MEPTS - 1617 | TX_RTT Changes for December 2024 Release

api/src/main/java/org/openmrs/module/eptsreports/reporting/cohort/evaluator/ResumoMensalTransferredOutCohortDefinitionEvaluator.java

@@ -96,6 +96,7 @@ public EvaluatedCohort evaluate(CohortDefinition cohortDefinition, EvaluationCon
       q.append("                              ON         e.encounter_id=o.encounter_id");
       q.append("                             WHERE      p.voided = 0");
       q.append("                                 AND        e.voided = 0");
+      q.append("                                 AND        o.voided = 0");
       q.append("                       AND        o.concept_id =   :preArtStateOfStay  ");
       q.append("                       AND        o.value_coded =   :transfOutConcept  ");
       q.append("                                AND        e.encounter_type =   :masterCard  ");

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

@@ -2647,6 +2647,48 @@
     public abstract String getSearchKey();
   }
 
+  public enum semiQuantitativeCd4CountComparison {
+    LessThanOrEqualTo200mm3 {
+      @Override
+      public String getProposition() {
+        return "o.value_coded = ${165513}";
+      }
+
+      @Override
+      public String getCompositionString() {
+        return getSearchKey();
+      }
+
+      @Override
+      public String getSearchKey() {
+        return "AA";
+      }
+    },
+
+    GreaterThanOrEqualTo200mm3 {
+      @Override
+      public String getProposition() {
+        return "o.value_coded =${1254}";
+      }
+
+      @Override
+      public String getCompositionString() {
+        return getSearchKey();
+      }
+
+      @Override
+      public String getSearchKey() {
+        return "BB";
+      }
+    };
+
+    public abstract String getProposition();
+
+    public abstract String getCompositionString();
+
+    public abstract String getSearchKey();
+  }
+
   private Map<String, Integer> getMetadata() {
     Map<String, Integer> map = new HashMap<>();
     map.put("6", hivMetadata.getAdultoSeguimentoEncounterType().getEncounterTypeId());

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

@@ -3797,6 +3797,8 @@ public CohortDefinition getPatientsWhoAreTransferredIn(boolean isExclusion) {
             hivMetadata
                 .getTransferredFromOtherHealthFacilityWorkflowState()
                 .getProgramWorkflowStateId(),
+            hivMetadata.getTypeOfPatientTransferredFrom().getConceptId(),
+            hivMetadata.getArtStatus().getConceptId(),
             isExclusion));
     return cd;
   }

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

@@ -13,8 +13,6 @@
  */
 package org.openmrs.module.eptsreports.reporting.library.cohorts;
 
-import static org.openmrs.module.eptsreports.reporting.utils.EptsReportUtils.map;
-
 import java.util.*;
 import org.apache.commons.text.StringSubstitutor;
 import org.openmrs.EncounterType;
@@ -390,6 +388,7 @@
 
   public CohortDefinition getPatientsWithCd4AndAge(
       AdvancedDiseaseAndTBCascadeCohortQueries.Cd4CountComparison cd4,
+      AdvancedDiseaseAndTBCascadeCohortQueries.semiQuantitativeCd4CountComparison semiCd4,
       Integer minAge,
       Integer maxAge) {
     CompositionCohortDefinition cd = new CompositionCohortDefinition();
@@ -398,7 +397,7 @@
     cd.addParameter(new Parameter("startDate", "Start Date", Date.class));
     cd.addParameter(new Parameter("endDate", "End Date", Date.class));
 
-    CohortDefinition getCd4Result = getCd4Result(cd4);
+    CohortDefinition getCd4Result = getCd4Result(cd4, semiCd4);
     CohortDefinition age = ageCohortQueries.createXtoYAgeCohort("Age", minAge, maxAge);
 
     cd.addSearch(
@@ -413,33 +412,37 @@
   }
 
   /**
-   * <b>Patients with an absolute CD4 result <200/mm3 registered in the following sources:</b>
+   * <b>Patients with an absolute CD4 result <200/mm3 or Semi-Quantitative registered in the
+   * following sources:</b>
    *
    * <ul>
-   *   <li>CD4 absolute value at ART initiation marked on Ficha Resumo OR
-   *   <li>Last CD4 absolute value marked on Ficha Resumo OR
-   *   <li>CD4 absolute result marked in the Investigações - Resultados Laboratoriais section on
-   *       Ficha Clínica OR
-   *   <li>CD4 absolute result registered on the Lab Form OR
-   *   <li>CD4 absolute result registered on the e-Lab Form
+   *   <li>CD4 absolute value or semi-quantitative at ART initiation marked on Ficha Resumo OR
+   *   <li>Last CD4 absolute value or semi-quantitative marked on Ficha Resumo OR
+   *   <li>CD4 absolute result or semi-quantitative marked in the Investigações - Resultados
+   *       Laboratoriais section on Ficha Clínica OR
+   *   <li>CD4 absolute result or semi-quantitative registered on the Lab Form OR
+   *   <li>CD4 absolute result or semi-quantitative registered on the e-Lab Form
    * </ul>
    *
-   * <p>The system will consider the oldest CD4 result date falling between patient ART Start Date -
-   * 90 days and ART Start Date + 28 days from the different sources listed above for the evaluation
-   * of the result (< 200).
+   * <p>The system will consider the oldest CD4 result date between patient ART Start Date - 90 days
+   * and ART Start Date + 28 days from the different sources listed above for the evaluation of the
+   * result (< 200).
    *
    * <p><b>Notes: </b>For the CD4 at ART initiation registered on Ficha Resumo, the “ART Start Date”
    * that is registered on the same Ficha Resumo will be considered as the CD4 result date. For
    * clients who have CD4 results ≥200/mm3 and <200/mm3 on the same, oldest date, the CD4 result
    * <200/mm3 will be prioritized.
    *
    * @param cd4CountComparison
+   * @param semiQuantitativeCd4CountComparison
    */
   public CohortDefinition getCd4Result(
-      AdvancedDiseaseAndTBCascadeCohortQueries.Cd4CountComparison cd4CountComparison) {
+      AdvancedDiseaseAndTBCascadeCohortQueries.Cd4CountComparison cd4CountComparison,
+      AdvancedDiseaseAndTBCascadeCohortQueries.semiQuantitativeCd4CountComparison
+          semiQuantitativeCd4CountComparison) {
 
     SqlCohortDefinition cd = new SqlCohortDefinition();
-    cd.setName("Number of patientes who initiated TARV - Fila and ARV Pickup");
+    cd.setName("CD4 Results");
     cd.addParameter(new Parameter("endDate", "End Date", Date.class));
     cd.addParameter(new Parameter("location", "Location", Location.class));
 
@@ -456,78 +459,108 @@
     map.put("1695", hivMetadata.getCD4AbsoluteOBSConcept().getConceptId());
     map.put("23896", hivMetadata.getArtInitiationCd4Concept().getConceptId());
     map.put("1190", hivMetadata.getARVStartDateConcept().getConceptId());
+    map.put("165515", hivMetadata.getCD4SemiQuantitativeConcept().getConceptId());
+    map.put("165513", hivMetadata.getCD4CountLessThanOrEqualTo200Concept().getConceptId());
+    map.put("1254", hivMetadata.getCD4CountGreaterThan200Concept().getConceptId());
 
     CommonQueries commonQueries = new CommonQueries(new CommonMetadata(), new HivMetadata());
 
     String query =
         "SELECT p.patient_id "
-            + "FROM   patient p "
-            + "       INNER JOIN encounter e ON e.patient_id = p.patient_id "
-            + "       INNER JOIN obs o ON o.encounter_id = e.encounter_id "
-            + "       INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
-            + "       INNER JOIN (SELECT e.patient_id,MIN(DATE(cd4.cd4_date)) cd4_date "
-            + "                   FROM   encounter e "
-            + "                          INNER JOIN obs o ON o.encounter_id = e.encounter_id "
-            + "                          INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
-            + "                          INNER JOIN ( "
+            + "FROM patient p "
+            + "INNER JOIN encounter e ON e.patient_id = p.patient_id "
+            + "INNER JOIN obs o ON o.encounter_id = e.encounter_id "
+            + "INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
+            + "INNER JOIN ( "
+            + "SELECT e.patient_id, MIN(DATE(cd4.cd4_date)) cd4_date "
+            + "FROM encounter e "
+            + "INNER JOIN obs o ON o.encounter_id = e.encounter_id "
+            + "INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
+            + "INNER JOIN ( "
             + commonQueries.getARTStartDate(true)
-            + "                 ) art "
-            + "  ON art.patient_id = e.patient_id "
-            + "  INNER JOIN (SELECT e.patient_id,DATE(e.encounter_datetime) cd4_date "
-            + "            FROM   encounter e "
-            + "            INNER JOIN obs o ON o.encounter_id = e.encounter_id "
-            + "            WHERE  e.encounter_type IN ( ${6}, ${13}, ${51} ) "
-            + "            AND e.location_id = :location "
-            + "            AND DATE(e.encounter_datetime) <= :endDate "
-            + "            AND o.concept_id = ${1695} "
-            + "            AND e.voided = 0 "
-            + "            AND o.voided = 0 "
-            + "            UNION "
-            + "            SELECT e.patient_id,DATE(o.obs_datetime) AS cd4_date "
-            + "            FROM   encounter e "
-            + "            INNER JOIN obs o ON o.encounter_id = e.encounter_id "
-            + "            WHERE  e.encounter_type = ${53} "
-            + "            AND e.location_id = :location "
-            + "            AND e.voided = 0 "
-            + "            AND o.voided = 0 "
-            + "            AND o.concept_id = ${1695} "
-            + "            AND o.obs_datetime <= :endDate"
-            + "            UNION "
-            + "            SELECT e.patient_id,DATE(o2.value_datetime) AS cd4_date "
-            + "            FROM   encounter e "
-            + "            INNER JOIN obs o ON o.encounter_id = e.encounter_id "
-            + "            INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
-            + "            WHERE  e.encounter_type = ${53} "
-            + "            AND e.location_id = :location "
-            + "            AND e.voided = 0 "
-            + "            AND o.voided = 0 "
-            + "            AND o2.voided = 0 "
-            + "            AND o.concept_id = ${23896} "
-            + "            AND o2.concept_id = ${1190} "
-            + "            AND o2.value_datetime <= :endDate"
-            + "     ) cd4 ON cd4.patient_id = e.patient_id "
-            + "   WHERE  e.voided = 0 "
-            + "   AND o.voided = 0 "
-            + "   AND e.location_id = :location "
-            + "   AND o.value_numeric IS NOT NULL "
-            + "   AND ( ( DATE(e.encounter_datetime) BETWEEN DATE_SUB(art.first_pickup, INTERVAL 90 day) AND DATE_ADD(art.first_pickup, INTERVAL 28 day) "
-            + "             AND e.encounter_type IN ( ${6}, ${13}, ${51}) AND o.concept_id = ${1695}  ) "
-            + "          OR (   ( DATE(o.obs_datetime) BETWEEN DATE_SUB(art.first_pickup, INTERVAL 90 day) AND DATE_ADD(art.first_pickup, INTERVAL 28 day) AND e.encounter_type = ${53} AND o.concept_id = ${1695} ) "
-            + "            OR ( DATE(o2.value_datetime) BETWEEN DATE_SUB(art.first_pickup, INTERVAL 90 day) AND DATE_ADD(art.first_pickup, INTERVAL 28 day) AND e.encounter_type = ${53} AND o.concept_id = ${23896} AND o2.concept_id = ${1190} AND o2.voided = 0) "
-            + "          ) "
+            + " ) art ON art.patient_id = e.patient_id "
+            + "INNER JOIN ( "
+            + "SELECT e.patient_id, DATE(e.encounter_datetime) cd4_date "
+            + "FROM encounter e "
+            + "INNER JOIN obs o ON o.encounter_id = e.encounter_id "
+            + "WHERE e.encounter_type IN (${6}, ${13}, ${51}) "
+            + "AND e.location_id = :location "
+            + "AND DATE(e.encounter_datetime) <= :endDate "
+            + "AND o.concept_id IN (${1695}, ${165515}) "
+            + "AND e.voided = 0 "
+            + "AND o.voided = 0 "
+            + "UNION "
+            + "SELECT e.patient_id, DATE(o.obs_datetime) AS cd4_date "
+            + "FROM encounter e "
+            + "INNER JOIN obs o ON o.encounter_id = e.encounter_id "
+            + "WHERE e.encounter_type = ${53} "
+            + "AND e.location_id = :location "
+            + "AND e.voided = 0 "
+            + "AND o.voided = 0 "
+            + "AND o.concept_id IN (${1695}, ${165515}) "
+            + "AND o.obs_datetime <= :endDate "
+            + "UNION "
+            + "SELECT e.patient_id, DATE(o2.value_datetime) AS cd4_date "
+            + "FROM encounter e "
+            + "INNER JOIN obs o ON o.encounter_id = e.encounter_id "
+            + "INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
+            + "WHERE e.encounter_type = ${53} "
+            + "AND e.location_id = :location "
+            + "AND e.voided = 0 "
+            + "AND o.voided = 0 "
+            + "AND o2.voided = 0 "
+            + "AND o.concept_id = ${23896} "
+            + "AND o2.concept_id = ${1190} "
+            + "AND o2.value_datetime <= :endDate "
+            + ") cd4 ON cd4.patient_id = e.patient_id "
+            + "WHERE e.voided = 0 "
+            + "AND o.voided = 0 "
+            + "AND e.location_id = :location "
+            + "AND o.value_numeric IS NOT NULL "
+            + "AND ( "
+            + "(DATE(e.encounter_datetime) BETWEEN DATE_SUB(art.first_pickup, INTERVAL 90 day) AND DATE_ADD(art.first_pickup, INTERVAL 28 day) "
+            + "AND e.encounter_type IN (${6}, ${13}, ${51}) AND o.concept_id IN (${1695}, ${165515})) "
+            + "OR ( "
+            + "(DATE(o.obs_datetime) BETWEEN DATE_SUB(art.first_pickup, INTERVAL 90 day) AND DATE_ADD(art.first_pickup, INTERVAL 28 day) "
+            + "AND e.encounter_type = ${53} AND o.concept_id IN (${1695}, ${165515})) "
+            + "OR ( "
+            + "DATE(o2.value_datetime) BETWEEN DATE_SUB(art.first_pickup, INTERVAL 90 day) AND DATE_ADD(art.first_pickup, INTERVAL 28 day) "
+            + "AND e.encounter_type = ${53} AND o.concept_id = ${23896} AND o2.concept_id = ${1190} AND o2.voided = 0 "
+            + ") "
+            + ") "
+            + ") "
+            + "GROUP BY e.patient_id "
+            + ") min_cd4 ON min_cd4.patient_id = p.patient_id "
+            + "WHERE p.voided = 0 "
+            + "AND e.voided = 0 "
+            + "AND o.voided = 0 "
+            + "AND e.location_id = :location "
+            + "AND ( "
+            + "(DATE(e.encounter_datetime) = min_cd4.cd4_date AND e.encounter_type IN (${6}, ${13}, ${51}) AND o.concept_id = ${1695} "
+            + "AND "
+            + cd4CountComparison.getProposition()
+            + ") "
+            + "OR ( "
+            + "DATE(e.encounter_datetime) = min_cd4.cd4_date AND e.encounter_type IN (${6}, ${13}, ${51}) AND o.concept_id = ${165515} "
+            + "AND "
+            + semiQuantitativeCd4CountComparison.getProposition()
+            + ") "
+            + "OR ( "
+            + "DATE(o.obs_datetime) = min_cd4.cd4_date AND e.encounter_type = ${53} AND o.concept_id = ${1695} "
+            + "AND "
+            + cd4CountComparison.getProposition()
+            + ") "
+            + "OR ( "
+            + "DATE(o.obs_datetime) = min_cd4.cd4_date AND e.encounter_type = ${53} AND o.concept_id = ${165515} "
+            + "AND "
+            + semiQuantitativeCd4CountComparison.getProposition()
+            + ") "
+            + "OR ( "
+            + "DATE(o2.value_datetime) = min_cd4.cd4_date AND e.encounter_type = ${53} "
+            + "AND o.concept_id = ${23896} AND o2.concept_id = ${1190} AND o2.voided = 0 "
+            + ") "
             + ") "
-            + "   GROUP  BY e.patient_id) min_cd4 ON min_cd4.patient_id = p.patient_id "
-            + " WHERE  p.voided = 0 "
-            + "       AND e.voided = 0 "
-            + "       AND o.voided = 0 "
-            + "       AND e.location_id = :location "
-            + "       AND  ".concat(cd4CountComparison.getProposition())
-            + "       AND ( ( DATE(e.encounter_datetime) = min_cd4.cd4_date AND e.encounter_type IN ( ${6}, ${13}, ${51} ) AND o.concept_id = ${1695}  ) "
-            + "              OR ( ( DATE(o.obs_datetime) = min_cd4.cd4_date AND e.encounter_type = ${53} AND o.concept_id = ${1695} )  "
-            + "                OR ( DATE(o2.value_datetime) = min_cd4.cd4_date AND e.encounter_type = ${53} AND o.concept_id = ${23896} AND o2.concept_id = ${1190} AND o2.voided = 0 )"
-            + "               ) "
-            + "             ) "
-            + "GROUP  BY p.patient_id";
+            + "GROUP BY p.patient_id";
 
     StringSubstitutor sb = new StringSubstitutor(map);
     cd.setQuery(sb.replace(query));
@@ -588,6 +621,8 @@
     CohortDefinition cd4Under200 =
         getPatientsWithCd4AndAge(
             AdvancedDiseaseAndTBCascadeCohortQueries.Cd4CountComparison.LessThanOrEqualTo200mm3,
+            AdvancedDiseaseAndTBCascadeCohortQueries.semiQuantitativeCd4CountComparison
+                .LessThanOrEqualTo200mm3,
             5,
             null);
 
@@ -653,12 +688,16 @@
     CohortDefinition cd4Above200AndAge =
         getPatientsWithCd4AndAge(
             AdvancedDiseaseAndTBCascadeCohortQueries.Cd4CountComparison.GreaterThanOrEqualTo200mm3,
+            AdvancedDiseaseAndTBCascadeCohortQueries.semiQuantitativeCd4CountComparison
+                .GreaterThanOrEqualTo200mm3,
             5,
             null);
 
     CohortDefinition cd4Under200AndAge =
         getPatientsWithCd4AndAge(
             AdvancedDiseaseAndTBCascadeCohortQueries.Cd4CountComparison.LessThanOrEqualTo200mm3,
+            AdvancedDiseaseAndTBCascadeCohortQueries.semiQuantitativeCd4CountComparison
+                .LessThanOrEqualTo200mm3,
             5,
             null);
 
@@ -705,12 +744,16 @@
     CohortDefinition cd4Under200AndAge =
         getPatientsWithCd4AndAge(
             AdvancedDiseaseAndTBCascadeCohortQueries.Cd4CountComparison.LessThanOrEqualTo200mm3,
+            AdvancedDiseaseAndTBCascadeCohortQueries.semiQuantitativeCd4CountComparison
+                .LessThanOrEqualTo200mm3,
             5,
             null);
 
     CohortDefinition cd4Above200AndAge =
         getPatientsWithCd4AndAge(
             AdvancedDiseaseAndTBCascadeCohortQueries.Cd4CountComparison.GreaterThanOrEqualTo200mm3,
+            AdvancedDiseaseAndTBCascadeCohortQueries.semiQuantitativeCd4CountComparison
+                .GreaterThanOrEqualTo200mm3,
             5,
             null);