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Update flat hiv summary script #251

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Update flat hiv summary script #251

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acab587
Update flat hiv summary script
jecihjoy Jun 3, 2021
f420255
GBV screening result and last non transit location indicators
jecihjoy Aug 9, 2021
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91 changes: 75 additions & 16 deletions etl-scripts/stored-procedures/generate_flat_hiv_summary.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ CREATE TABLE IF NOT EXISTS flat_hiv_summary_v15b (
is_transit INT,
is_clinical_encounter INT,
location_id INT,
last_non_transit_location_id INT NULL,
location_uuid VARCHAR(100),
visit_num INT,
mdt_session_number INT,
Expand Down Expand Up @@ -147,7 +148,7 @@ CREATE TABLE IF NOT EXISTS flat_hiv_summary_v15b (
is_cross_border_country INT,
cross_border_service_offered INT,
cross_border_country_travelled INT,
is_cross_border_county INT,
is_cross_border_county INT,
is_cross_border INT,
tb_tx_stop_date DATETIME,
country_of_residence INT,
Expand All @@ -158,6 +159,10 @@ CREATE TABLE IF NOT EXISTS flat_hiv_summary_v15b (
ca_cx_screening_result INT,
ca_cx_screening_result_datetime DATETIME,
ca_cx_screening_datetime DATETIME,
tb_modality_test INT,
tb_test_result INT,
tb_test_date DATETIME,
gbv_screening_result INT NULL,
PRIMARY KEY encounter_id (encounter_id),
INDEX person_date (person_id , encounter_datetime),
INDEX person_uuid (uuid),
Expand All @@ -172,10 +177,10 @@ CREATE TABLE IF NOT EXISTS flat_hiv_summary_v15b (



if(@query_type="build") then
if(@query_type="build") then
select 'BUILDING..........................................';
set @write_table = concat("flat_hiv_summary_temp_",queue_number);
set @queue_table = concat("flat_hiv_summary_build_queue_",queue_number);
set @queue_table = concat("flat_hiv_summary_build_queue_",queue_number);

SET @dyn_sql=CONCAT('Create table if not exists ',@write_table,' like ',@primary_table);
PREPARE s1 from @dyn_sql;
Expand All @@ -189,7 +194,7 @@ CREATE TABLE IF NOT EXISTS flat_hiv_summary_v15b (
DEALLOCATE PREPARE s1;


SET @dyn_sql=CONCAT('delete t1 from flat_hiv_summary_build_queue t1 join ',@queue_table, ' t2 using (person_id);');
SET @dyn_sql=CONCAT('delete t1 from flat_hiv_summary_sync_queue t1 join ',@queue_table, ' t2 using (person_id);');
PREPARE s1 from @dyn_sql;
EXECUTE s1;
DEALLOCATE PREPARE s1;
Expand Down Expand Up @@ -316,7 +321,7 @@ SELECT @person_ids_count AS 'num patients to sync';
t1.obs,
t1.obs_datetimes,

case
case
when t1.encounter_type in (1,2,3,4,10,14,15,17,19,26,32,33,34,47,105,106,112,113,114,117,120,127,128,138,140,153,154,158,162,163,225,226) then 1
when t1.encounter_type in (186) AND v.visit_type_id not in (24,25,80,104) AND v.visit_type_id is NOT NULL then 1
when t1.encounter_type in (158) AND v.visit_type_id not in (104) AND v.visit_type_id is NOT NULL then 1
Expand All @@ -341,7 +346,7 @@ SELECT @person_ids_count AS 'num patients to sync';
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)
or (t1.encounter_type in (186) and v.visit_type_id not in (80,104)))
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 @@ -430,6 +435,7 @@ SELECT @person_ids_count AS 'num patients to sync';
set @ovc_exit_date = null;
set @hiv_start_date = null;
set @cur_location = null;
set @cur_last_non_transit_location_id = null;
set @cur_rtc_date = null;
set @prev_rtc_date = null;
set @med_pickup_rtc_date = null;
Expand Down Expand Up @@ -513,6 +519,10 @@ SELECT @person_ids_count AS 'num patients to sync';
set @ca_cx_screening_result = null;
set @ca_cx_screening_result_datetime = null;
set @ca_cx_screening_datetime = null;
set @tb_modality_test = null;
set @tb_test_result = null;
set @tb_test_date = null;
set @gbv_screening_result = null;



Expand Down Expand Up @@ -587,7 +597,11 @@ SELECT @person_ids_count AS 'num patients to sync';
when @prev_id = @cur_id then @cur_location
else null
end as location_id,

case
when @prev_id = @cur_id and @cur_last_non_transit_location_id is not null and visit_type in (23, 24, 119, 124, 129,43,80,118,120,123) then @cur_last_non_transit_location_id
when location_id then @cur_last_non_transit_location_id := location_id
else null
end as last_non_transit_location_id,
case
when @prev_id=@cur_id and t1.encounter_type not in (5,6,7,8,9,21) then @visit_num:= @visit_num + 1
when @prev_id != @cur_id then @visit_num := 1
Expand Down Expand Up @@ -1810,8 +1824,51 @@ SELECT @person_ids_count AS 'num patients to sync';
when obs regexp "!!10400=1065" then @ca_cx_screening_datetime := encounter_datetime
when @cur_id = @prev_id then @ca_cx_screening_datetime
else @ca_cx_screening_datetime := null
end as ca_cx_screening_datetime

end as ca_cx_screening_datetime,

case
when obs regexp "!!8070=" then @tb_modality_test := 8070
when obs regexp "!!307=" then @tb_modality_test := 307
when obs regexp "!!2311=" then @tb_modality_test := 2311
when obs regexp "!!1506=" then @tb_modality_test := 1506
when obs regexp "!!12=" then @tb_modality_test := 12
when @prev_id = @cur_id then @tb_modality_test
else @tb_modality_test := 0
end as tb_modality_test,

case
when obs regexp "!!8070=" then @tb_test_result :=
replace(replace((substring_index(substring(obs,locate("!!8070=",obs)),@sep,1)),"!!8070=",""),"!!","")
when obs regexp "!!307=" then @tb_test_result :=
replace(replace((substring_index(substring(obs,locate("!!307=",obs)),@sep,1)),"!!307=",""),"!!","")
when obs regexp "!!2311=" then @tb_test_result :=
replace(replace((substring_index(substring(obs,locate("!!2311=",obs)),@sep,1)),"!!2311=",""),"!!","")
when obs regexp "!!1506=" then @tb_test_result :=
replace(replace((substring_index(substring(obs,locate("!!1506=",obs)),@sep,1)),"!!1506=",""),"!!","")
when obs regexp "!!12=" then @tb_test_result :=
replace(replace((substring_index(substring(obs,locate("!!12=",obs)),@sep,1)),"!!12=",""),"!!","")
when @prev_id = @cur_id then @tb_test_result
else @tb_test_result := 0
end as tb_test_result,

case
when obs regexp "!!8070=" then @tb_test_date := date(encounter_datetime)
when obs regexp "!!307=" then @tb_test_date := date(encounter_datetime)
when obs regexp "!!2311=" then @tb_test_date := date(encounter_datetime)
when obs regexp "!!1506=" then @tb_test_date := date(encounter_datetime)
when obs regexp "!!12=" then @tb_test_date := date(encounter_datetime)
when @prev_id = @cur_id then @tb_test_date
else @tb_test_date := null
end as tb_test_date,

case
when obs regexp "!!11866=1065" OR obs regexp "!!11565=1065" OR obs regexp "!!11865=1065" OR obs regexp "!!11855=1065"
OR obs regexp "!!9303=1065" OR obs regexp "!!11867=1065" then @gbv_screening_result := 1
when obs regexp "!!11866=1066" OR obs regexp "!!11565=1066" OR obs regexp "!!11865=1066" OR obs regexp "!!11855=1066"
OR obs regexp "!!9303=1066" OR obs regexp "!!11867=1066" then @gbv_screening_result := 0
when @prev_id = @cur_id then @gbv_screening_result
else @gbv_screening_result := null
end as gbv_screening_result

from flat_hiv_summary_0 t1
join amrs.person p using (person_id)
Expand Down Expand Up @@ -2114,20 +2171,20 @@ 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)) 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 (23,24,33,124)) and (prev_visit_type is null or prev_visit_type not in (23,24,33)) 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)) 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 (23,24,33,124)) and (prev_visit_type is null or prev_visit_type not in (23,24,33)) 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)) 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 (23,24,33,124)) 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 @cur_id = @prev_id then @transfer_in_location_id
else @transfer_in_location_id := null
end transfer_in_location_id,
Expand Down Expand Up @@ -2187,6 +2244,7 @@ SELECT @total_rows_written;
is_transit,
is_clinical_encounter,
location_id,
last_non_transit_location_id,
t2.uuid as location_uuid,
visit_num,
mdt_session_number,
Expand Down Expand Up @@ -2314,7 +2372,11 @@ SELECT @total_rows_written;
ca_cx_screen,
ca_cx_screening_result,
ca_cx_screening_result_datetime,
ca_cx_screening_datetime
ca_cx_screening_datetime,
tb_modality_test,
tb_test_result,
tb_test_date,
gbv_screening_result

from flat_hiv_summary_4 t1
join amrs.location t2 using (location_id))');
Expand Down Expand Up @@ -2408,9 +2470,6 @@ SELECT
' second(s)');

set @end = now();
#if (@query_type="sync") then
#insert into etl.flat_log values (@start,@last_date_created,@table_version,timestampdiff(second,@start,@end));
#end if;
SELECT
CONCAT(@table_version,
' : Time to complete: ',
Expand Down