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Merge pull request #1281 from AMPATH/ml-weekly-predictions
ML weekly predictions API endpoint for patient list
2 parents a4f3a04 + 295bb0c commit 99dff0f

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‎app/reporting-framework/base-mysql.report.js

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@@ -225,6 +225,10 @@ import * as hiv_cervical_cancer_monthly_summary_lesions_pcf_aggregate from './js
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import * as defaulter_list_aggregate from './json-reports/defaulter-list-aggregate.json';
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import * as defaulter_list_base from './json-reports/defaulter-list-base.json';
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// ML Weekly Predictions
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import * as ml_weekly_predictions_aggregate from './json-reports/ml-predictions/ml-weekly-predictions-aggregate.json';
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import * as ml_weekly_predictions_base from './json-reports/ml-predictions/ml-weekly-predictions-base.json';
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//clinic clow report
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import * as clinic_flow_provider_statistics_aggregate from './json-reports/clinic-flow-provider-statistics-aggregate.json';
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import * as clinic_flow_provider_statistics_base from './json-reports/clinic-flow-provider-statistics-base.json';
@@ -1272,6 +1276,14 @@ export class BaseMysqlReport {
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defaulterListBase: this.cloneJsonSchema(defaulter_list_base)
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});
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break;
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case 'mlWeeklyPredictionsAggregate':
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resolve({
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main: this.cloneJsonSchema(ml_weekly_predictions_aggregate),
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mlWeeklyPredictionsBase: this.cloneJsonSchema(
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ml_weekly_predictions_base
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)
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});
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break;
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case 'clinicFlowProviderStatisticsAggregate':
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resolve({
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main: this.cloneJsonSchema(

‎app/reporting-framework/json-reports/ml-predictions/ml-weekly-predictions-aggregate.json

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{
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"name": "mlWeeklyPredictionsAggregate",
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"version": "1.0",
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"tag": "",
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"description": "",
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"uses": [
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{
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"name": "mlWeeklyPredictionsBase",
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"version": "1.0",
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"type": "dataset_def"
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}
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],
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"sources": [
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{
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"dataSet": "mlWeeklyPredictionsBase",
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"alias": "t2"
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}
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],
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"columns": [
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{
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"type": "simple_column",
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"alias": "person_id",
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"column": "t2.person_id"
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},
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{
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"type": "simple_column",
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"alias": "total_predictions",
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"column": "count(distinct t2.person_id)"
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}
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],
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"groupBy": {
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"groupParam": "groupByParam",
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"columns": ["person_id"],
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"excludeParam": "excludeParam"
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},
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"dynamicJsonQueryGenerationDirectives": {
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"patientListGenerator": {
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"useTemplate": "patient-list-template",
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"useTemplateVersion": "1.0",
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"generatingDirectives": {
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"joinDirectives": {
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"joinType": "INNER",
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"joinCondition": "<<base_column>> = <<template_column>>",
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"baseColumn": "person_id",
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"templateColumn": "person_id"
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}
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}
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}
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}
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}

‎app/reporting-framework/json-reports/ml-predictions/ml-weekly-predictions-base.json

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{
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"name": "mlWeeklyPredictionsBase",
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"version": "1.0",
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"tag": "",
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"description": "",
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"uses": [],
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"sources": [
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{
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"table": "predictions.ml_weekly_predictions",
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"alias": "ml"
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},
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{
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"table": "etl.flat_hiv_summary_v15b",
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"alias": "de",
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"join": {
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"type": "LEFT",
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"joinCondition": "de.encounter_id = ml.encounter_id"
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}
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},
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{
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"table": "etl.flat_patient_identifiers_v1",
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"alias": "fi",
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"join": {
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"type": "LEFT",
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"joinCondition": "de.person_id = fi.patient_id"
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}
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},
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{
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"table": "etl.program_visit_map",
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"alias": "pm",
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"join": {
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"type": "LEFT",
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"joinCondition": "de.visit_type = pm.visit_type_id"
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}
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},
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{
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"table": "amrs.program",
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"alias": "p",
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"join": {
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"type": "LEFT",
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"joinCondition": "p.program_id = pm.program_type_id"
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}
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},
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{
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"table": "etl.pre_appointment_summary",
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"alias": "pre",
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"join": {
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"type": "LEFT",
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"joinCondition": "pre.person_id = ml.person_id"
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}
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}
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],
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"columns": [
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{
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"type": "simple_column",
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"alias": "person_id",
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"column": "ml.person_id"
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},
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{
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"type": "simple_column",
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"alias": "ccc_number",
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"column": "fi.ccc"
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},
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{
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"type": "simple_column",
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"alias": "ovcid_id",
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"column": "fi.ovcid"
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},
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{
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"type": "simple_column",
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"alias": "upi_number",
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"column": "fi.nupi"
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},
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{
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"type": "simple_column",
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"alias": "program",
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"column": "p.name"
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},
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{
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"type": "simple_column",
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"alias": "predicted_risk",
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"column": "ml.predicted_risk"
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},
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{
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"type": "simple_column",
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"alias": "week",
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"column": "ml.week"
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},
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{
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"type": "simple_column",
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"alias": "predicted_prob_disengage",
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"column": "ml.predicted_prob_disengage"
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},
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{
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"type": "simple_column",
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"alias": "prediction_generated_date",
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"column": "DATE_FORMAT(ml.prediction_generated_date,'%Y-%m-%d')"
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},
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{
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"type": "simple_column",
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"alias": "rtc_date",
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"column": "DATE_FORMAT(ml.rtc_date,'%Y-%m-%d')"
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},
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{
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"type": "simple_column",
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"alias": "follow_up_type",
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"column": "pre.follow_up_type"
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},
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{
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"type": "simple_column",
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"alias": "follow_up_reason",
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"column": "pre.follow_up_reason"
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},
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{
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"type": "simple_column",
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"alias": "rescheduled_date",
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"column": "pre.rescheduled_date"
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},
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{
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"type": "simple_column",
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"alias": "reschedule_appointment",
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"column": "pre.reschedule_appointment"
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},
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{
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"type": "simple_column",
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"alias": "contact_reached",
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"column": "pre.contact_reached_phone_follow_up"
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},
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{
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"type": "simple_column",
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"alias": "attempted_home_visit",
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"column": "pre.attempted_home_visit"
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},
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{
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"type": "simple_column",
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"alias": "reason_not_attempted_home_visit",
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"column": "pre.reason_not_attempted_home_visit"
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},
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{
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"type": "simple_column",
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"alias": "was_client_found",
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"column": "pre.was_client_found"
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},
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{
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"type": "simple_column",
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"alias": "reason_client_not_found",
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"column": "pre.reason_client_not_found"
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},
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{
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"type": "simple_column",
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"alias": "home_visit_personnel",
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"column": "pre.home_visit_personnel"
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},
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{
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"type": "derived_column",
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"alias": "was_follow_up_successful",
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"expressionType": "simple_expression",
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"expressionOptions": {
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"expression": "if((pre.is_successful_phone_follow_up = 'YES' OR (pre.attempted_home_visit = 'YES' AND pre.was_client_found = 'YES')), 1, 0)"
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}
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},
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{
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"type": "simple_column",
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"alias": "comments",
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"column": "pre.comments"
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}
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],
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"filters": {
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"conditionJoinOperator": "and",
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"conditions": [
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{
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"filterType": "tableColumns",
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"conditionExpression": "ml.location_id in (?)",
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"parameterName": "locations"
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},
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{
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"filterType": "tableColumns",
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"conditionExpression": "ml.week = ?",
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"parameterName": "yearWeek"
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},
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{
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"filterType": "tableColumns",
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"conditionExpression": "(if((pre.is_successful_phone_follow_up = 'YES' OR (pre.attempted_home_visit = 'YES' AND pre.was_client_found = 'YES')), 1, 0)) = ?",
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"parameterName": "successfulOutcome"
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},
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{
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"filterType": "tableColumns",
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"conditionExpression": "(if((pre.is_successful_phone_follow_up = 'NO' OR (pre.attempted_home_visit = 'YES' AND pre.was_client_found = 'NO')), 1, 0)) = ?",
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"parameterName": "failedOutcome"
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},
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{
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"filterType": "tableColumns",
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"conditionExpression": "ml.predicted_risk is not null"
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}
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]
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},
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"orderBy": {
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"orderByParam": "orderByParam",
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"columns": [
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{
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"column": "ml.predicted_prob_disengage",
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"order": "desc"
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},
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{
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"column": "ml.prediction_generated_date",
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"order": "desc"
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},
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{
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"column": "pre.encounter_datetime",
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"order": "desc"
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}
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]
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}
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}

‎app/routes/ml-weekly-predictions.route.js

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const preRequest = require('../../pre-request-processing');
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const etlHelpers = require('../../etl-helpers');
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const Boom = require('boom');
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const {
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MlWeeklyPredictionsService
7+
} = require('../../service/ml-weekly-predictions.service');
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const routes = [];
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exports.routes = (server) => server.route(routes);

‎etl-routes.js

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@@ -79,6 +79,8 @@ import { DefaulterListService } from './service/defaulter-list-service';
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import { ClinicFlowService } from './service/clinic-flow-service';
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import { getPatientCovidVaccinationStatus } from './service/covid-19/covid-19-vaccination-summary';
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import { Covid19MonthlyReport } from './service/covid-19/covid-19-monthly-report';
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import { MlWeeklyPredictionsService } from './service/ml-weekly-predictions.service';
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import { getPatientPredictedScore } from './service/predictions/ml-prediction-service';
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module.exports = (function () {
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var routes = [
@@ -6211,6 +6213,85 @@ module.exports = (function () {
62116213
'Returns patient list of vaccinated i.e fully,partial and not vaccinated',
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tags: ['api']
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}
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},
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{
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method: 'GET',
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path: '/etl/ml-weekly-predictions',
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config: {
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auth: 'simple',
6222+
handler: function (request, reply) {
6223+
if (request.query.locationUuids) {
6224+
request.query.reportName = 'defaulter-list';
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preRequest.resolveLocationIdsToLocationUuids(request, function () {
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let requestParams = Object.assign(
6227+
{},
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request.query,
6229+
request.params
6230+
);
6231+
6232+
const mlWeeklyPredictionsService = new MlWeeklyPredictionsService();
6233+
6234+
mlWeeklyPredictionsService
6235+
.getPatientListReport(requestParams)
6236+
.then((results) => {
6237+
_.each(results.result, (item) => {
6238+
item.cur_meds = etlHelpers.getARVNames(item.cur_meds);
6239+
});
6240+
reply(results);
6241+
})
6242+
.catch((err) => {
6243+
reply(Boom.internal('An error occured', err));
6244+
});
6245+
});
6246+
}
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},
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plugins: {
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hapiAuthorization: {
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role: privileges.canViewClinicDashBoard
6251+
},
6252+
openmrsLocationAuthorizer: {
6253+
locationParameter: [
6254+
{
6255+
type: 'query',
6256+
name: 'locationUuids' //name of the location parameter
6257+
}
6258+
]
6259+
}
6260+
},
6261+
description: "Get a location's ml weekly predictions list.",
6262+
notes: "Returns a location's ml weekly predictions list.",
6263+
tags: ['api'],
6264+
validate: {
6265+
options: {
6266+
allowUnknown: true
6267+
}
6268+
}
6269+
}
6270+
},
6271+
{
6272+
method: 'GET',
6273+
path: '/etl/predicted-score',
6274+
config: {
6275+
auth: 'simple',
6276+
plugins: {},
6277+
handler: function (request, reply) {
6278+
if (request.query.patientUuid) {
6279+
const patientUuid = request.query.patientUuid;
6280+
getPatientPredictedScore(patientUuid)
6281+
.then((results) => {
6282+
reply(results);
6283+
})
6284+
.catch((error) => {
6285+
reply(Boom.internal('An error occured', error));
6286+
});
6287+
} else {
6288+
reply(Boom.internal('Request misssing patient uuid'));
6289+
}
6290+
},
6291+
description: 'Patient predicted score of missing appointment.',
6292+
notes: 'Returns the patients predictions data.',
6293+
tags: ['api']
6294+
}
62146295
}
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];
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