Merge pull request #1711 from njorocs/KHP3-2399

Revised clients tested to include only those who had a valid test res…
palladiumkenya · Oct 19, 2023 · eaf2f8b · eaf2f8b
2 parents b772131 + 2478795
commit eaf2f8b
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Showing 3 changed files with 14 additions and 13 deletions.
diff --git a/.../kenyaemr/reporting/cohort/definition/evaluator/HTSRegisterCohortDefinitionEvaluator.java b/.../kenyaemr/reporting/cohort/definition/evaluator/HTSRegisterCohortDefinitionEvaluator.java
@@ -40,7 +40,7 @@ public EncounterQueryResult evaluate(EncounterQuery definition, EvaluationContex
 		context = ObjectUtil.nvl(context, new EvaluationContext());
 		EncounterQueryResult queryResult = new EncounterQueryResult(definition, context);
 
-		String qry = "SELECT encounter_id from kenyaemr_etl.etl_hts_test t inner join person p on p.person_id=t.patient_id and p.voided=0 where t.test_type = 1 and t.voided = 0 and date(t.visit_date) BETWEEN date(:startDate) AND date(:endDate) ; ";
+		String qry = "SELECT encounter_id from kenyaemr_etl.etl_hts_test t inner join person p on p.person_id=t.patient_id and p.voided=0 where t.test_type = 1 and t.final_test_result in ('Positive','Negative') and t.voided = 0 and date(t.visit_date) BETWEEN date(:startDate) AND date(:endDate) ; ";
 
 		SqlQueryBuilder builder = new SqlQueryBuilder();
 		builder.append(qry);

diff --git a/...enyaemr/reporting/library/ETLReports/MOH731Greencard/ETLMoh731GreenCardCohortLibrary.java b/...enyaemr/reporting/library/ETLReports/MOH731Greencard/ETLMoh731GreenCardCohortLibrary.java
@@ -899,8 +899,9 @@ public CohortDefinition htsNumberTested() {
     }
     // HIV testing cohort. includes all those who tested during the reporting period
     public CohortDefinition htsAllNumberTested() {
-        String sqlQuery = "select t.patient_id from kenyaemr_etl.etl_hts_test t inner join kenyaemr_etl.etl_patient_demographics d on d.patient_id = t.patient_id where test_type =1 and t.voided = 0 and t.visit_date between date(:startDate) and date(:endDate)\n" +
-                "group by t.patient_id;";
+        String sqlQuery = "select t.patient_id from kenyaemr_etl.etl_hts_test t inner join kenyaemr_etl.etl_patient_demographics d on d.patient_id = t.patient_id where test_type = 1 and\n" +
+                "    t.final_test_result in ('Positive','Negative') and t.voided = 0 and t.visit_date between date (:startDate) and date (:endDate)\n" +
+                "    group by t.patient_id;";
         SqlCohortDefinition cd = new SqlCohortDefinition();
         cd.setName("htsNumberTested");
         cd.setQuery(sqlQuery);
@@ -934,7 +935,7 @@ public CohortDefinition htsAllNumberTestedAtFacility() {
         String sqlQuery = "select patient_id\n" +
                 "from kenyaemr_etl.etl_hts_test\n" +
                 "WHERE test_type = 1\n" +
-                "  AND setting = 'Facility'\n" +
+                "  AND setting = 'Facility' AND final_test_result in ('Positive','Negative')\n" +
                 "  AND visit_date between date(:startDate) and date(:endDate);";
         SqlCohortDefinition cd = new SqlCohortDefinition();
         cd.setName("htsNumberTestedAtFacility");
@@ -969,7 +970,7 @@ public CohortDefinition htsAllNumberTestedAtCommunity() {
         String sqlQuery = "select patient_id\n" +
                 "FROM kenyaemr_etl.etl_hts_test\n" +
                 "WHERE test_type = 1\n" +
-                "  AND setting = 'Community'\n" +
+                "  AND setting = 'Community' AND final_test_result in ('Positive','Negative')\n" +
                 "  AND visit_date between date(:startDate) and date(:endDate);";
         SqlCohortDefinition cd = new SqlCohortDefinition();
         cd.setName("htsNumberTestedAtCommunity");
@@ -1000,7 +1001,7 @@ protected CohortDefinition htsNumberTestedAsCouple() {
      * @return
      */
     protected CohortDefinition htsAllNumberTestedAsCouple() {
-        String sqlQuery = "select patient_id from kenyaemr_etl.etl_hts_test where test_type =1\n" +
+        String sqlQuery = "select patient_id from kenyaemr_etl.etl_hts_test where test_type =1 AND final_test_result in ('Positive','Negative')\n" +
                 " and client_tested_as ='Couple' and date(visit_date) between date(:startDate) and date(:endDate)";
         SqlCohortDefinition cd = new SqlCohortDefinition();
         cd.setName("htsNumberTestedAsCouple");
@@ -1030,7 +1031,7 @@ protected CohortDefinition htsNumberTestedKeyPopulation() {
      * @return
      */
     protected CohortDefinition htsAllNumberTestedKeyPopulation() {
-        String sqlQuery = "select patient_id from kenyaemr_etl.etl_hts_test where test_type =1 \n" +
+        String sqlQuery = "select patient_id from kenyaemr_etl.etl_hts_test where test_type =1 AND final_test_result in ('Positive','Negative')\n" +
                 " and population_type ='Key Population' and visit_date between date(:startDate) and date(:endDate)";
         SqlCohortDefinition cd = new SqlCohortDefinition();
         cd.setName("htsNumberTestedKeyPopulation");
@@ -1133,7 +1134,7 @@ protected CohortDefinition htsNumberTestedDiscordant() {
      */
     public CohortDefinition htsAllNumberTestedDiscordant() {
         String sqlQuery = "select patient_id from kenyaemr_etl.etl_hts_test where test_type =1\n" +
-                " and couple_discordant ='Yes' and date(visit_date) between date(:startDate) and date(:endDate)";
+                " and couple_discordant ='Yes' and final_test_result in ('Positive','Negative') and date(visit_date) between date(:startDate) and date(:endDate)";
         SqlCohortDefinition cd = new SqlCohortDefinition();
         cd.setName("htsNumberTestedDiscordant");
         cd.setQuery(sqlQuery);
@@ -1364,7 +1365,7 @@ public CohortDefinition htsClientsForTheFirstTimeEver() {
                 "                  patient_id,\n" +
                 "                  visit_date      AS test_date\n" +
                 "                FROM kenyaemr_etl.etl_hts_test\n" +
-                "                WHERE test_type = 1\n" +
+                "                WHERE test_type = 1 and final_test_result in ('Positive','Negative')\n" +
                 "                and ever_tested_for_hiv = 'No'\n" +
                 "                GROUP BY patient_id\n" +
                 "                       having count(patient_id) = 1\n" +
@@ -1388,7 +1389,7 @@ public CohortDefinition htsClientsForTheFirstTimeEver() {
     public CohortDefinition htsClientsWithPreviousTestOver12MonthsAgo() {
         String sqlQuery = "SELECT patient_id\n" +
                 "FROM kenyaemr_etl.etl_hts_test\n" +
-                "WHERE test_type = 1\n" +
+                "WHERE test_type = 1 AND final_test_result in ('Positive','Negative')\n" +
                 "  and ever_tested_for_hiv = 'Yes'\n" +
                 "  and months_since_last_test > 12\n" +
                 "  and date(visit_date) between date(:startDate) and date(:endDate);";
@@ -1427,7 +1428,7 @@ public CohortDefinition htsRepeatTestsMuxEnc() {
                 "                         max(visit_date)      AS latest_test_date,\n" +
                 "                         min(visit_date) AS first_test_date\n" +
                 "                       FROM kenyaemr_etl.etl_hts_test\n" +
-                "                       WHERE test_type = 1\n" +
+                "                       WHERE test_type = 1 AND final_test_result in ('Positive','Negative')\n" +
                 "                       GROUP BY patient_id\n" +
                 "                       having latest_test_date between date(:startDate) and date(:endDate)\n" +
                 "                          and (latest_test_date > first_test_date and timestampdiff(MONTH,first_test_date,latest_test_date) <= 12)\n" +
@@ -1449,7 +1450,7 @@ public CohortDefinition htsRepeatTestsMuxEnc() {
     public CohortDefinition htsRepeatClientReported() {
         String sqlQuery = "SELECT patient_id\n" +
                 "FROM kenyaemr_etl.etl_hts_test\n" +
-                "WHERE test_type = 1\n" +
+                "WHERE test_type = 1 AND final_test_result in ('Positive','Negative')\n" +
                 "  and ever_tested_for_hiv = 'Yes'\n" +
                 "  and months_since_last_test <= 12\n" +
                 "  and date(visit_date) between date(:startDate) and date(:endDate);";

diff --git a/...openmrs/module/kenyaemr/reporting/library/ETLReports/RevisedDatim/DatimCohortLibrary.java b/...openmrs/module/kenyaemr/reporting/library/ETLReports/RevisedDatim/DatimCohortLibrary.java
@@ -6281,7 +6281,7 @@ public CohortDefinition kpPrevOfferedHTSServices() {
     public CohortDefinition kpPrevNewlyTestedOrReferredSql() {
         String sqlQuery = "select a.client_id from (select v.client_id as client_id from (select v.client_id from kenyaemr_etl.etl_clinical_visit v where timestampdiff(MONTH,v.visit_date,date(:endDate)) <3 and v.hiv_tested in ('Yes','Referred for testing'))v\n" +
                 "left join\n" +
-                "    (select t.patient_id from kenyaemr_etl.etl_hts_test t where timestampdiff(MONTH,t.visit_date,date(:endDate)) <3)t on v.client_id = t.patient_id)a group by a.client_id;";
+                "    (select t.patient_id from kenyaemr_etl.etl_hts_test t where t.final_test_result in ('Positive','Negative') and timestampdiff(MONTH,t.visit_date,date(:endDate)) <3)t on v.client_id = t.patient_id)a group by a.client_id;";
         SqlCohortDefinition cd = new SqlCohortDefinition();
         cd.setName("kpPrevNewlyTestedOrReferred");
         cd.setQuery(sqlQuery);