Skip to content

Commit

Permalink
Refactored hei_immunization name to align with etl
Browse files Browse the repository at this point in the history
  • Loading branch information
njorocs committed Jul 4, 2024
1 parent 3013608 commit 79ea41c
Show file tree
Hide file tree
Showing 8 changed files with 32 additions and 32 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ public EncounterQueryResult evaluate(EncounterQuery definition, EvaluationContex
EncounterQueryResult queryResult = new EncounterQueryResult(definition, context);

String qry = "select i.encounter_id \n" +
"from kenyaemr_etl.etl_hei_immunization i inner join kenyaemr_etl.etl_hei_enrollment e on e.patient_id=i.patient_id\n" +
"from kenyaemr_etl.etl_immunization i inner join kenyaemr_etl.etl_hei_enrollment e on e.patient_id=i.patient_id\n" +
"where e.visit_date between date(:startDate) and (:endDate) ; ";

SqlQueryBuilder builder = new SqlQueryBuilder();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ public class DateOfFullImmunizationDataEvaluator implements EncounterDataEvaluat
public EvaluatedEncounterData evaluate(EncounterDataDefinition definition, EvaluationContext context) throws EvaluationException {
EvaluatedEncounterData c = new EvaluatedEncounterData(definition, context);

String qry = "select encounter_id, NULLIF(date(fully_immunized),'0000-00-00') as immunization_date from kenyaemr_etl.etl_hei_immunization ";
String qry = "select encounter_id, NULLIF(date(fully_immunized),'0000-00-00') as immunization_date from kenyaemr_etl.etl_immunization ";

SqlQueryBuilder queryBuilder = new SqlQueryBuilder();
queryBuilder.append(qry);
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ public EvaluatedEncounterData evaluate(EncounterDataDefinition definition, Evalu

String tableColumn = def.getVaccineTableColumn();

String qry = "select encounter_id, (CASE WHEN :vaccineColumn != '' THEN STR_TO_DATE(:vaccineColumn, '%Y-%m-%d') ELSE NULL END) from kenyaemr_etl.etl_hei_immunization ";
String qry = "select encounter_id, (CASE WHEN :vaccineColumn != '' THEN STR_TO_DATE(:vaccineColumn, '%Y-%m-%d') ELSE NULL END) from kenyaemr_etl.etl_immunization ";

qry = qry.replaceAll(":vaccineColumn", tableColumn);
SqlQueryBuilder queryBuilder = new SqlQueryBuilder();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ public EvaluatedEncounterData evaluate(EncounterDataDefinition definition, Evalu
"\tif(VitaminA_2_yr != '', STR_TO_DATE(VitaminA_2_yr, '%Y/%m/%d'),\"\"),\n" +
"\tif(VitaminA_2_to_5_yr != '', STR_TO_DATE(VitaminA_2_to_5_yr, '%Y/%m/%d'),\"\")\n" +
"\t) as dates\n" +
"from kenyaemr_etl.etl_hei_immunization ";
"from kenyaemr_etl.etl_immunization ";

SqlQueryBuilder queryBuilder = new SqlQueryBuilder();
queryBuilder.append(qry);
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ public class VaccinatedAgainstInfluenzaDataEvaluator implements PersonDataEvalua

public EvaluatedPersonData evaluate(PersonDataDefinition definition, EvaluationContext context) throws EvaluationException {
EvaluatedPersonData c = new EvaluatedPersonData(definition, context);
String qry = "select i.patient_id, if(timestampdiff(YEAR, DATE(i.influenza), DATE(:endDate)) <= 12, 'Y','N') as is_vaccinated from kenyaemr_etl.etl_hei_immunization i;";
String qry = "select i.patient_id, if(timestampdiff(YEAR, DATE(i.influenza), DATE(:endDate)) <= 12, 'Y','N') as is_vaccinated from kenyaemr_etl.etl_immunization i;";
SqlQueryBuilder queryBuilder = new SqlQueryBuilder();
queryBuilder.append(qry);
Date startDate = (Date)context.getParameterValue("startDate");
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ public EvaluatedEncounterData evaluate(EncounterDataDefinition definition, Evalu
String qry = "select v.encounter_id,\n" +
" if(m.fully_immunized = 1065,'Y','N') as fully_immunized\n" +
"from kenyaemr_etl.etl_clinical_encounter v\n" +
" INNER JOIN kenyaemr_etl.etl_hei_immunization m ON v.patient_id = m.patient_id\n" +
" INNER JOIN kenyaemr_etl.etl_immunization m ON v.patient_id = m.patient_id\n" +
" and date(v.visit_date) between date(:startDate) and date(:endDate);";

SqlQueryBuilder queryBuilder = new SqlQueryBuilder();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2648,7 +2648,7 @@ public CohortDefinition knownExposureAtPenta1(){
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select distinct he.patient_id\n" +
"from kenyaemr_etl.etl_hei_enrollment he\n" +
" inner join kenyaemr_etl.etl_hei_immunization hi on hi.patient_id=he.patient_id\n" +
" inner join kenyaemr_etl.etl_immunization hi on hi.patient_id=he.patient_id\n" +
"where date(hi.visit_date) between (:startDate) and (:endDate)\n" +
" and he.child_exposed != 1067 AND\n" +
" hi.PCV_10_1 = \"Yes\" ;";
Expand All @@ -2668,7 +2668,7 @@ public CohortDefinition totalGivenPenta1(){
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select distinct he.patient_id\n" +
" from kenyaemr_etl.etl_hei_enrollment he\n" +
" inner join kenyaemr_etl.etl_hei_immunization hi on hi.patient_id=he.patient_id\n" +
" inner join kenyaemr_etl.etl_immunization hi on hi.patient_id=he.patient_id\n" +
" where date(hi.visit_date) between (:startDate) and (:endDate)\n" +
" and hi.PCV_10_1 = \"Yes\" ;";

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -918,7 +918,7 @@ public CohortDefinition vaccinatedBetweenDates() {
/*Given BCG*/
public CohortDefinition givenBCGVaccineCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.BCG) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.BCG) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("BCG");
cd.setQuery(sqlQuery);
Expand All @@ -932,7 +932,7 @@ public CohortDefinition givenBCGVaccineCl() {
/*Given OPV at birth*/
public CohortDefinition givenOPVCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.OPV_birth) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.OPV_birth) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("OPV-0");
cd.setQuery(sqlQuery);
Expand All @@ -946,7 +946,7 @@ public CohortDefinition givenOPVCl() {
/*Given OPV 1*/
public CohortDefinition givenOPV1Cl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.OPV_1) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.OPV_1) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("OPV-1");
cd.setQuery(sqlQuery);
Expand All @@ -960,7 +960,7 @@ public CohortDefinition givenOPV1Cl() {
/*Given OPV 2*/
public CohortDefinition givenOPV2Cl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.OPV_2) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.OPV_2) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("OPV-2");
cd.setQuery(sqlQuery);
Expand All @@ -974,7 +974,7 @@ public CohortDefinition givenOPV2Cl() {
/*Given OPV 3*/
public CohortDefinition givenOPV3Cl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.OPV_3) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.OPV_3) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("OPV-3");
cd.setQuery(sqlQuery);
Expand All @@ -988,7 +988,7 @@ public CohortDefinition givenOPV3Cl() {
/*Given IPV*/
public CohortDefinition givenIpvCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.IPV) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.IPV) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("IPV");
cd.setQuery(sqlQuery);
Expand All @@ -1002,7 +1002,7 @@ public CohortDefinition givenIpvCl() {
/*Given Dpt-Hep-Hib 1*/
public CohortDefinition givenDptHepHibVaccine1Cl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.DPT_Hep_B_Hib_1) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.DPT_Hep_B_Hib_1) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("DHH-1");
cd.setQuery(sqlQuery);
Expand All @@ -1016,7 +1016,7 @@ public CohortDefinition givenDptHepHibVaccine1Cl() {
/*Given Dpt-Hep-Hib 2*/
public CohortDefinition givenDptHepHibVaccine2Cl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.DPT_Hep_B_Hib_2) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.DPT_Hep_B_Hib_2) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("DHH-2");
cd.setQuery(sqlQuery);
Expand All @@ -1030,7 +1030,7 @@ public CohortDefinition givenDptHepHibVaccine2Cl() {
/*Given Dpt-Hep-Hib 3*/
public CohortDefinition givenDptHepHibVaccine3Cl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.DPT_Hep_B_Hib_3) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.DPT_Hep_B_Hib_3) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("DHH-3");
cd.setQuery(sqlQuery);
Expand All @@ -1044,7 +1044,7 @@ public CohortDefinition givenDptHepHibVaccine3Cl() {
/*Given Pneumococcal 1*/
public CohortDefinition givenPneumococcal1VaccineCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.PCV_10_1) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.PCV_10_1) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("PCV-1");
cd.setQuery(sqlQuery);
Expand All @@ -1058,7 +1058,7 @@ public CohortDefinition givenPneumococcal1VaccineCl() {
/*Given Pneumococcal 2*/
public CohortDefinition givenPneumococcal2VaccineCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.PCV_10_2) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.PCV_10_2) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("PCV-2");
cd.setQuery(sqlQuery);
Expand All @@ -1072,7 +1072,7 @@ public CohortDefinition givenPneumococcal2VaccineCl() {
/*Given Pneumococcal 3*/
public CohortDefinition givenPneumococcal3VaccineCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.PCV_10_3) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.PCV_10_3) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("PCV-3");
cd.setQuery(sqlQuery);
Expand All @@ -1086,7 +1086,7 @@ public CohortDefinition givenPneumococcal3VaccineCl() {
/*Given Rota 1 vaccine*/
public CohortDefinition givenRota1VirusVaccineCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.ROTA_1) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.ROTA_1) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("ROTA-1");
cd.setQuery(sqlQuery);
Expand All @@ -1100,7 +1100,7 @@ public CohortDefinition givenRota1VirusVaccineCl() {
/*Given Rota 2 vaccine*/
public CohortDefinition givenRota2VirusVaccineCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.ROTA_2) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.ROTA_2) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("ROTA-2");
cd.setQuery(sqlQuery);
Expand All @@ -1114,7 +1114,7 @@ public CohortDefinition givenRota2VirusVaccineCl() {
/*Given Rota 3 vaccine*/
public CohortDefinition givenRota3VirusVaccineCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.ROTA_3) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.ROTA_3) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("ROTA-3");
cd.setQuery(sqlQuery);
Expand All @@ -1128,7 +1128,7 @@ public CohortDefinition givenRota3VirusVaccineCl() {
/*Given Vitamin A at 6 Months*/
public CohortDefinition givenVitAAt6MAgeCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.VitaminA_6_months) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.VitaminA_6_months) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("VA6M");
cd.setQuery(sqlQuery);
Expand All @@ -1142,7 +1142,7 @@ public CohortDefinition givenVitAAt6MAgeCl() {
/*Given Yellow Fever vaccine*/
public CohortDefinition givenYellowFeverVaccineCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id,i.Measles_rubella_1 from kenyaemr_etl.etl_hei_immunization i where date(i.Yellow_fever) between date(:startDate) and date(:endDate);";
String sqlQuery = "select i.patient_id,i.Measles_rubella_1 from kenyaemr_etl.etl_immunization i where date(i.Yellow_fever) between date(:startDate) and date(:endDate);";

cd.setName("YF");
cd.setQuery(sqlQuery);
Expand All @@ -1156,7 +1156,7 @@ public CohortDefinition givenYellowFeverVaccineCl() {
/*Given Measles-Rubella 1 vaccine*/
public CohortDefinition givenMeaslesRubella1VaccineCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.Measles_rubella_1) between date(:startDate) and date(:endDate);";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.Measles_rubella_1) between date(:startDate) and date(:endDate);";

cd.setName("MR-1");
cd.setQuery(sqlQuery);
Expand All @@ -1170,7 +1170,7 @@ public CohortDefinition givenMeaslesRubella1VaccineCl() {
/*Fully immunized child*/
public CohortDefinition fullyImmunizedCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.fully_immunized) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.fully_immunized) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("FIC");
cd.setQuery(sqlQuery);
Expand All @@ -1184,7 +1184,7 @@ public CohortDefinition fullyImmunizedCl() {
/*Given Vitamin A at 1 years (200,000IU)*/
public CohortDefinition givenVitAAt12MonthsCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.VitaminA_1_yr) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.VitaminA_1_yr) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("VA-1Y");
cd.setQuery(sqlQuery);
Expand All @@ -1198,7 +1198,7 @@ public CohortDefinition givenVitAAt12MonthsCl() {
/*Given Vitamin A at 2 years to 5 years (200,000IU)*/
public CohortDefinition givenVitAAt18MonthsCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.VitaminA_1_and_half_yr) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.VitaminA_1_and_half_yr) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("VA-2Y-5Y");
cd.setQuery(sqlQuery);
Expand All @@ -1212,7 +1212,7 @@ public CohortDefinition givenVitAAt18MonthsCl() {
/*Given Measles - Rubella 2(at 1 1/2 - 2 years)*/
public CohortDefinition givenVitAAt2To5YearsCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.VitaminA_2_to_5_yr) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.VitaminA_2_to_5_yr) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("MR-2-1.5Y>2Y");
cd.setQuery(sqlQuery);
Expand All @@ -1226,7 +1226,7 @@ public CohortDefinition givenVitAAt2To5YearsCl() {
/*Measles - Rubella 2(at 1 1/2 - 2 years)*/
public CohortDefinition givenMeaslesRubella2VaccineAge18To24MonthsCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.Measles_rubella_2) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.Measles_rubella_2) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("MR-2-1.5Y>2Y");
cd.setQuery(sqlQuery);
Expand All @@ -1240,7 +1240,7 @@ public CohortDefinition givenMeaslesRubella2VaccineAge18To24MonthsCl() {
/*Measles-Rubella 2 Above 2 years*/
public CohortDefinition givenMeaslesRubellaVaccine2AndAgedOver2YearsCl() {
SqlCohortDefinition cd = new SqlCohortDefinition();
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_hei_immunization i where date(i.Measles_rubella_2) between date(:startDate) and date(:endDate) group by i.patient_id;";
String sqlQuery = "select i.patient_id from kenyaemr_etl.etl_immunization i where date(i.Measles_rubella_2) between date(:startDate) and date(:endDate) group by i.patient_id;";

cd.setName("MR-2->2Y");
cd.setQuery(sqlQuery);
Expand Down

0 comments on commit 79ea41c

Please sign in to comment.