsd.addColumn(
+        "F2",
+        "Number of patients who had clinical appointment during the reporting month and were screened for TB",
+        map(
+            eptsGeneralIndicator.getIndicator(
+                "F2",
+                map(
+                    resumoMensalCohortQueries
+                        .getNumberOfPatientsWhoHadClinicalAppointmentDuringTheReportingMonthAndScreenedFoTb(),
+                    mappings)),
+            mappings),
+        "");
+    // F3
+    dsd.addColumn(
+        "F3",
+        "Number of patients who had at least one clinical appointment during the year",
+        map(
+            eptsGeneralIndicator.getIndicator(
+                "F3",
+                map(
+                    resumoMensalCohortQueries
+                        .getNumberOfPatientsWithAtLeastOneClinicalAppointmentDuringTheYear(),
+                    mappings)),
+            mappings),
+        "");
+
     return dsd;
   }
 

api/src/main/java/org/openmrs/module/eptsreports/reporting/library/dimensions/EptsCommonDimension.java

@@ -84,6 +84,9 @@ public CohortDefinitionDimension age(final AgeDimensionCohortInterface ageDimens
     dim.addCohortDefinition(
         "0-4",
         ageDimensionCohort.createXtoYAgeCohort("patients with age between 0 and 4 years", 0, 4));
+    dim.addCohortDefinition(
+        "0-14",
+        ageDimensionCohort.createXtoYAgeCohort("patients with age between 0 and 14 years", 0, 14));
     dim.addCohortDefinition(
         "0-15",
         ageDimensionCohort.createXtoYAgeCohort("patients with age between 0 and 15 years", 0, 15));

api/src/main/java/org/openmrs/module/eptsreports/reporting/library/disaggregations/ResumoMensalAandBdisaggregations.java

@@ -28,13 +28,13 @@ public List<ColumnParameters> getUnder14YearsColumns() {
         new ColumnParameters("fiveTo9years", "5 to  9 years patients", "age=5-9", "02");
     ColumnParameters tenTo14yearsMale =
         new ColumnParameters(
-            "tenTo14yearsMale", "10 to  14 years male patients", "gender=M|age=10-15", "03");
+            "tenTo14yearsMale", "10 to  14 years male patients", "gender=M|age=10-14", "03");
     ColumnParameters tenTo14yearsFemale =
         new ColumnParameters(
-            "tenTo14yearsFemale", "10 to  14 years female patients", "gender=F|age=10-15", "04");
+            "tenTo14yearsFemale", "10 to  14 years female patients", "gender=F|age=10-14", "04");
     ColumnParameters under14yearsTotal =
         new ColumnParameters(
-            "under14yearsTotal", "Under 15 years patients - Totals", "age=0-15", "05");
+            "under14yearsTotal", "Under 15 years patients - Totals", "age=0-14", "05");
 
     return Arrays.asList(
         under4years, fiveTo9years, tenTo14yearsMale, tenTo14yearsFemale, under14yearsTotal);
@@ -62,9 +62,9 @@ public List<ColumnParameters> getAdultPatients() {
 
   public List<ColumnParameters> getAdolescentesColumns() {
     ColumnParameters tenTo14Male =
-        new ColumnParameters("tenTo14Male", "10 to 14 years male", "gender=M|age=10-15", "01");
+        new ColumnParameters("tenTo14Male", "10 to 14 years male", "gender=M|age=10-14", "01");
     ColumnParameters tenTo14Female =
-        new ColumnParameters("tenTo14Female", "10 to 14 years female", "gender=F|age=10-15", "02");
+        new ColumnParameters("tenTo14Female", "10 to 14 years female", "gender=F|age=10-14", "02");
     ColumnParameters fifteenTo19Female =
         new ColumnParameters(
             "fifteenTo19Female", "15 to 19 years female", "gender=F|age=15-19", "03");
@@ -76,4 +76,16 @@ public List<ColumnParameters> getAdolescentesColumns() {
     return Arrays.asList(
         tenTo14Male, tenTo14Female, fifteenTo19Female, fifteenTo19Male, adolescentTotals);
   }
+
+  /**
+   * Get teh disaggregations for the patients under 14 years and those above 14 yeara
+   *
+   * @return List of ColumnParameters
+   */
+  public List<ColumnParameters> disAggForE() {
+    ColumnParameters under14Years =
+        new ColumnParameters("under14", "Under 14 years", "age=0-14", "01");
+    ColumnParameters over14Years = new ColumnParameters("over14", "15+ years", "age=15+", "02");
+    return Arrays.asList(under14Years, over14Years);
+  }
 }

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

@@ -120,4 +120,243 @@ public static String getPatientsTransferredFromAnotherHealthFacilityByEndOfPrevi
         typeOfPantientConcept,
         tarvConcept);
   }
+
+  public static String getPatientsForF2ForExclusionFromMainQuery(
+      int encounterType, int tbSymptomsConcept, int yesConcept, int tbTreatmentPlanConcept) {
+    String query =
+        "SELECT p.patient_id "
+            + "FROM   patient p "
+            + " JOIN encounter e "
+            + " ON p.patient_id = e.patient_id "
+            + " JOIN obs o "
+            + " ON o.encounter_id = e.encounter_id "
+            + " JOIN (SELECT pat.patient_id AS patient_id, enc.encounter_datetime AS endDate FROM encounter enc JOIN patient pat ON pat.patient_id=enc.patient_id "
+            + " JOIN obs ob ON enc.encounter_id=ob.encounter_id WHERE pat.voided = 0 AND enc.voided = 0 AND ob.voided = 0 "
+            + " AND enc.location_id = :location AND enc.encounter_datetime BETWEEN :startDate AND :endDate "
+            + " AND enc.encounter_type= %d AND ob.concept_id=%d AND ob.value_coded=%d) ed "
+            + " ON p.patient_id=ed.patient_id"
+            + " WHERE  p.voided = 0 "
+            + " AND e.voided = 0 "
+            + " AND e.encounter_type = %d "
+            + " AND e.location_id = :location "
+            + " AND e.encounter_datetime = ed.endDate "
+            + " AND o.voided = 0 "
+            + " AND o.concept_id = %d ";
+    return String.format(
+        query, encounterType, tbSymptomsConcept, yesConcept, encounterType, tbTreatmentPlanConcept);
+  }
+
+  /**
+   * Get patients with encounters within start and end date F1: Number of patients who had clinical
+   * appointment during the reporting month
+   *
+   * @return String
+   */
+  public static String getPatientsWithGivenEncounterType(int encounterType) {
+    String query =
+        "SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id "
+            + " WHERE e.encounter_type=%d AND e.location_id=:location "
+            + " AND e.encounter_datetime BETWEEN :startDate AND :endDate AND p.voided=0 AND e.voided=0 ";
+    return String.format(query, encounterType);
+  }
+
+  /**
+   * Get patients with viral load suppression
+   *
+   * @return String
+   */
+  public static String getPatientsHavingViralLoadSuppression(
+      int viralLoadConcept, int encounterType) {
+    String query =
+        "SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id JOIN obs o ON e.encounter_id=o.encounter_id "
+            + " WHERE p.voided=0 AND e.voided=0 AND o.voided=0 AND e.location_id=:location "
+            + " AND e.encounter_datetime BETWEEN :startDate AND :endDate "
+            + " AND o.value_numeric IS NOT NULL "
+            + " AND o.concept_id=%d "
+            + " AND e.encounter_type=%d "
+            + " AND o.value_numeric < 1000";
+    return String.format(query, viralLoadConcept, encounterType);
+  }
+
+  /**
+   * getPatientsWithCodedObsAndAnswers
+   *
+   * @return String
+   */
+  public static String getPatientsWithCodedObsAndAnswers(
+      int encounterType, int questionConceptId, int answerConceptId) {
+    String query =
+        "SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id JOIN obs o ON e.encounter_id=o.encounter_id "
+            + " WHERE p.voided = 0 AND e.voided = 0 AND o.voided = 0 "
+            + " AND e.location_id = :location AND e.encounter_datetime BETWEEN :startDate AND :endDate AND e.encounter_type=%d "
+            + " AND o.concept_id=%d AND o.value_coded=%d";
+    return String.format(query, encounterType, questionConceptId, answerConceptId);
+  }
+
+  /**
+   * Get patients with viral load suppression
+   *
+   * @return String
+   */
+  public static String getPatientsHavingViralLoadResults(int viralLoadConcept, int encounterType) {
+    String query =
+        "SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id JOIN obs o ON e.encounter_id=o.encounter_id "
+            + " WHERE p.voided=0 AND e.voided=0 AND o.voided=0 AND e.location_id=:location "
+            + " AND e.encounter_datetime BETWEEN :startDate AND :endDate "
+            + " AND o.value_numeric IS NOT NULL "
+            + " AND o.concept_id=%d "
+            + " AND e.encounter_type=%d ";
+    return String.format(query, viralLoadConcept, encounterType);
+  }
+
+  /**
+   * Get patients with any coded obs value
+   *
+   * @return String
+   */
+  public static String gePatientsWithCodedObs(int encounterType, int conceptId) {
+    String query =
+        "SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id JOIN obs o ON e.encounter_id=o.encounter_id "
+            + " WHERE p.voided = 0 AND e.voided = 0 AND o.voided = 0 "
+            + " AND e.location_id = :location AND e.encounter_datetime BETWEEN :startDate AND :endDate AND e.encounter_type=%d "
+            + " AND o.concept_id=%d ";
+    return String.format(query, encounterType, conceptId);
+  }
+
+  /**
+   * E1 exclusions
+   *
+   * @return String
+   */
+  public static String getE1ExclusionCriteria(
+      int encounterType, int questionConceptId, int answerConceptId) {
+    String query =
+        "SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id JOIN obs o ON e.encounter_id=o.encounter_id "
+            + " JOIN (SELECT pat.patient_id AS patient_id, enc.encounter_datetime AS endDate FROM patient pat "
+            + " JOIN encounter enc ON pat.patient_id=enc.patient_id JOIN obs ob ON enc.encounter_id=ob.encounter_id "
+            + " WHERE pat.voided = 0 AND enc.voided = 0 AND ob.voided = 0 AND enc.location_id = :location "
+            + " AND enc.encounter_datetime BETWEEN :startDate AND :endDate AND enc.encounter_type=%d AND "
+            + " ob.concept_id=%d AND ob.value_coded=%d) ed "
+            + " ON p.patient_id=ed.patient_id "
+            + " WHERE p.voided = 0 AND e.voided = 0 AND o.voided = 0 "
+            + " AND e.location_id = :location AND e.encounter_datetime BETWEEN "
+            + " IF(MONTH(:startDate) = 12  && DAY(:startDate) = 21, :startDate, CONCAT(YEAR(:startDate)-1, '-12','-21')) "
+            + " AND ed.endDate AND e.encounter_type=%d "
+            + " AND o.concept_id=%d AND o.value_coded=%d";
+    return String.format(
+        query,
+        encounterType,
+        questionConceptId,
+        answerConceptId,
+        encounterType,
+        questionConceptId,
+        answerConceptId);
+  }
+
+  /**
+   * E2 exclusions
+   *
+   * @param viralLoadConcept
+   * @param encounterType
+   * @param qualitativeConcept
+   * @return String
+   */
+  public static String getE2ExclusionCriteria(
+      int viralLoadConcept, int encounterType, int qualitativeConcept) {
+
+    String query =
+        "SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id JOIN obs o ON e.encounter_id=o.encounter_id "
+            + "JOIN (SELECT pat.patient_id AS patient_id, enc.encounter_datetime AS endDate FROM patient pat JOIN encounter enc ON pat.patient_id=enc.patient_id JOIN obs ob "
+            + " ON enc.encounter_id=ob.encounter_id "
+            + " WHERE pat.voided=0 AND enc.voided=0 AND ob.voided=0 AND enc.location_id=:location AND enc.encounter_datetime "
+            + " BETWEEN :startDate AND :endDate AND ob.concept_id IN(%d, %d) AND enc.encounter_type=%d) ed "
+            + " ON p.patient_id=ed.patient_id "
+            + " WHERE p.voided=0 AND e.voided=0 AND o.voided=0 AND e.location_id=:location "
+            + " AND e.encounter_datetime BETWEEN "
+            + " IF(MONTH(:startDate) = 12  && DAY(:startDate) = 21, :startDate, CONCAT(YEAR(:startDate)-1, '-12','-21')) "
+            + " AND ed.endDate "
+            + " AND o.concept_id IN (%d, %d)"
+            + " AND e.encounter_type=%d ";
+    return String.format(
+        query,
+        viralLoadConcept,
+        qualitativeConcept,
+        encounterType,
+        viralLoadConcept,
+        qualitativeConcept,
+        encounterType);
+  }
+
+  /**
+   * E3 exclusion
+   *
+   * @param viralLoadConcept
+   * @param encounterType
+   * @param qualitativeConcept
+   * @return
+   */
+  public static String getE3ExclusionCriteria(
+      int viralLoadConcept, int encounterType, int qualitativeConcept) {
+    String query =
+        "SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id JOIN obs o ON e.encounter_id=o.encounter_id "
+            + " JOIN (SELECT pat.patient_id AS patient_id, enc.encounter_datetime AS endDate FROM patient pat "
+            + " JOIN encounter enc ON pat.patient_id=enc.patient_id JOIN obs ob ON enc.encounter_id=ob.encounter_id "
+            + " WHERE pat.voided=0 AND enc.voided=0 AND ob.voided=0 AND enc.location_id=:location "
+            + " AND enc.encounter_datetime BETWEEN :startDate AND :endDate AND ob.value_numeric IS NOT NULL "
+            + " AND ob.concept_id=%d AND enc.encounter_type=%d AND ob.value_numeric < 1000) ed "
+            + " ON p.patient_id=ed.patient_id"
+            + " WHERE p.voided=0 AND e.voided=0 AND o.voided=0 AND e.location_id=:location "
+            + " AND e.encounter_datetime BETWEEN "
+            + " IF(MONTH(:startDate) = 12  && DAY(:startDate) = 21, :startDate, CONCAT(YEAR(:startDate)-1, '-12','-21')) "
+            + " AND ed.endDate "
+            + " AND o.value_numeric IS NOT NULL "
+            + " AND o.concept_id=%d "
+            + " AND e.encounter_type=%d "
+            + " AND o.value_numeric < 1000"
+            + " UNION "
+            + " SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id JOIN obs o ON e.encounter_id=o.encounter_id "
+            + " JOIN (SELECT pat.patient_id AS patient_id, enc.encounter_datetime AS endDate FROM patient pat "
+            + " JOIN encounter enc ON pat.patient_id=enc.patient_id JOIN obs ob ON enc.encounter_id=ob.encounter_id "
+            + " WHERE pat.voided = 0 AND enc.voided = 0 AND ob.voided = 0 AND enc.location_id = :location AND "
+            + " enc.encounter_datetime BETWEEN :startDate AND :endDate AND enc.encounter_type=%d AND ob.concept_id=%d) ed "
+            + " ON p.patient_id=ed.patient_id "
+            + " WHERE p.voided = 0 AND e.voided = 0 AND o.voided = 0 "
+            + " AND e.location_id = :location AND e.encounter_datetime BETWEEN "
+            + " IF(MONTH(:startDate) = 12  && DAY(:startDate) = 21, :startDate, CONCAT(YEAR(:startDate)-1, '-12','-21')) "
+            + " AND ed.endDate "
+            + " AND e.encounter_type=%d "
+            + " AND o.concept_id=%d ";
+
+    return String.format(
+        query,
+        viralLoadConcept,
+        encounterType,
+        viralLoadConcept,
+        encounterType,
+        encounterType,
+        qualitativeConcept,
+        encounterType,
+        qualitativeConcept);
+  }
+
+  /**
+   * F3 exclusions
+   *
+   * @param encounterType
+   * @return
+   */
+  public static String getF3Exclusion(int encounterType) {
+    String query =
+        " SELECT p.patient_id FROM patient p JOIN encounter e ON p.patient_id=e.patient_id JOIN ( "
+            + " SELECT pat.patient_id AS patient_id, enc.encounter_datetime AS endDate FROM encounter enc JOIN patient pat "
+            + " ON enc.patient_id=pat.patient_id WHERE enc.encounter_type=%d AND enc.location_id=:location "
+            + " AND enc.encounter_datetime BETWEEN :startDate AND :endDate AND pat.voided=0 AND enc.voided=0) ed "
+            + " ON p.patient_id=ed.patient_id"
+            + " WHERE e.encounter_type=%d AND e.location_id=:location "
+            + " AND e.encounter_datetime BETWEEN "
+            + " IF(MONTH(:startDate) = 12  && DAY(:startDate) = 21, :startDate, CONCAT(YEAR(:startDate)-1, '-12','-21')) "
+            + " AND ed.endDate "
+            + "AND p.voided=0 AND e.voided=0 ";
+    return String.format(query, encounterType, encounterType);
+  }
 }