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POC-341: Revise Patient Requiring Viral Order report to Generate the … #1304

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0971b81
POC-341: Revise Patient Requiring Viral Order report to Generate the …
Alfred-Mutai Aug 2, 2023
312ecee
POC-341: Patients requiring VL
Alfred-Mutai Aug 10, 2023
da02f2d
Merge branch 'AMPATH:master' into POC-341
Alfred-Mutai Jan 19, 2024
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2 changes: 1 addition & 1 deletion app/reporting-framework/json-reports/clinical-reminder-report.json
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Expand Up @@ -134,7 +134,7 @@
"alias": "needs_vl_coded",
"expressionType": "simple_expression",
"expressionOptions": {
"expression": "CASE WHEN (ls.cur_arv_meds IS NULL) THEN 0 WHEN (TIMESTAMPDIFF(MONTH, ls.vl_1_date, DATE('{referenceDate}')) > 3) AND ls.vl_1 > 1000 AND ls.arv_start_date < ls.vl_1_date THEN 1 WHEN ls.vl_1 > 200 AND (TIMESTAMPDIFF(MONTH,ls.vl_1_date,DATE('{referenceDate}')) > 3) THEN 2 WHEN (TIMESTAMPDIFF(MONTH, ls.arv_start_date, '{referenceDate}') >= 12) AND (ls.vl_2 IS NULL) THEN 3 WHEN (ls.is_pregnant OR (t6.relationship = 2 AND TIMESTAMPDIFF(MONTH, t6.date_created, '{referenceDate}') BETWEEN 0 AND 24)) AND (TIMESTAMPDIFF(MONTH, ls.vl_1_date, '{referenceDate}') >= 6) THEN 4 WHEN (t1.is_pregnant OR (t6.relationship = 2 AND TIMESTAMPDIFF(MONTH, t6.date_created, '{referenceDate}') BETWEEN 0 AND 24)) AND ls.vl_1 >= 200 AND (TIMESTAMPDIFF(MONTH, ls.vl_1_date, '{referenceDate}') >= 3) THEN 5 WHEN (TIMESTAMPDIFF(MONTH, ls.arv_start_date, '{referenceDate}') = 3) AND (ls.vl_1_date IS NULL) THEN 6 WHEN (ls.cur_arv_meds <> ls.prev_arv_meds) AND ls.prev_arv_meds IS NOT NULL THEN 7 WHEN ls.vl_1 < 200 AND (TIMESTAMPDIFF(MONTH, ls.vl_1_date, DATE('{referenceDate}')) >= 12) THEN 8 ELSE 0 END"
"expression": "CASE WHEN (ls.cur_arv_meds IS NULL) THEN 0 WHEN (TIMESTAMPDIFF(MONTH, ls.vl_1_date, DATE('{referenceDate}')) > 3) AND ls.vl_1 > 1000 AND ls.arv_start_date < ls.vl_1_date THEN 1 WHEN ls.vl_1 > 200 AND (TIMESTAMPDIFF(MONTH,ls.vl_1_date,DATE('{referenceDate}')) > 3) THEN 2 WHEN (TIMESTAMPDIFF(MONTH, ls.arv_start_date, '{referenceDate}') >= 12) AND (ls.vl_2 IS NULL) THEN 3 WHEN (ls.is_pregnant OR (t6.relationship = 2 AND TIMESTAMPDIFF(MONTH, t6.date_created, '{referenceDate}') BETWEEN 0 AND 24)) AND (TIMESTAMPDIFF(MONTH, ls.vl_1_date, '{referenceDate}') >= 6) THEN 4 WHEN (t1.is_pregnant OR (t6.relationship = 2 AND TIMESTAMPDIFF(MONTH, t6.date_created, '{referenceDate}') BETWEEN 0 AND 24)) AND ls.vl_1 >= 200 AND (TIMESTAMPDIFF(MONTH, ls.vl_1_date, '{referenceDate}') >= 3) THEN 5 WHEN (TIMESTAMPDIFF(MONTH, ls.arv_start_date, '{referenceDate}') = 3) AND (ls.vl_1_date IS NULL) THEN 6 WHEN (ls.cur_arv_meds <> ls.prev_arv_meds) AND ls.prev_arv_meds IS NOT NULL AND TIMESTAMPDIFF(MONTH, ls.encounter_datetime, DATE('{referenceDate}')) >= 3 THEN 7 WHEN ls.vl_1 < 200 AND (TIMESTAMPDIFF(MONTH, ls.vl_1_date, DATE('{referenceDate}')) >= 12) THEN 8 ELSE 0 END"
}
},
{
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12 changes: 2 additions & 10 deletions app/reporting-framework/json-reports/differentiated-care-program-base.json
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Expand Up @@ -11,18 +11,10 @@
},
{
"table": "(SELECT fli.person_id, fli.hiv_viral_load as vl_1, fli.test_datetime as vl_1_date FROM etl.flat_labs_and_imaging fli INNER JOIN (SELECT person_id, MAX(test_datetime) AS max_vl_1_date FROM etl.flat_labs_and_imaging fli where fli.hiv_viral_load is not null GROUP BY person_id) max_dates ON fli.person_id = max_dates.person_id AND fli.test_datetime = max_dates.max_vl_1_date and fli.hiv_viral_load is not null)",
"alias": "fli_latest_vl",
"alias": "fli1",
"join": {
"type": "LEFT",
"joinCondition": "fli_latest_vl.person_id = dcr.person_id"
}
},
{
"table": "etl.flat_patient_identifiers_v1",
"alias": "flat_identifiers",
"join": {
"type": "LEFT",
"joinCondition": "dcr.person_id = flat_identifiers.patient_id"
"joinCondition": "fli1.person_id = dcr.person_id"
}
}
],
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2 changes: 1 addition & 1 deletion app/reporting-framework/json-reports/labs-report-aggregate.json
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Expand Up @@ -72,7 +72,7 @@
{
"filterType": "tableColumns",
"conditionExpression": "(t1.next_clinical_datetime_hiv is null or date(t1.next_clinical_datetime_hiv) > ?)",
"parameterName": "endDate"
"parameterName": "reportMonth"
},
{
"filterType": "tableColumns",
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98 changes: 28 additions & 70 deletions app/reporting-framework/json-reports/labs-report-base.json
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Expand Up @@ -7,70 +7,46 @@
"sources": [
{
"table": "etl.flat_hiv_summary_v15b",
"alias": "t2"
"alias": "fhs"
},
{
"table": "etl.flat_patient_identifiers_v1",
"alias": "flat_identifiers",
"join": {
"type": "LEFT",
"joinCondition": "t2.person_id = flat_identifiers.patient_id"
}
},
{
"table": "amrs.location",
"alias": "l",
"table": "(SELECT a.person_id, MAX(encounter_id) AS max_encounter_id FROM etl.flat_hiv_summary_v15b a LEFT JOIN amrs.person p ON p.person_id = a.person_id WHERE p.dead = 0 and p.birthdate is not null GROUP BY a.person_id)",
"alias": "max_encounters",
"join": {
"type": "INNER",
"joinCondition": "t2.location_uuid = l.uuid"
"joinCondition": "fhs.person_id = max_encounters.person_id AND fhs.encounter_id = max_encounters.max_encounter_id"
}
},
{
"table": "amrs.person",
"alias": "t3",
"alias": "p",
"join": {
"type": "INNER",
"joinCondition": "t3.person_id = t2.person_id"
"joinCondition": "p.person_id = fhs.person_id"
}
},
{
"table": "amrs.person_attribute",
"alias": "contacts",
"join": {
"type": "LEFT",
"joinCondition": "t2.person_id = contacts.person_id AND (contacts.voided IS NULL || contacts.voided = 0) AND contacts.person_attribute_type_id in (10, 48)"
}
},
{
"table": "amrs.encounter_type",
"alias": "et",
"table": "etl.flat_patient_identifiers_v1",
"alias": "flat_identifiers",
"join": {
"type": "LEFT",
"joinCondition": "t2.encounter_type = et.encounter_type_id"
"joinCondition": "fhs.person_id = flat_identifiers.patient_id"
}
},
{
"table": "amrs.person_address",
"alias": "pa",
"table": "amrs.location",
"alias": "l",
"join": {
"type": "LEFT",
"joinCondition": "t2.person_id = pa.person_id"
"type": "INNER",
"joinCondition": "fhs.location_uuid = l.uuid"
}
}
],
"columns": [
{
"type": "simple_column",
"alias": "person_id",
"column": "t2.person_id"
},
{
"type": "derived_column",
"alias": "needs_vl_in_period",
"expressionType": "simple_expression",
"expressionOptions": {
"expression": "if(case when (t2.cur_arv_meds is not null and t2.vl_1 > 1000) and (timestampdiff(day,t2.vl_1_date, '{endDate}') >= 90) then true when (timestampdiff(month,t2.arv_start_date, '{endDate}') <= 12) and (t2.vl_1_date is null or timestampdiff(month,t2.vl_1_date, '{endDate}') >= 6) and (timestampdiff(month,t2.arv_start_date, '{endDate}')>=6) then true when (timestampdiff(month,t2.arv_start_date, '{endDate}') >= 12) and (t2.vl_1_date is null or timestampdiff(month,t2.vl_1_date, '{endDate}') >= 12) then true else false end,1,0)"
}
"column": "fhs.person_id"
},
{
"type": "simple_column",
Expand All @@ -89,80 +65,62 @@
},
{
"type": "simple_column",
"alias": "location",
"column": "l.name"
"alias": "location_id",
"column": "fhs.location_id"
},
{
"type": "simple_column",
"alias": "location_id",
"column": "t2.location_id"
"alias": "location",
"column": "l.name"
},
{
"type": "simple_column",
"alias": "location_uuid",
"column": "t2.location_uuid"
"column": "fhs.location_uuid"
},
{
"type": "simple_column",
"alias": "encounter_datetime",
"column": "t2.encounter_datetime"
"column": "fhs.encounter_datetime"
},
{
"type": "simple_column",
"alias": "month",
"column": "MONTH(t2.encounter_datetime)"
"column": "MONTH(fhs.encounter_datetime)"
},
{
"type": "simple_column",
"alias": "reporting_month",
"column": "date_format(t2.encounter_datetime, '%m/%Y')"
"column": "date_format(fhs.encounter_datetime, '%m/%Y')"
},
{
"type": "simple_column",
"alias": "year",
"column": "YEAR(t2.encounter_datetime)"
},
{
"type": "derived_column",
"alias": "phone_number",
"expressionType": "simple_expression",
"expressionOptions": {
"expression": " GROUP_CONCAT(DISTINCT contacts.value SEPARATOR ', ')"
}
"column": "YEAR(fhs.encounter_datetime)"
},
{
"type": "simple_column",
"alias": "latest_rtc_date",
"column": "date_format(t2.rtc_date, '%Y-%m-%d')"
},
{
"type": "simple_column",
"alias": "last_appointment",
"column": "CONCAT(COALESCE(DATE_FORMAT(t2.encounter_datetime, '%Y-%m-%d'),''),' ',COALESCE(et.name, ''))"
"column": "date_format(fhs.rtc_date, '%Y-%m-%d')"
},
{
"type": "simple_column",
"alias": "cur_meds",
"column": "t2.cur_arv_meds"
"column": "fhs.cur_arv_meds"
}
],
"filters": {
"conditionJoinOperator": "and",
"conditions": [
{
"filterType": "tableColumns",
"conditionExpression": "(t2.next_clinical_datetime_hiv is null or date(t2.next_clinical_datetime_hiv) > ?)",
"parameterName": "endDate"
},
{
"filterType": "tableColumns",
"conditionExpression": "t2.location_uuid in ?",
"conditionExpression": "fhs.location_uuid in ? AND fhs.transfer_out is null AND fhs.out_of_care is null",
"parameterName": "locationUuids"
},
{
"filterType": "tableColumns",
"conditionExpression": "coalesce(t2.death_date, t2.out_of_care) is null",
"parameterName": ""
"conditionExpression": "(TIMESTAMPDIFF(YEAR, p.birthdate, DATE('{reportMonth}')) BETWEEN 0 AND 24 AND ((TIMESTAMPDIFF(MONTH, fhs.arv_start_date, DATE('{reportMonth}')) >= 3 AND fhs.vl_1 IS NULL AND fhs.arv_start_date) OR (TIMESTAMPDIFF(MONTH, fhs.vl_1_date, '{reportMonth}') >= 6 AND fhs.vl_1 IS NOT NULL AND fhs.vl_1_date IS NOT NULL))) OR (TIMESTAMPDIFF(YEAR, p.birthdate, DATE('{reportMonth}')) >= 25 AND ((TIMESTAMPDIFF(MONTH, fhs.arv_start_date, DATE('{reportMonth}')) >= 3 AND fhs.arv_start_date IS NOT NULL AND fhs.vl_1 IS NULL) OR (TIMESTAMPDIFF(MONTH, fhs.arv_start_date, DATE('{reportMonth}')) >= 12 AND fhs.arv_start_date IS NOT NULL AND fhs.vl_1 IS NOT NULL AND fhs.vl_2 IS NULL) OR (TIMESTAMPDIFF(MONTH, fhs.vl_1_date, DATE('{reportMonth}')) >= 12 AND fhs.vl_1 IS NOT NULL AND fhs.vl_2 IS NOT NULL AND fhs.vl_1_date IS NOT NULL AND fhs.vl_1 < 200) OR (TIMESTAMPDIFF(MONTH, fhs.vl_1_date, DATE('{reportMonth}')) >= 3 AND fhs.vl_1 IS NOT NULL AND fhs.vl_2 IS NOT NULL AND fhs.vl_1_date IS NOT NULL AND fhs.vl_1 >= 200) OR ((fhs.is_pregnant = 1 OR fhs.is_mother_breastfeeding = 1) AND TIMESTAMPDIFF(MONTH, fhs.vl_1_date, DATE('{reportMonth}')) >= 6 AND fhs.vl_1_date IS NOT NULL))) OR (fhs.prev_arv_meds <> fhs.cur_arv_meds AND TIMESTAMPDIFF(MONTH, fhs.encounter_datetime, DATE('{reportMonth}')) >= 3)",
"parameterName": "reportMonth"
}
]
}
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44 changes: 18 additions & 26 deletions app/reporting-framework/json-reports/patients-requiring-viral-load-template.json
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Expand Up @@ -12,7 +12,7 @@
"table": "amrs.person_name",
"alias": "person_name",
"join": {
"type": "INNER",
"type": "LEFT",
"joinCondition": "t1.person_id = person_name.person_id AND (person_name.voided IS NULL || person_name.voided = 0) AND person_name.preferred = 1"
}
},
Expand All @@ -32,20 +32,12 @@
"joinCondition": "t1.person_id = contact.person_id AND (contact.voided IS NULL || contact.voided = 0) AND contact.person_attribute_type_id in (10, 48)"
}
},
{
"table": "etl.flat_hiv_summary_v15b",
"alias": "fhsh",
"join": {
"type": "LEFT",
"joinCondition": "t1.person_id = fhsh.person_id AND fhsh.next_clinical_location_id IS NULL AND fhsh.encounter_type NOT IN (99999) "
}
},
{
"table": "amrs.encounter_type",
"alias": "ety",
"join": {
"type": "LEFT",
"joinCondition": "fhsh.encounter_type = ety.encounter_type_id"
"joinCondition": "fhs.encounter_type = ety.encounter_type_id"
}
},
{
Expand Down Expand Up @@ -107,39 +99,39 @@
"alias": "has_pending_vl_test",
"expressionType": "simple_expression",
"expressionOptions": {
"expression": "case when (timestampdiff(day,t2.vl_order_date,now()) between 0 and 14) and (t2.vl_1_date is null or t2.vl_order_date > t2.vl_1_date) then true else false end"
"expression": "case when (timestampdiff(day,fhs.vl_order_date,now()) between 0 and 14) and (fhs.vl_1_date is null or fhs.vl_order_date > fhs.vl_1_date) then true else false end"
}
},
{
"type": "derived_column",
"alias": "current_vl",
"expressionType": "simple_expression",
"expressionOptions": {
"expression": "t2.vl_1 "
"expression": "fhs.vl_1 "
}
},
{
"type": "derived_column",
"alias": "current_vl_date",
"expressionType": "simple_expression",
"expressionOptions": {
"expression": "date_format(t2.vl_1_date,'%d-%m-%Y')"
"expression": "date_format(fhs.vl_1_date,'%d-%m-%Y')"
}
},
{
"type": "derived_column",
"alias": "last_vl_order_date",
"expressionType": "simple_expression",
"expressionOptions": {
"expression": "date_format(t2.vl_order_date,'%d-%m-%Y')"
"expression": "date_format(fhs.vl_order_date,'%d-%m-%Y')"
}
},
{
"type": "derived_column",
"alias": "days_since_last_order",
"expressionType": "simple_expression",
"expressionOptions": {
"expression": "timestampdiff(day, t2.vl_order_date, now())"
"expression": "timestampdiff(day, fhs.vl_order_date, now())"
}
},
{
Expand All @@ -153,12 +145,12 @@
{
"type": "simple_column",
"alias": "latest_rtc_date",
"column": "date_format(fhsh.rtc_date, '%Y-%m-%d')"
"column": "date_format(fhs.rtc_date, '%Y-%m-%d')"
},
{
"type": "simple_column",
"alias": "latest_vl",
"column": "fhsh.vl_1"
"column": "fhs.vl_1"
},
{
"type": "derived_column",
Expand All @@ -167,19 +159,19 @@
"expressionOptions": {
"caseOptions": [
{
"condition": "fhsh.vl_1 < 50",
"condition": "fhs.vl_1 < 50",
"value": "LDL"
},
{
"condition": "(fhsh.vl_1 >= 50 and fhsh.vl_1 < 200)",
"condition": "(fhs.vl_1 >= 50 and fhs.vl_1 < 200)",
"value": "Low Risk Low Level Viremia"
},
{
"condition": "(fhsh.vl_1 >= 200 and fhsh.vl_1 < 1000)",
"condition": "(fhs.vl_1 >= 200 and fhs.vl_1 < 1000)",
"value": "High Risk Low Level Viremia"
},
{
"condition": "(fhsh.vl_1 > 1000)",
"condition": "(fhs.vl_1 > 1000)",
"value": "Suspected Treatment Failure"
}
]
Expand All @@ -188,27 +180,27 @@
{
"type": "simple_column",
"alias": "latest_vl_date",
"column": "date_format(fhsh.vl_1_date, '%Y-%m-%d')"
"column": "date_format(fhs.vl_1_date, '%Y-%m-%d')"
},
{
"type": "simple_column",
"alias": "last_appointment",
"column": "CONCAT(COALESCE(DATE_FORMAT(fhsh.encounter_datetime, '%Y-%m-%d'),''),' ',COALESCE(ety.name, ''))"
"column": "CONCAT(COALESCE(DATE_FORMAT(fhs.encounter_datetime, '%Y-%m-%d'),''),' ',COALESCE(ety.name, ''))"
},
{
"type": "simple_column",
"alias": "cur_meds",
"column": "fhsh.cur_arv_meds"
"column": "fhs.cur_arv_meds"
},
{
"type": "simple_column",
"alias": "previous_vl",
"column": "fhsh.vl_2"
"column": "fhs.vl_2"
},
{
"type": "simple_column",
"alias": "previous_vl_date",
"column": "date_format(fhsh.vl_2_date, '%Y-%m-%d')"
"column": "date_format(fhs.vl_2_date, '%Y-%m-%d')"
},
{
"type": "simple_column",
Expand Down
3 changes: 3 additions & 0 deletions etl-routes.js
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Expand Up @@ -4375,6 +4375,9 @@ module.exports = (function () {
endDate: Joi.string()
.optional()
.description('The end date to filter by'),
reportMonth: Joi.string()
.required()
.description('The report month in the format "YYYY-MM-DD"'),
startIndex: Joi.number()
.required()
.description('The startIndex to control pagination'),
Expand Down
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