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Cross border report phase II improvements #249

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11825b2
Added pmtct indicators to program monthly enrolment script
jecihjoy Apr 21, 2021
a22b136
Added cross border columns to etl hei datasets
jecihjoy Apr 30, 2021
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81 changes: 77 additions & 4 deletions etl-scripts/stored-procedures/generate_flat_hei_summary_v1_0.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,14 @@ CREATE TABLE IF NOT EXISTS flat_hei_summary (
ovc_non_enrolment_date DATETIME,
ovc_exit_reason INT,
ovc_exit_date DATETIME,
travelled_outside_last_3_months INT,
travelled_outside_last_6_months INT,
travelled_outside_last_12_months INT,
last_cross_boarder_screening_datetime DATETIME,
is_cross_border_country INT,
cross_border_service_offered INT,
is_cross_border INT,
country_of_residence INT,
PRIMARY KEY encounter_id (encounter_id),
INDEX person_date (person_id , encounter_datetime),
INDEX location_id_rtc_date (location_id),
Expand Down Expand Up @@ -225,7 +233,7 @@ SELECT 'created table successfully ...';
set @total_time=0;
set @cycle_number = 0;


while @person_ids_count > 0 do

set @loop_start_time = now();
Expand Down Expand Up @@ -276,7 +284,7 @@ SELECT 'created table successfully ...';
join amrs.location l using (location_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 (21,67,110,111,114,115,116,121,123,154,158,168,186,116,212,214,220)
where t1.encounter_type in (21,67,110,111,114,115,116,121,123,154,158,168,186,116,212,214,220,218)
AND NOT obs regexp "!!5303=703!!"
);

Expand Down Expand Up @@ -820,7 +828,64 @@ SELECT 'created table successfully ...';
when t1.encounter_type = 220 then @ovc_exit_date := encounter_datetime
when @prev_id = @cur_id then @ovc_exit_date
else @ovc_exit_date := null
end as ovc_exit_date
end as ovc_exit_date,

case
when obs regexp "!!11237=1065" then @travelled_outside_last_3_months := 1
when obs regexp "!!11237=1066" then @travelled_outside_last_3_months := 0
when @prev_id = @cur_id then @travelled_outside_last_3_months
else @travelled_outside_last_3_months := null
end as travelled_outside_last_3_months,

case
when obs regexp "!!11238=1065" then @travelled_outside_last_6_months := 1
when obs regexp "!!11238=1066" then @travelled_outside_last_6_months := 0
when @prev_id = @cur_id then @travelled_outside_last_6_months
else @travelled_outside_last_6_months := null
end as travelled_outside_last_6_months,

case
when obs regexp "!!11239=1065" then @travelled_outside_last_12_months := 1
when obs regexp "!!11239=1066" then @travelled_outside_last_12_months := 0
when @prev_id = @cur_id then @travelled_outside_last_12_months
else @travelled_outside_last_12_months := null
end as travelled_outside_last_12_months,

case
when t1.encounter_type = 218 then @last_cross_boarder_screening_datetime := encounter_datetime
when @prev_id = @cur_id then @last_cross_boarder_screening_datetime
else @last_cross_boarder_screening_datetime := null
end as last_cross_boarder_screening_datetime,

case
when @travelled_outside_last_3_months = 1 or @travelled_outside_last_6_months = 1 or @travelled_outside_last_12_months = 1 then @is_cross_border_country := 1
else @is_cross_border_country := 0
end as is_cross_border_country,

case
when obs regexp "!!11243=10739" then @cross_border_service_offered := 10739
when obs regexp "!!11243=10649" then @cross_border_service_offered := 10649
when obs regexp "!!11243=5483" then @cross_border_service_offered := 5483
when obs regexp "!!11243=2050" then @cross_border_service_offered := 2050
when obs regexp "!!11243=11244" then @cross_border_service_offered := 11244
when obs regexp "!!11243=1964" then @cross_border_service_offered := 1964
when obs regexp "!!11243=7913" then @cross_border_service_offered := 7913
when obs regexp "!!11243=5622" then @cross_border_service_offered := 5622
when @prev_id = @cur_id then @cross_border_service_offered
else @cross_border_service_offered := null
end as cross_border_service_offered,

case
when obs regexp "!!11252=11197" then @country_of_residence := 11197
when obs regexp "!!11252=11118" then @country_of_residence := 11118
when @prev_id = @cur_id then @country_of_residence
else @country_of_residence := null
end as country_of_residence,

case
when @is_cross_border_country = 1 then @is_cross_border := 1
else @is_cross_border := 0
end as is_cross_border

from flat_hei_summary_0 t1
join amrs.person p using (person_id)
Expand Down Expand Up @@ -1087,7 +1152,15 @@ SELECT @total_rows_written;
ovc_non_enrolment_reason,
ovc_non_enrolment_date,
ovc_exit_reason,
ovc_exit_date
ovc_exit_date,
travelled_outside_last_3_months,
travelled_outside_last_6_months,
travelled_outside_last_12_months,
last_cross_boarder_screening_datetime,
is_cross_border_country,
cross_border_service_offered,
is_cross_border,
country_of_residence
from flat_hei_summary_4 t1)');

PREPARE s1 from @dyn_sql;
Expand Down
53 changes: 51 additions & 2 deletions etl-scripts/stored-procedures/generate_hei_monthly_report_dataset_v1_0.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,14 @@ CREATE TABLE IF NOT EXISTS hei_monthly_report_dataset (
ovc_non_enrolment_out_of_catchment_area tinyint,
newly_exited_from_ovc_this_month tinyint,
exited_from_ovc_this_month tinyint,
is_cross_border_country_this_month int,
is_cross_border_county_this_month int,
is_cross_border_this_month int,
last_cross_boarder_screening_datetime date,
travelled_outside_last_3_months int,
travelled_outside_last_6_months int,
travelled_outside_last_12_months int,
country_of_residence int,
PRIMARY KEY elastic_id (elastic_id),
INDEX person_enc_date (person_id , encounter_date),
INDEX person_report_date (person_id , endDate),
Expand Down Expand Up @@ -281,7 +289,40 @@ CREATE TABLE IF NOT EXISTS hei_monthly_report_dataset (
case
when t2.ovc_exit_date is not null then 1
else 0
end as exited_from_ovc_this_month
end as exited_from_ovc_this_month,
t2.is_cross_border_country as is_cross_border_country_this_month,

case
when t2.is_cross_border_country = 0 and t2.location_id in (20,19,55,83,12,23,100,130,78,91,106,65,90) and t4.address1 != 'Busia' then @is_cross_border_county_this_month := 1
else @is_cross_border_county_this_month := 0
end as is_cross_border_county_this_month,

IF(t2.is_cross_border_country = 1 or @is_cross_border_county_this_month = 1, 1, 0) as is_cross_border_this_month,

date(t2.last_cross_boarder_screening_datetime) as last_cross_boarder_screening_datetime,

case
when t2.travelled_outside_last_3_months = 1
AND timestampdiff(month,t2.last_cross_boarder_screening_datetime,t1.endDate) <= 3
then 1
else 0
end as travelled_outside_last_3_months,

case
when (t2.travelled_outside_last_6_months = 1 or t2.travelled_outside_last_3_months = 1)
AND timestampdiff(month,t2.last_cross_boarder_screening_datetime,t1.endDate) <= 6
then 1
else 0
end as travelled_outside_last_6_months,

case
when ( t2.travelled_outside_last_12_months = 1 or t2.travelled_outside_last_6_months = 1 or t2.travelled_outside_last_3_months = 1)
AND timestampdiff(month,t2.last_cross_boarder_screening_datetime,t1.endDate) <= 12
then 1
else 0
end as travelled_outside_last_12_months,

t2.country_of_residence

from etl.dates t1
join etl.flat_hei_summary t2
Expand Down Expand Up @@ -392,7 +433,15 @@ FROM
ovc_non_enrolment_declined,
ovc_non_enrolment_out_of_catchment_area,
newly_exited_from_ovc_this_month,
exited_from_ovc_this_month
exited_from_ovc_this_month,
is_cross_border_country_this_month,
is_cross_border_county_this_month,
is_cross_border_this_month,
last_cross_boarder_screening_datetime,
travelled_outside_last_3_months,
travelled_outside_last_6_months,
travelled_outside_last_12_months,
country_of_residence
from hei_monthly_report_dataset_2
);

Expand Down
90 changes: 84 additions & 6 deletions etl-scripts/stored-procedures/generate_patient_monthly_enrollment.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,13 @@ CREATE TABLE if not exists `patient_monthly_enrollment` (
`newly_enrolled_ovc_this_month` int(4) DEFAULT NULL,
`exited_ovc_this_month` int(4) DEFAULT NULL,
`in_ovc_this_month` int(0) DEFAULT NULL,
`pmtct_date_enrolled` datetime DEFAULT NULL,
`pmtct_date_completed` datetime DEFAULT NULL,
`pmtct_location_id` int(11) DEFAULT NULL,
`pmtct_patient_program_id` int(11) DEFAULT '0',
`newly_enrolled_pmtct_this_month` int(4) DEFAULT NULL,
`exited_pmtct_this_month` int(4) DEFAULT NULL,
`in_pmtct_this_month` int(0) DEFAULT NULL,
KEY `person_id` (`person_id`),
KEY `person_id_2` (`person_id`, `endDate`),
KEY `endDate` (`endDate`)
Expand Down Expand Up @@ -197,7 +204,6 @@ while @person_ids_count > 0 do
) p
group by person_id, endDate);
select count(*) from ovc_patient_date_enrollments;
select * from ovc_patient_date_enrollments;

set @prev_id = -1;
set @cur_id = -1;
Expand Down Expand Up @@ -232,7 +238,71 @@ while @person_ids_count > 0 do
ovc_patient_date_enrollments e
);
select count(*) from ovc_patient_enrollments_1;
select * from ovc_patient_enrollments_1;

drop temporary table if exists pmtct_patient_date_enrollments;
create temporary table pmtct_patient_date_enrollments
(index (person_id), index (endDate), UNIQUE e_person_id_date(person_id, endDate))
(
select
person_id,
endDate,
date_enrolled as pmtct_date_enrolled,
date_completed as pmtct_date_completed,
program_id as pmtct_program_id,
location_id as pmtct_location_id,
patient_program_id as pmtct_patient_program_id
from
(select
h.person_id,
d.endDate,
date_enrolled,
date_completed,
patient_program_id,
program_id,
location_id
from
dates d
join
enrollments_in_queue h
WHERE
h.date_enrolled < DATE_ADD(endDate, INTERVAL 1 DAY)
and program_id IN (4)
ORDER BY h.person_id , d.endDate, h.date_enrolled desc
) p
group by person_id, endDate);

set @prev_id = -1;
set @cur_id = -1;
drop temporary table if exists pmtct_patient_enrollments_1;
create temporary table pmtct_patient_enrollments_1
(index (person_id), index (endDate), UNIQUE e_person_id_date(person_id, endDate))
(
select
e.*,
@prev_id := @cur_id AS prev_id,
@cur_id := person_id AS cur_id,
case
when EXTRACT( YEAR_MONTH FROM endDate ) = EXTRACT( YEAR_MONTH FROM pmtct_date_enrolled ) then
@newly_enrolled_pmtct_this_month := 1
else
@newly_enrolled_pmtct_this_month := 0
end as newly_enrolled_pmtct_this_month,
case
when EXTRACT( YEAR_MONTH FROM endDate ) = EXTRACT( YEAR_MONTH FROM pmtct_date_completed ) then
@exited_pmtct_this_month := 1
else
@exited_pmtct_this_month := 0
end as exited_pmtct_this_month,
case
when EXTRACT( YEAR_MONTH FROM pmtct_date_enrolled ) <= EXTRACT( YEAR_MONTH FROM endDate ) and
(!(EXTRACT( YEAR_MONTH FROM pmtct_date_completed ) <= EXTRACT( YEAR_MONTH FROM endDate )) or pmtct_date_completed is null) then
1
else
0
end as in_pmtct_this_month
from
pmtct_patient_date_enrollments e
);

drop temporary table if exists retention_patient_date_enrollments;
create temporary table retention_patient_date_enrollments
Expand Down Expand Up @@ -266,7 +336,6 @@ while @person_ids_count > 0 do
) p
group by person_id, endDate);
select count(*) from retention_patient_date_enrollments;
select * from retention_patient_date_enrollments;

set @prev_id = -1;
set @cur_id = -1;
Expand Down Expand Up @@ -301,15 +370,16 @@ while @person_ids_count > 0 do
retention_patient_date_enrollments e
);
select count(*) from retention_patient_enrollments_1;
select * from retention_patient_enrollments_1;

drop temporary table if exists patient_dates;
create temporary table patient_dates
(index (person_id), index(person_id, endDate), index(endDate))
(select * from
(select person_id, endDate from retention_patient_enrollments_1
union
select person_id, endDate from ovc_patient_enrollments_1) pd
select person_id, endDate from ovc_patient_enrollments_1
union
select person_id, endDate from pmtct_patient_enrollments_1) pd
);

replace into patient_monthly_enrollment
Expand All @@ -330,11 +400,19 @@ while @person_ids_count > 0 do
ovc_patient_program_id,
newly_enrolled_ovc_this_month,
exited_ovc_this_month,
in_ovc_this_month
in_ovc_this_month,
pmtct_date_enrolled,
pmtct_date_completed,
pmtct_location_id,
pmtct_patient_program_id,
newly_enrolled_pmtct_this_month,
exited_pmtct_this_month,
in_pmtct_this_month
from
patient_dates pd
left outer join retention_patient_enrollments_1 re on (pd.person_id = re.person_id and pd.endDate = re.endDate)
left outer join ovc_patient_enrollments_1 ovc on (pd.person_id = ovc.person_id and pd.endDate = ovc.endDate)
left outer join pmtct_patient_enrollments_1 pmtct on (pd.person_id = pmtct.person_id and pd.endDate = pmtct.endDate)
order by pd.person_id, pd.endDate
);

Expand Down