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Index last clinical location and other non synched changes #262

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Index last clinical location and other non synched changes #262

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95 changes: 74 additions & 21 deletions etl-scripts/stored-procedures/build_flat_hiv_summary.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -163,6 +163,10 @@ CREATE TABLE IF NOT EXISTS flat_hiv_summary_v15b (
tb_test_result INT,
tb_test_date DATETIME,
gbv_screening_result INT NULL,
on_modern_contraceptive INT,
modern_contraceptive_reporting_date DATETIME,
continue_on_fp INT,
with_pregnancy_intentions INT,
PRIMARY KEY encounter_id (encounter_id),
INDEX person_date (person_id , encounter_datetime),
INDEX person_uuid (uuid),
Expand All @@ -172,7 +176,9 @@ CREATE TABLE IF NOT EXISTS flat_hiv_summary_v15b (
INDEX location_uuid_rtc_date (location_uuid , rtc_date),
INDEX loc_id_enc_date_next_clinical (location_id , encounter_datetime , next_clinical_datetime_hiv),
INDEX encounter_type (encounter_type),
INDEX date_created (date_created)
INDEX date_created (date_created),
INDEX last_non_transit_location_id_rtc_date (last_non_transit_location_id , rtc_date),
INDEX last_non_transit_location_id_enc_date_next_clinical (last_non_transit_location_id , encounter_datetime , next_clinical_datetime_hiv)
);


Expand Down Expand Up @@ -345,7 +351,7 @@ SELECT @person_ids_count AS 'num patients to sync';
join flat_hiv_summary_build_queue__0 t0 using (person_id)
left join etl.flat_orders t2 using(encounter_id)
left join amrs.visit v on (v.visit_id = t1.visit_id)
where (t1.encounter_type in (1,2,3,4,10,14,15,17,19,22,23,26,32,33,43,47,21,105,106,110,111,112,113,114,116,117,120,127,128,129,138,140,153,154,158,161,162,163,212,214,218,220,225,226)
where (t1.encounter_type in (1,2,3,4,10,14,15,17,19,22,23,26,32,33,43,47,21,105,106,110,111,112,113,114,116,117,120,127,128,129,138,140,153,154,158,161,162,163,212,214,218,220,225,226,253)
or (t1.encounter_type in (186) and (v.visit_type_id not in (80,104) OR v.visit_type_id IS NULL) ))
AND NOT obs regexp "!!5303=(822|664|1067)!!"
AND NOT obs regexp "!!9082=9036!!"
Expand Down Expand Up @@ -523,6 +529,8 @@ SELECT @person_ids_count AS 'num patients to sync';
set @tb_test_result = null;
set @tb_test_date = null;
set @gbv_screening_result = null;
set @gbv_screening_result = null;
set @on_modern_contraceptive = null;



Expand Down Expand Up @@ -1260,7 +1268,7 @@ SELECT @person_ids_count AS 'num patients to sync';
when obs regexp "!!1265=(1256|1850)!!" then @ipt_start_date := encounter_datetime
when obs regexp "!!1265=(1257|981|1406|1849)!!" and @ipt_start_date is null then @ipt_start_date := encounter_datetime
when obs regexp "!!10591=1065" AND obs regexp "!!6984=" then @ipt_start_date := replace(replace((substring_index(substring(obs,locate("!!6984=",obs)),@sep,1)),"!!6984=",""),"!!","")
when obs regexp "!!10591=1065" and obs regexp "!!1190=" then @ipt_start_date := replace(replace((substring_index(substring(obs,locate("!!1190=",obs)),@sep,1)),"!!1190=",""),"!!","")
-- when obs regexp "!!10591=1065" and obs regexp "!!1190=" then @ipt_start_date := replace(replace((substring_index(substring(obs,locate("!!1190=",obs)),@sep,1)),"!!1190=",""),"!!","")
when @cur_id != @prev_id then @ipt_start_date := null
else @ipt_start_date
end as ipt_start_date,
Expand Down Expand Up @@ -1588,37 +1596,78 @@ SELECT @person_ids_count AS 'num patients to sync';
else @condoms_provided_date := null
end as condoms_provided_date,






case
when obs regexp "!!7240=(5275|6220|780|5279|907|6218|6700|6701|5274|9510|9511|9734|9735|6217)!!"
then @modern_contraceptive_method_start_date := date(encounter_datetime)
when obs regexp "!!7240=!!"
then @modern_contraceptive_method_start_date := null
when obs regexp "!!374=(5275|6220|780|5279|907|6218|6700|6701|5274|9510|9511|9734|9735|6217)!!" and obs regexp "!!1190="
when obs regexp "!!374=(5275|6220|780|5279|907|6218|6700|6701|5274|9510|9511|9734|9735|6217)!!" and obs regexp "!!1190="
then @modern_contraceptive_method_start_date := date(replace(replace((substring_index(substring(obs,locate("!!1190=",obs)),@sep,1)),"!!1190=",""),"!!",""))
when obs regexp "!!374=(5275|6220|780|5279|907|6218|6700|6701|5274|9510|9511|9734|9735|6217)!!"
then @modern_contraceptive_method_start_date := date(encounter_datetime)
when obs regexp "!!374=!!"
when obs regexp "!!7240=(5275|6220|780|5279|907|6218|6700|6701|5274|9510|9511|9734|9735|6217)!!" and obs regexp "!!1190="
then @modern_contraceptive_method_start_date := date(replace(replace((substring_index(substring(obs,locate("!!1190=",obs)),@sep,1)),"!!1190=",""),"!!",""))
when obs regexp "!!7240=(5275|6220|780|5279|907|6218|6700|6701|5274|9510|9511|9734|9735|6217)!!"
then @modern_contraceptive_method_start_date := date(encounter_datetime)
when obs regexp "!!374=!!"
then @modern_contraceptive_method_start_date := null
when obs regexp "!!7240=!!"
then @modern_contraceptive_method_start_date := null
when @prev_id = @cur_id then @modern_contraceptive_method_start_date
else @modern_contraceptive_method_start_date := null
end as modern_contraceptive_method_start_date,


case
when obs regexp "!!9738=1066!!" then @contraceptive_method := null
when obs regexp "!!7240=1107!!" then @contraceptive_method := null
when obs regexp "!!7240="
when obs regexp "!!7240=1107!!" or obs regexp "!!374=1107!!" then @contraceptive_method := 1107
when (obs regexp "!!9737=!!" or obs regexp "!!9737=1065!!") and obs regexp "!!7240="
then @contraceptive_method := replace(replace((substring_index(substring(obs,locate("!!7240=",obs)),@sep,1)),"!!7240=",""),"!!","")
when obs regexp "!!374="
then @contraceptive_method := replace(replace((substring_index(substring(obs,locate("!!374=",obs)),@sep,1)),"!!374=",""),"!!","")
when obs regexp "!!9738=1066!!" then @contraceptive_method := 1107
when @prev_id = @cur_id then @contraceptive_method
else @contraceptive_method := null
end as contraceptive_method,

case
when obs regexp "!!374=(5275|6220|780|5279|907|6218|6700|6701|5274|9510|9511|9734|9735|6217|5279|8300)!!"
then @modern_contraceptive_reporting_date := date(encounter_datetime)
when obs regexp "!!7240=(5275|6220|780|5279|907|6218|6700|6701|5274|9510|9511|9734|9735|6217|5279|8300)!!"
then @modern_contraceptive_reporting_date := date(encounter_datetime)
when (obs regexp "!!7240=!!" or obs regexp "!!7240=1107!!")
then @modern_contraceptive_reporting_date := null
when (obs regexp "!!374=!!" or obs regexp "!!374=1107!!")
then @modern_contraceptive_reporting_date := null
when @prev_id = @cur_id then @modern_contraceptive_reporting_date
else @modern_contraceptive_reporting_date := null
end as modern_contraceptive_reporting_date,

case
when obs regexp "!!9737=1066!!" then @continue_fp := 0
when obs regexp "!!9737=1065!!" then @continue_fp := 1
when @prev_id = @cur_id then @continue_fp
else @continue_fp := 0
end as continue_fp,

case
when (@contraceptive_method = 1107 or @contraceptive_method is null) then @on_modern_contraceptive := null
when @contraceptive_method in (6701, 5276) and @continue_fp = 1 and @modern_contraceptive_method_start_date <= date(encounter_datetime) then @on_modern_contraceptive := 1
when @contraceptive_method = 9510 and @continue_fp = 1 and date(encounter_datetime) between @modern_contraceptive_method_start_date and date_add(@modern_contraceptive_method_start_date, interval 3 year)
and date(encounter_datetime) between @modern_contraceptive_reporting_date and date_add(@modern_contraceptive_reporting_date, interval 6 month) then @on_modern_contraceptive := 1
when @contraceptive_method = 9511 and @continue_fp = 1 and date(encounter_datetime) between @modern_contraceptive_method_start_date and date_add(@modern_contraceptive_method_start_date, interval 5 year)
and date(encounter_datetime) between @modern_contraceptive_reporting_date and date_add(@modern_contraceptive_reporting_date, interval 6 month) then @on_modern_contraceptive := 1
when @contraceptive_method in (9734,9735) and @continue_fp = 1 and date(encounter_datetime) between @modern_contraceptive_method_start_date and date_add(@modern_contraceptive_method_start_date, interval 10 year)
and date(encounter_datetime) between @modern_contraceptive_reporting_date and date_add(@modern_contraceptive_reporting_date, interval 6 month) then @on_modern_contraceptive := 1
when @contraceptive_method = 8300 and date(encounter_datetime) between @modern_contraceptive_method_start_date and date_add(@modern_contraceptive_method_start_date, interval 6 month)
and date(encounter_datetime) between @modern_contraceptive_reporting_date and date_add(@modern_contraceptive_reporting_date, interval 3 month) then @on_modern_contraceptive := 1
when @contraceptive_method = 5279 and @continue_fp = 1 and date(encounter_datetime) between @modern_contraceptive_method_start_date and date_add(@modern_contraceptive_method_start_date, interval 3 month) then @on_modern_contraceptive := 1
when @contraceptive_method in (6218,6217) and date(encounter_datetime) <= date(@cur_rtc_date) then @on_modern_contraceptive := 1
when @prev_id = @cur_id and @contraceptive_method in (6701, 5276) then @on_modern_contraceptive
else @on_modern_contraceptive := null
end as on_modern_contraceptive,

case
when obs regexp "!!11887=1065!!" then @with_pregnancy_intentions := 1
when obs regexp "!!6687=11662!!" then @with_pregnancy_intentions := 1
when @prev_id = @cur_id then @with_pregnancy_intentions
else @with_pregnancy_intentions := null
end as with_pregnancy_intentions,

case
when obs regexp "!!2061=1115!!" then @menstruation_status := 1115
Expand Down Expand Up @@ -2172,20 +2221,20 @@ SELECT @person_ids_count AS 'num patients to sync';

case
when obs regexp "!!7015=" then @transfer_in := 1
when prev_clinical_location_id != location_id and (visit_type is null or visit_type not in (23,24,33,124)) and (prev_visit_type is null or prev_visit_type not in (23,24,33)) then @transfer_in := 1
when prev_clinical_location_id != location_id and (visit_type is null or visit_type not in (23,24,33,43,80,119,124,129,118,120,123)) and (prev_visit_type is null or prev_visit_type not in (23,24,33,43,80,119,124,129,118,120,123)) then @transfer_in := 1
else @transfer_in := null
end as transfer_in,

case
when obs regexp "!!7015=" then @transfer_in_date := date(encounter_datetime)
when prev_clinical_location_id != location_id and (visit_type is null or visit_type not in (23,24,33,124)) and (prev_visit_type is null or prev_visit_type not in (23,24,33)) then @transfer_in_date := date(encounter_datetime)
when prev_clinical_location_id != location_id and (visit_type is null or visit_type not in (23,24,33,43,80,119,124,129,118,120,123)) and (prev_visit_type is null or prev_visit_type not in (23,24,33,43,80,119,124,129,118,120,123)) then @transfer_in_date := date(encounter_datetime)
when @cur_id = @prev_id then @transfer_in_date
else @transfer_in_date := null
end transfer_in_date,

case
when obs regexp "!!7015=1287" then @transfer_in_location_id := 9999
when prev_clinical_location_id != location_id and (visit_type is null or visit_type not in (23,24,33,124)) and (prev_visit_type is null or prev_visit_type not in (23,24,33)) then @transfer_in_location_id := cur_clinical_location_id
when prev_clinical_location_id != location_id and (visit_type is null or visit_type not in (23,24,33,43,80,119,124,129,118,120,123)) and (prev_visit_type is null or prev_visit_type not in (23,24,33,43,80,119,124,129,118,120,123)) then @transfer_in_location_id := cur_clinical_location_id
when @cur_id = @prev_id then @transfer_in_location_id
else @transfer_in_location_id := null
end transfer_in_location_id,
Expand Down Expand Up @@ -2377,7 +2426,11 @@ SELECT @total_rows_written;
tb_modality_test,
tb_test_result,
tb_test_date,
gbv_screening_result
gbv_screening_result,
on_modern_contraceptive,
modern_contraceptive_reporting_date,
continue_fp as continue_on_fp,
with_pregnancy_intentions

from flat_hiv_summary_4 t1
join amrs.location t2 using (location_id))');
Expand Down