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Merge pull request #1367 from henrykorir/POC-651
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POC-651: Enhancement of DQA Report
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@hiqedme
hiqedme authored Feb 14, 2024
2 parents ad7a876 + 92ecab0 commit 97bd738
Showing 1 changed file with 226 additions and 135 deletions.
361 changes: 226 additions & 135 deletions reports/DQA/dqa-chart-abstraction-report-dao.js
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Original file line number Diff line number Diff line change
Expand Up @@ -26,159 +26,250 @@ export class DQAChartAbstractionDAO {

const limitOffSetDefinition =
limit === 'all' ? '' : `limit ` + limit + ` offset ` + offset;

let sqlQuery =
`
SELECT
h.person_uuid AS uuid,
fpiv.ccc AS ccc_number,
IF((fpiv.nupi IS NOT NULL), fpiv.nupi, 'Missing') AS NUPI,
TIMESTAMPDIFF(year,h.birthdate,'` +
`SELECT
h.person_uuid AS uuid,
fpiv.ccc AS ccc_number,
IF((fpiv.nupi IS NOT NULL),
fpiv.nupi,
'Missing') AS NUPI,
TIMESTAMPDIFF(YEAR,
h.birthdate,
'2023-12-31') AS age,
CASE
WHEN e.tb_screen = 1 THEN 'Yes'
ELSE 'No'
END AS 'tb_screened_this_visit',
CASE
WHEN (h.gender = 'F') THEN 'Female'
WHEN (h.gender = 'M') THEN 'Male'
ELSE 'Missing'
END AS 'sex_gender',
e.height,
e.weight,
DATE_FORMAT(h.birthdate, '%d/%m/%Y') AS birthdate,
h.encounter_id,
DATE_FORMAT(h.encounter_date, '%d/%m/%Y') AS last_appointment_date,
h.rtc_date,
h.location_id,
h.cur_arv_meds,
CASE
WHEN (h.cur_arv_meds_names REGEXP '[[:<:]]DTG[[:>:]]') THEN 'DTG-based'
WHEN (h.cur_arv_meds_names NOT REGEXP '[[:<:]]DTG[[:>:]]') THEN 'Non-DTG-based'
ELSE 'NON DTG'
END AS cur_arv_med_basis,
h.tb_screen,
DATE_FORMAT(h.tb_screening_datetime, '%d/%m/%Y') AS tb_screening_datetime,
CASE
WHEN (e.hiv_start_date <= '1900-01-01') THEN ''
ELSE DATE_FORMAT(e.hiv_start_date, '%d/%m/%Y')
END AS hiv_start_date,
h.arv_start_date,
CASE
WHEN (h.arv_first_regimen_start_date <= '1900-01-01') THEN ''
ELSE DATE_FORMAT(h.arv_first_regimen_start_date,
'%d/%m/%Y')
END AS arv_first_regimen_start_date,
e.cd4_1,
IF((e.cd4_1 IS NOT NULL), 'Yes', 'No') AS has_cd4_1,
DATE_FORMAT(e.encounter_datetime, '%d/%m/%Y') AS last_clinical_encounter,
DATE_FORMAT(h.rtc_date, '%d/%m/%Y') AS next_appointment,
h.vl_1,
CASE
WHEN
(TIMESTAMPDIFF(MONTH,
h.arv_start_date,
'` +
endDate +
`') AS age,
CASE
WHEN e.tb_screen = 1 then 'Yes'
-- WHEN e.tb_screen = 0 then 'No'
ELSE 'No'
END AS 'tb_screened_this_visit',
CASE
WHEN (h.gender = 'F') then 'Female'
WHEN (h.gender = 'M') then 'Male'
ELSE 'Missing'
END AS 'sex_gender',
e.height,
e.weight,
DATE_FORMAT(h.birthdate, '%d/%m/%Y') AS birthdate,
h.encounter_id,
DATE_FORMAT(h.encounter_date, '%d/%m/%Y') AS last_appointment_date,
h.rtc_date,
h.location_id,
h.cur_arv_meds,
CASE
WHEN (h.cur_arv_meds_names regexp '[[:<:]]DTG[[:>:]]') THEN 'DTG-based'
WHEN (h.cur_arv_meds_names NOT regexp '[[:<:]]DTG[[:>:]]') THEN 'Non-DTG-based'
ELSE 'NON DTG'
END as cur_arv_med_basis,
h.tb_screen,
DATE_FORMAT(h.tb_screening_datetime,'%d/%m/%Y') as tb_screening_datetime,
CASE
WHEN (e.hiv_start_date <= '1900-01-01') THEN ''
ELSE DATE_FORMAT(e.hiv_start_date,'%d/%m/%Y')
END as hiv_start_date,
h.arv_start_date,
CASE
WHEN (h.arv_first_regimen_start_date <= '1900-01-01') THEN ''
ELSE DATE_FORMAT(h.arv_first_regimen_start_date,'%d/%m/%Y')
END as arv_first_regimen_start_date,
e.cd4_1,
IF((e.cd4_1 IS NOT NULL), 'Yes', 'No') as has_cd4_1,
DATE_FORMAT(e.encounter_datetime, '%d/%m/%Y') AS last_clinical_encounter,
DATE_FORMAT(h.rtc_date, '%d/%m/%Y') AS next_appointment,
h.vl_1,
CASE
WHEN (TIMESTAMPDIFF(MONTH,h.arv_start_date,'` +
`') < 6)
THEN
'NA'
WHEN (h.vl_1 IS NOT NULL) THEN 'Yes'
ELSE 'Missing'
END AS viral_load_validity,
h.cur_arv_meds_names AS drugs_given,
CASE
WHEN
e.height IS NOT NULL
AND e.weight IS NOT NULL
THEN
e.weight / ((e.height / 100) * (e.height / 100))
ELSE NULL
END AS BMI,
TIMESTAMPDIFF(DAY,
h.encounter_date,
h.rtc_date) AS drugs_duration,
IF(h.ipt_start_date = h.encounter_date,
1,
0) AS ipt_started_this_visit,
DATE_FORMAT(h.ipt_start_date, '%d/%m/%Y') AS last_ipt_start_date,
CASE
WHEN h.on_ipt_this_month = 1 THEN 'Continuing'
WHEN
h.ipt_completion_date IS NULL
AND h.ipt_stop_date IS NOT NULL
THEN
'Discontinued'
WHEN h.ipt_completion_date IS NOT NULL THEN 'INH Completed'
WHEN
(h.on_ipt_this_month = 0
AND h.on_tb_tx_this_month = 0)
THEN
'Missing'
WHEN
((TIMESTAMPDIFF(MONTH,
h.ipt_start_date,
'` +
endDate +
`') < 6 ) THEN 'NA'
WHEN (h.vl_1 is NOT NULL) THEN 'Yes'
ELSE 'Missing'
END AS viral_load_validity,
h.cur_arv_meds_names AS drugs_given,
CASE
WHEN
e.height IS NOT NULL
AND e.weight IS NOT NULL
THEN
e.weight / ((e.height / 100) * (e.height / 100))
ELSE NULL
END AS BMI,
TIMESTAMPDIFF(DAY,
h.encounter_date,
h.rtc_date) AS drugs_duration,
IF(h.ipt_start_date = h.encounter_date,
1,
0) AS ipt_started_this_visit,
DATE_FORMAT(h.ipt_start_date, '%d/%m/%Y') AS last_ipt_start_date,
CASE
WHEN h.on_ipt_this_month = 1 THEN 'Continuing'
WHEN
h.ipt_completion_date IS NULL
AND h.ipt_stop_date IS NOT NULL
THEN
'Discontinued'
WHEN h.ipt_completion_date IS NOT NULL THEN 'INH Completed'
WHEN (h.on_ipt_this_month = 0 AND h.on_tb_tx_this_month = 0) THEN 'Missing'
WHEN ((TIMESTAMPDIFF(MONTH,h.ipt_start_date,'` +
`') < 3)
AND h.on_ipt_this_month = 1)
THEN
'Defaulted'
ELSE 'NA'
END AS tpt_status,
DATE_FORMAT(h.ipt_stop_date, '%d/%m/%Y') AS ipt_stop_date,
DATE_FORMAT(h.ipt_completion_date, '%d/%m/%Y') AS ipt_completion_date,
fv.muac AS muac,
IF(h.ipt_stop_date = h.encounter_date
OR h.ipt_completion_date = h.encounter_date,
1,
0) AS ipt_ended_this_visit,
h.status,
IF((o.value_coded IS NULL), 'No', 'Yes') AS is_crag_screened,
CASE
WHEN (h.vl_1 < 200) THEN 'Yes'
WHEN (h.vl_1 >= 200) THEN 'No'
ELSE 'Missing'
END AS vl_suppression,
CASE
WHEN (e.tb_screening_result IN (6621 , 1118)) THEN 'TB Screening not done'
WHEN (e.tb_screening_result = 6971) THEN 'Presumed TB'
WHEN (e.tb_screening_result IN (6137 , 6176, 10767)) THEN 'TB confirmed'
WHEN (e.tb_screening_result IN (1107 , 10678)) THEN 'No TB signs'
ELSE 'Missing'
END AS tb_screening_result,
CASE
WHEN (p.program_id = 4) THEN 'PMTCT'
WHEN
(TIMESTAMPDIFF(YEAR,
h.birthdate,
'` +
endDate +
`') < 3) AND h.on_ipt_this_month = 1) THEN 'Defaulted'
ELSE 'NA'
END AS tpt_status,
DATE_FORMAT(h.ipt_stop_date,'%d/%m/%Y') as ipt_stop_date,
DATE_FORMAT(h.ipt_completion_date, '%d/%m/%Y') as ipt_completion_date,
fv.muac as muac,
IF(h.ipt_stop_date = h.encounter_date
OR h.ipt_completion_date = h.encounter_date,
1,
0) AS ipt_ended_this_visit,
h.status,
IF((o.value_coded IS NULL), 'No', 'Yes') AS is_crag_screened,
CASE
WHEN (h.vl_1 < 200) THEN 'Yes'
WHEN (h.vl_1 >= 200) THEN 'No'
ELSE 'Missing'
END AS vl_suppression,
CASE
WHEN (e.tb_screening_result IN (6621,1118)) THEN 'TB Screening not done'
WHEN (e.tb_screening_result = 6971) THEN 'Presumed TB'
WHEN (e.tb_screening_result IN (6137, 6176, 10767)) THEN 'TB confirmed'
WHEN (e.tb_screening_result IN (1107 , 10678)) THEN 'No TB signs'
ELSE 'Missing'
END AS tb_screening_result,
CASE
WHEN (p.program_id = 4) THEN 'PMTCT'
WHEN (TIMESTAMPDIFF(YEAR, h.birthdate, '` +
`') < 15)
THEN
'Paeds (0-14yrs)'
WHEN
(TIMESTAMPDIFF(YEAR,
h.birthdate,
'` +
endDate +
`') < 15) THEN 'Paeds (0-14yrs)'
WHEN (TIMESTAMPDIFF(YEAR, h.birthdate, '` +
endDate +
`') >= 15) THEN 'Adults (>15 yrs)'
END AS category
`') >= 15)
THEN
'Adults (>15 yrs)'
END AS category,
CASE
WHEN
o.concept_id = 1109
AND o.value_coded = 916
THEN
'COTRIMOXAZOLE'
WHEN
o.concept_id = 1109
AND o.value_coded = 92
THEN
'DAPSONE'
ELSE NULL
END AS pcp_prophylaxis,
CASE
WHEN o.value_coded IN (916) THEN 'Yes'
ELSE 'No'
END AS ctx_dispensed,
case
WHEN (h.gender = 'M') then 'Not Applicable'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (1170)) then 'SVD'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (1171)) then 'C-Section'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (1172)) then 'Breech'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (5622)) then 'Other'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (1067)) then 'Uknown'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (2167)) then 'Vacuum Assisted'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (2166)) then 'Forceps Delivery'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (6263)) then 'Elective C-Section'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (6442)) then 'Emergency C-Section'
WHEN (h.gender = 'F' AND o.concept_id IN (5630) AND o.value_coded IN (8316)) then 'Vertex Delivery'
ELSE NULL
end as delivery_method,
case
WHEN (h.gender = 'M') then 'Not Applicable'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (1844)) then 'Early Neonatal Mortality'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (48)) then 'Miscarriage'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (46)) then 'Ectopic'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (1993)) then 'Stillbirth'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (1845)) then 'Late Neonatal Mortality'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (5622)) then 'Other'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (1843)) then 'Live Birth'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (6782)) then 'Normal Term Deliver'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (6648)) then 'Preterm Deliery'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (10424)) then 'Macerated Stillbirth'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (10877)) then 'Fresh Stillbirth'
WHEN (h.gender = 'F' AND o.concept_id IN (6224) AND o.value_coded IN (10878)) then 'Spontaneous Abortion'
ELSE NULL
end as pregnancy_outcome,
case
WHEN (h.gender = 'F' AND o.concept_id IN (5630, 6224)
AND o.value_coded IN (1170, 1843)) THEN 'Yes'
WHEN h.gender = 'M' THEN 'Not Applicable'
ELSE null
END as svd_and_live_birth
FROM
etl.hiv_monthly_report_dataset_v1_2 h
LEFT JOIN
etl.flat_hiv_summary_v15b e ON (h.encounter_id = e.encounter_id)
LEFT JOIN
etl.flat_vitals fv ON (e.person_id = fv.person_id)
INNER JOIN
amrs.person t1 ON (h.person_id = t1.person_id)
inner JOIN
etl.flat_patient_identifiers_v1 fpiv ON (t1.person_id = fpiv.patient_id)
LEFT JOIN
amrs.patient_program p ON (p.patient_id = h.person_id
AND p.program_id IN (4)
AND p.date_completed IS NULL
AND p.voided = 0)
LEFT JOIN
amrs.obs o ON (o.encounter_id = e.encounter_id
AND o.person_id = h.person_id
AND o.concept_id in (9812)
AND o.voided = 0
)
etl.hiv_monthly_report_dataset_v1_2 h
LEFT JOIN
etl.flat_hiv_summary_v15b e ON (h.encounter_id = e.encounter_id)
LEFT JOIN
etl.flat_vitals fv ON (e.person_id = fv.person_id)
INNER JOIN
amrs.person t1 ON (h.person_id = t1.person_id)
INNER JOIN
etl.flat_patient_identifiers_v1 fpiv ON (t1.person_id = fpiv.patient_id)
LEFT JOIN
amrs.patient_program p ON (p.patient_id = h.person_id
AND p.program_id IN (4)
AND p.date_completed IS NULL
AND p.voided = 0)
Left JOIN
amrs.obs o ON (o.encounter_id = e.encounter_id
AND o.person_id = h.person_id
AND o.location_id IN (` +
locations +
`)
AND (o.obs_datetime between '` +
startDate +
`'AND '` +
endDate +
`')
AND o.concept_id IN (5630, 6224, 1109, 9812, 1109)
AND o.value_coded in (1170, 1843, 916)
AND o.voided = 0
)
WHERE
h.status = "active" AND
h.status = 'active' AND
h.endDate >= '` +
startDate +
`'
AND h.endDate <= '` +
endDate +
`'
AND h.location_id IN (` +
AND h.location_id IN (` +
locations +
`)
AND ` +
AND ` +
where +
`
GROUP BY
h.person_id
` +
h.person_id
` +
limitOffSetDefinition;

return new Promise((resolve, reject) => {
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