MEPTS - 1577 | PMTCT EID & HEI Differences

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

@@ -259,29 +259,52 @@
     map.put("165510", hivMetadata.getFollowingtSampleBetween9To17MonthsConcept().getConceptId());
 
     String query =
-        "SELECT patient_id FROM ( "
-            + " SELECT p.patient_id, "
-            + "       Min(o.value_datetime) AS collection_date "
-            + "FROM patient p "
-            + "         INNER JOIN encounter e ON p.patient_id = e.patient_id "
-            + "         INNER JOIN obs o ON o.encounter_id = e.encounter_id "
-            + "         INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
-            + "WHERE p.voided = 0 "
-            + "  AND e.voided = 0 "
-            + "  AND o.voided = 0 "
-            + "  AND o2.voided = 0 "
-            + "  AND e.location_id = :location "
-            + "  AND e.encounter_type = ${13} "
-            + "  AND ( (o.concept_id = ${23821} "
-            + "    AND o.value_datetime >= :startDate "
-            + "    AND o.value_datetime <= :endDate ) "
-            + "    AND (o2.concept_id = ${165502} ";
+        "SELECT "
+            + "  hiv_sample.patient_id "
+            + "FROM "
+            + "  ( "
+            + "    SELECT "
+            + "      p.patient_id, "
+            + "      Min(o.value_datetime) AS collection_date "
+            + "    FROM patient p "
+            + "      INNER JOIN encounter e ON p.patient_id = e.patient_id "
+            + "      INNER JOIN obs o ON o.encounter_id = e.encounter_id "
+            + "      INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
+            + "    WHERE p.voided = 0 "
+            + "      AND e.voided = 0 "
+            + "      AND o.voided = 0 "
+            + "      AND o2.voided = 0 "
+            + "      AND e.location_id = :location "
+            + "      AND e.encounter_type = ${13} "
+            + "      AND ( "
+            + "        ( "
+            + "          o.concept_id = ${23821} "
+            + "          AND o.value_datetime >= :startDate "
+            + "          AND o.value_datetime <= :endDate "
+            + "        ) "
+            + "        AND ( "
+            + "          o2.concept_id = ${165502} "
+            + "          AND o2.value_coded IN (${165503}, ${165506}, ${165507}, ${165510}) "
+            + "        ) "
+            + "      ) "
+            + "    GROUP BY p.patient_id "
+            + "  ) hiv_sample "
+            + "  INNER JOIN encounter ee ON hiv_sample.patient_id = ee.patient_id "
+            + "  INNER JOIN obs oo ON oo.encounter_id = ee.encounter_id "
+            + "  INNER JOIN obs oo2 ON oo2.encounter_id = ee.encounter_id "
+            + "WHERE ee.voided = 0 "
+            + "  AND oo.voided = 0 "
+            + "  AND oo2.voided = 0 "
+            + "  AND ee.location_id = :location "
+            + "  AND ee.encounter_type = ${13} "
+            + "  AND oo.concept_id = ${23821} "
+            + "  AND oo.value_datetime = hiv_sample.collection_date "
+            + "  AND oo2.concept_id = ${165502} ";
     if (firstSample) {
-      query = query + "        AND o2.value_coded IN (${165503}, ${165507}) ) ) ";
+      query = query + " AND oo2.value_coded IN (${165503}, ${165507}) ";
     } else {
-      query = query + "        AND o2.value_coded IN (${165506}, ${165510}) ) ) ";
+      query = query + " AND oo2.value_coded IN (${165506}, ${165510}) ";
     }
-    query = query + "GROUP BY p.patient_id ) hiv_sample";
 
     StringSubstitutor stringSubstitutor = new StringSubstitutor(map);
 
@@ -316,7 +339,7 @@
    * @param maxAge Maximum age in Days of a patient based on Specimen Collection Date
    * @return CohortDefinition
    */
-  public CohortDefinition getInfantAge(Integer minAge, Integer maxAge) {
+  public CohortDefinition getInfantAge(Integer minAge, Integer maxAge, boolean eidOrHei) {
     SqlCohortDefinition sqlCohortDefinition = new SqlCohortDefinition();
     sqlCohortDefinition.setName("Infant Age");
     sqlCohortDefinition.addParameter(new Parameter("startDate", "Start Date", Date.class));
@@ -334,50 +357,43 @@
     map.put("minAge", minAge);
     map.put("maxAge", maxAge);
 
-    String query =
-        "SELECT "
-            + "  pr.person_id "
-            + "FROM "
-            + "  person pr "
-            + "  INNER JOIN ( "
-            + "    SELECT "
-            + "      p.patient_id, "
-            + "      Min(o.value_datetime) AS collection_date "
-            + "    FROM "
-            + "      patient p "
-            + "      INNER JOIN encounter e ON p.patient_id = e.patient_id "
-            + "      INNER JOIN obs o ON o.encounter_id = e.encounter_id "
-            + "      INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
-            + "    WHERE "
-            + "      p.voided = 0 "
-            + "      AND e.voided = 0 "
-            + "      AND o.voided = 0 "
-            + "      AND o2.voided = 0 "
-            + "      AND e.location_id = :location "
-            + "      AND e.encounter_type = ${13} "
-            + "      AND ( "
-            + "        ( "
-            + "          o.concept_id = ${23821} "
-            + "          AND o.value_datetime >= :startDate "
-            + "          AND o.value_datetime <= :endDate "
-            + "        ) "
-            + "        AND ( "
-            + "          o2.concept_id = ${165502} "
-            + "          AND o2.value_coded IN (${165503}, ${165506}, ${165507}, ${165510}) "
-            + "        ) "
-            + "      ) "
-            + "    GROUP BY "
-            + "      p.patient_id "
-            + "  ) specimen_collection ON pr.person_id = specimen_collection.patient_id "
-            + "WHERE "
-            + "  pr.birthdate IS NOT NULL "
-            + "  AND specimen_collection.collection_date IS NOT NULL "
-            + "  AND TIMESTAMPDIFF( "
-            + "    DAY, pr.birthdate, specimen_collection.collection_date "
-            + "  ) >= ${minAge} "
-            + "  AND TIMESTAMPDIFF( "
-            + "    DAY, pr.birthdate, specimen_collection.collection_date "
-            + "  ) <= ${maxAge}";
+    String query = "SELECT pr.person_id " + "FROM person pr " + "INNER JOIN ( ";
+    query +=
+        eidOrHei
+            ? "    SELECT p.patient_id, MIN(o.value_datetime) AS collection_date "
+            : "    SELECT p.patient_id, MAX(o.value_datetime) AS collection_date ";
+    query +=
+        "    FROM patient p "
+            + "    INNER JOIN encounter e ON p.patient_id = e.patient_id "
+            + "    INNER JOIN obs o ON o.encounter_id = e.encounter_id "
+            + "    INNER JOIN obs o2 ON o2.encounter_id = e.encounter_id "
+            + "    WHERE p.voided = 0 "
+            + "    AND e.voided = 0 "
+            + "    AND o.voided = 0 "
+            + "    AND o2.voided = 0 "
+            + "    AND e.location_id = :location "
+            + "    AND e.encounter_type = ${13} ";
+    query +=
+        eidOrHei
+            ? "    AND ( "
+                + "        (o.concept_id = ${23821} "
+                + "        AND o.value_datetime >= :startDate "
+                + "        AND o.value_datetime <= :endDate) "
+                + "        AND (o2.concept_id = ${165502} "
+                + "        AND o2.value_coded IN (${165503}, ${165506}, ${165507}, ${165510})) "
+                + "    ) "
+            : "    AND ( "
+                + "        o.concept_id = ${23821} "
+                + "        AND (o2.concept_id = ${165502} "
+                + "        AND o2.value_coded IN (${165503}, ${165506}, ${165507}, ${165510})) "
+                + "    ) ";
+    query +=
+        "    GROUP BY p.patient_id "
+            + ") specimen_collection ON pr.person_id = specimen_collection.patient_id "
+            + "WHERE pr.birthdate IS NOT NULL "
+            + "AND specimen_collection.collection_date IS NOT NULL "
+            + "AND TIMESTAMPDIFF(DAY, pr.birthdate, specimen_collection.collection_date) >= ${minAge} "
+            + "AND TIMESTAMPDIFF(DAY, pr.birthdate, specimen_collection.collection_date) <= ${maxAge}";
 
     StringSubstitutor stringSubstitutor = new StringSubstitutor(map);
 
@@ -422,7 +438,7 @@
         EptsReportUtils.map(
             getPatientsWhoUnderwentASampleCollectionForVirologicHivTest(), mappings));
 
-    cd.addSearch("infantAge", EptsReportUtils.map(getInfantAge(0, 365), mappings));
+    cd.addSearch("infantAge", EptsReportUtils.map(getInfantAge(0, 365, true), mappings));
 
     cd.setCompositionString("infantsInCcr AND sampleCollectionHiv AND infantAge");
     return cd;

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

@@ -166,7 +166,7 @@
             + "            ) "
             + "        GROUP BY "
             + "            p.patient_id "
-            + "    ) virologic_hiv;";
+            + "    ) virologic_hiv";
 
     StringSubstitutor stringSubstitutor = new StringSubstitutor(map);
 
@@ -264,7 +264,8 @@
         EptsReportUtils.map(getPatientsWhoHaveVirologivHivTestResult(), mappings));
 
     cd.addSearch(
-        "infantAge", EptsReportUtils.map(pmtctEidCohortQueries.getInfantAge(0, 365), mappings));
+        "infantAge",
+        EptsReportUtils.map(pmtctEidCohortQueries.getInfantAge(0, 365, false), mappings));
 
     cd.setCompositionString("infantsInCcr AND sampleCollectionHiv AND infantAge");
     return cd;
@@ -299,72 +300,59 @@
 
     String query =
         "SELECT "
-            + "  p.patient_id "
+            + "    hiv_sample.patient_id "
             + "FROM "
-            + "  patient p "
-            + "  INNER JOIN encounter e ON p.patient_id = e.patient_id "
-            + "  INNER JOIN obs o ON o.encounter_id = e.encounter_id "
-            + "  INNER JOIN ( "
-            + "    SELECT "
-            + "      p.patient_id, "
-            + "      MAX(o.value_datetime) AS pcr_result_date, "
-            + "      o2.value_coded AS pcr_result "
-            + "    FROM "
-            + "      patient p "
-            + "      INNER JOIN encounter e ON p.patient_id = e.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 obs o3 ON o3.encounter_id = e.encounter_id "
-            + "      INNER JOIN ( "
+            + "    ( "
             + "        SELECT "
-            + "          p.patient_id, "
-            + "          ps.birthdate AS birtday "
+            + "            p.patient_id, "
+            + "            MAX(e.encounter_datetime) AS collection_date "
             + "        FROM "
-            + "          patient p "
-            + "          INNER JOIN person ps ON p.patient_id = ps.person_id "
+            + "            patient p "
+            + "                INNER JOIN encounter e ON p.patient_id = e.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 "
+            + "                    p.patient_id, "
+            + "                    ps.birthdate AS birthday "
+            + "                FROM "
+            + "                    patient p "
+            + "                        INNER JOIN person ps ON p.patient_id = ps.person_id "
+            + "                WHERE "
+            + "                    p.voided = 0 "
+            + "                  AND ps.voided = 0 "
+            + "            ) pat ON pat.patient_id = p.patient_id "
             + "        WHERE "
-            + "          p.voided = 0 "
-            + "          AND ps.voided = 0 "
-            + "      ) pat ON pat.patient_id = p.patient_id "
-            + "    WHERE "
-            + "      p.voided = 0 "
-            + "      AND e.voided = 0 "
-            + "      AND o.voided = 0 "
-            + "      AND o2.voided = 0 "
-            + "      AND o3.voided = 0 "
-            + "      AND e.encounter_type = ${13} "
-            + "      AND e.encounter_datetime >= :startDate "
-            + "      AND e.encounter_datetime <= :endDate "
-            + "      AND e.location_id = :location "
-            + "      AND ( "
-            + "        ( "
-            + "          o.concept_id = ${23821} "
-            + "          AND o.value_datetime <= DATE_ADD(pat.birtday, INTERVAL 365 DAY) "
-            + "        ) "
-            + "        AND ( "
-            + "          o2.concept_id = ${1030} "
-            + "          AND o2.value_coded IN (${703}, ${664}) "
-            + "        ) "
-            + "        AND ( "
-            + "          o3.concept_id = ${165502} "
-            + "          AND o3.value_coded IN (${165503}, ${165506}, ${165507}, ${165510}) "
-            + "        ) "
-            + "      ) "
-            + "    GROUP BY "
-            + "      p.patient_id "
-            + "  ) virologic_hiv ON virologic_hiv.patient_id = p.patient_id "
-            + "  AND p.voided = 0 "
-            + "  AND e.voided = 0 "
-            + "  AND o.voided = 0 "
-            + "  AND e.encounter_type = ${13} "
-            + "  AND e.encounter_datetime >= :startDate "
-            + "  AND e.encounter_datetime <= :endDate "
-            + "  AND e.location_id = :location "
-            + "  AND o.concept_id = ${1030} ";
+            + "            p.voided = 0 "
+            + "          AND e.voided = 0 "
+            + "          AND o.voided = 0 "
+            + "          AND o2.voided = 0 "
+            + "          AND e.location_id = :location "
+            + "          AND e.encounter_type = ${13} "
+            + "          AND ( "
+            + "            o.concept_id = ${23821} "
+            + "                AND o.value_datetime <= DATE_ADD(pat.birthday, INTERVAL 365 DAY) "
+            + "            ) "
+            + "          AND ( "
+            + "            o2.concept_id = ${165502} "
+            + "                AND o2.value_coded IN (${165503}, ${165506}, ${165507}, ${165510}) "
+            + "            ) "
+            + "        GROUP BY "
+            + "            p.patient_id "
+            + "    ) hiv_sample "
+            + "        INNER JOIN encounter ee ON hiv_sample.patient_id = ee.patient_id "
+            + "        INNER JOIN obs oo ON oo.encounter_id = ee.encounter_id "
+            + "WHERE "
+            + "    ee.voided = 0 "
+            + "  AND oo.voided = 0 "
+            + "  AND ee.encounter_type = ${13} "
+            + "  AND ee.encounter_datetime = hiv_sample.collection_date "
+            + "  AND ee.location_id = :location "
+            + "  AND oo.concept_id = ${1030} ";
     if (posiveResult) {
-      query = query + "  AND virologic_hiv.pcr_result = ${703}";
+      query = query + " AND oo.value_coded = ${703} ";
     } else {
-      query = query + "  AND virologic_hiv.pcr_result = ${664}";
+      query = query + " AND oo.value_coded = ${664} ";
     }
 
     StringSubstitutor stringSubstitutor = new StringSubstitutor(map);

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

@@ -33,19 +33,19 @@
   @Autowired private PmtctHeiCohortQueries pmtctHeiCohortQueries;
 
   /**
-   * Construction of the PMTCT - EID dataset
+   * Construction of the PMTCT - HEI dataset
    *
    * @return @{@link DataSetDefinition}
    */
   public DataSetDefinition constructPmtctHeiDataSet() {
     CohortIndicatorDataSetDefinition dsd = new CohortIndicatorDataSetDefinition();
-    dsd.setName("PMTCT-EID Dataset");
+    dsd.setName("PMTCT-HEI Dataset");
     dsd.addParameters(getParameters());
 
     dsd.addDimension(
         "infantAgeInMonths",
         EptsReportUtils.map(
-            eptsCommonDimension.getInfantAgeInMonths(),
+            eptsCommonDimension.getHeiInfantAgeInMonths(),
             "startDate=${startDate},endDate=${endDate},location=${location}"));
 
     dsd.addDimension(
@@ -68,7 +68,7 @@
                 "startDate=${startDate},endDate=${endDate},location=${location}"));
 
     dsd.addColumn(
-        "TOTAL",
+        "HEITOTAL",
         "The PMTCT_HEI numerator reports the number of HIV-exposed infants, with a virologic HIV test result returned in the reporting period, whose diagnostic sample was collected by 12 months of age.",
         EptsReportUtils.map(
             TOTAL, "startDate=${startDate},endDate=${endDate},location=${location}"),

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

@@ -1158,13 +1158,34 @@
     dim.addCohortDefinition(
         "lessThan2Months",
         EptsReportUtils.map(
-            pmtctEidCohortQueries.getInfantAge(0, 59),
+            pmtctEidCohortQueries.getInfantAge(0, 59, true),
             "startDate=${startDate},endDate=${endDate},location=${location}"));
 
     dim.addCohortDefinition(
         "from2To12Months",
         EptsReportUtils.map(
-            pmtctEidCohortQueries.getInfantAge(60, 365),
+            pmtctEidCohortQueries.getInfantAge(60, 365, true),
+            "startDate=${startDate},endDate=${endDate},location=${location}"));
+    return dim;
+  }
+
+  public CohortDefinitionDimension getHeiInfantAgeInMonths() {
+    CohortDefinitionDimension dim = new CohortDefinitionDimension();
+    dim.setName("Infant Age in Number of Days");
+    dim.addParameter(new Parameter("startDate", "startDate", Date.class));
+    dim.addParameter(new Parameter("endDate", "endDate", Date.class));
+    dim.addParameter(new Parameter("location", "location", Location.class));
+
+    dim.addCohortDefinition(
+        "lessThan2Months",
+        EptsReportUtils.map(
+            pmtctEidCohortQueries.getInfantAge(0, 59, false),
+            "startDate=${startDate},endDate=${endDate},location=${location}"));
+
+    dim.addCohortDefinition(
+        "from2To12Months",
+        EptsReportUtils.map(
+            pmtctEidCohortQueries.getInfantAge(60, 365, false),
             "startDate=${startDate},endDate=${endDate},location=${location}"));
     return dim;
   }