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Merge branch 'master' into POC-352
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@drizzentic
drizzentic authored Oct 5, 2023
2 parents f57a2f5 + 3c1d21a commit 4aa289e
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6 changes: 6 additions & 0 deletions .prettierrc
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{
"trailingComma": "none",
"tabWidth": 2,
"semi": true,
"singleQuote": true
}
275 changes: 275 additions & 0 deletions app/reporting-framework/base-mysql.report.js
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Expand Up @@ -246,6 +246,86 @@ import * as ml_weekly_predictions_base from './json-reports/ml-predictions/ml-we
import * as clinic_flow_provider_statistics_aggregate from './json-reports/clinic-flow-provider-statistics-aggregate.json';
import * as clinic_flow_provider_statistics_base from './json-reports/clinic-flow-provider-statistics-base.json';

// (New) Prep monthly report
import * as eligible_for_prep_aggregate from './json-reports/prep-monthly/disaggregations/eligibility/eligible-for-prep-aggregate.json';
import * as eligible_for_prep_base from './json-reports/prep-monthly/disaggregations/eligibility/eligible-for-prep-base.json';
import * as reasons_for_initiation_prep_aggregate from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/prep-reasons-for-initiation-aggregate.json';
import * as reasons_for_initiation_prep_base from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/prep-reasons-for-initiation-base.json';

import * as new_for_prep_aggregate from './json-reports/prep-monthly/disaggregations/new/new-for-prep-aggregate.json';
import * as new_for_prep_base from './json-reports/prep-monthly/disaggregations/new/new-for-prep-base.json';

import * as prep_event_driven_aggregate from './json-reports/prep-monthly/disaggregations/event-driven/prep-event-driven-aggregate.json';
import * as prep_event_driven_base from './json-reports/prep-monthly/disaggregations/event-driven/prep-event-driven-base.json';

import * as restarting_prep_aggregate from './json-reports/prep-monthly/disaggregations/restarting/restarting-prep-aggregate.json';
import * as restarting_prep_base from './json-reports/prep-monthly/disaggregations/restarting/restarting-prep-base.json';

import * as while_on_prep_aggregate from './json-reports/prep-monthly/disaggregations/while-on-prep/while-on-prep-aggregate.json';
import * as while_on_prep_base from './json-reports/prep-monthly/disaggregations/while-on-prep/while-on-prep-base.json';

import * as discounted_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/discontinued-prep-aggregate.json';
import * as discounted_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/discontinued-prep-base.json';

import * as gbv_prep_aggregate from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/gbv-aggregate.json';
import * as gbv_prep_base from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/gbv-base.json';

import * as transactional_sex_prep_aggregate from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/transactional-sex-aggregate.json';
import * as transactional_sex_prep_base from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/transactional-sex-base.json';

import * as recent_sti_prep_aggregate from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/recent-sti-aggregate.json';
import * as recent_sti_prep_base from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/recent-sti-base.json';

import * as recurrent_use_of_pep_prep_aggregate from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/recurrent-use-of-pep-aggregate.json';
import * as recurrent_use_of_pep_prep_base from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/recurrent-use-of-pep-base.json';

import * as inconsistent_or_no_condom_use_prep_aggregate from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/inconsistent-or-no-condom-use-aggregate.json';
import * as inconsistent_or_no_condom_use_prep_base from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/inconsistent-or-no-condom-use-base.json';

import * as other_reasons_prep_aggregate from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/other-reasons-aggregate.json';
import * as other_reasons_prep_base from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/other-reasons-base.json';

import * as shared_needles_prep_aggregate from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/shared-needles-aggregate.json';
import * as shared_needles_prep_base from './json-reports/prep-monthly/disaggregations/reasons_for_initiation/shared-needles-base.json';

import * as tested_hiv_positive_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/tested-positive-aggregate.json';
import * as tested_hiv_positive_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/tested-positive-base.json';

import * as low_risk_for_hiv_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/low-risk-for-hiv-aggregate.json';
import * as low_risk_for_hiv_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/low-risk-for-hiv-base.json';

import * as prep_side_effects_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/prep-side-effects-aggregate.json';
import * as prep_side_effects_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/prep-side-effects-base.json';

import * as non_adherence_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/non-adherence-aggregate.json';
import * as non_adherence_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/non-adherence-base.json';

import * as viral_suppression_of_hiv_positive_partner_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/viral-suppression-of-hiv-positive-partner-aggregate.json';
import * as viral_suppression_of_hiv_positive_partner_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/viral-suppression-of-hiv-positive-partner-base.json';

import * as too_many_hiv_tests_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/too-many-hiv-tests-aggregate.json';
import * as too_many_hiv_tests_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/too-many-hiv-tests-base.json';

import * as partner_refusal_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/partner-refusal-aggregate.json';
import * as partner_refusal_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/partner-refusal-base.json';

import * as partner_violence_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/partner-violence-aggregate.json';
import * as partner_violence_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/partner-violence-base.json';

import * as died_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/died-aggregate.json';
import * as died_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/died-base.json';

import * as transfer_outs_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/transfer-outs-aggregate.json';
import * as transfer_outs_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/transfer-outs-base.json';

import * as missed_drug_pickups_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/missed-drug-pickups-aggregate.json';
import * as missed_drug_pickups_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/missed-drug-pickups-base.json';

import * as any_other_reason_prep_aggregate from './json-reports/prep-monthly/disaggregations/discontinued/any-other-reason-aggregate.json';
import * as any_other_reason_prep_base from './json-reports/prep-monthly/disaggregations/discontinued/any-other-reason-base.json';

import * as prep_monthly_report from './json-reports/prep-monthly/prep-report.json';

//covid 19 report
import * as patient_list_covid_template from './json-reports/patient-list-covid-template.json';
import * as covid_19_summary_aggregate from './json-reports/covid-19-summary-report-aggregate.json';
Expand Down Expand Up @@ -1391,6 +1471,201 @@ export class BaseMysqlReport {
)
});
break;
case 'prep-monthly-report':
resolve({
main: this.cloneJsonSchema(prep_monthly_report)
});
break;
case 'eligibleForPrepAggregate':
resolve({
main: this.cloneJsonSchema(eligible_for_prep_aggregate),
eligibleForPrepBase: this.cloneJsonSchema(eligible_for_prep_base)
});
break;
case 'reasonForInitiationPrepAggregate':
resolve({
main: this.cloneJsonSchema(reasons_for_initiation_prep_aggregate),
reasonForInitiationPrepBase: this.cloneJsonSchema(
reasons_for_initiation_prep_base
)
});
break;
case 'newForPrepAggregate':
resolve({
main: this.cloneJsonSchema(new_for_prep_aggregate),
newForPrepBase: this.cloneJsonSchema(new_for_prep_base)
});
break;
case 'eventDrivenPrepAggregate':
resolve({
main: this.cloneJsonSchema(prep_event_driven_aggregate),
eventDrivenPrepBase: this.cloneJsonSchema(prep_event_driven_base)
});
break;
case 'restartingPrepAggregate':
resolve({
main: this.cloneJsonSchema(restarting_prep_aggregate),
restartingPrepBase: this.cloneJsonSchema(restarting_prep_base)
});
break;
case 'whileOnPrepAggregate':
resolve({
main: this.cloneJsonSchema(while_on_prep_aggregate),
whileOnPrepBase: this.cloneJsonSchema(while_on_prep_base)
});
break;
case 'discontinuedPrepAggregate':
resolve({
main: this.cloneJsonSchema(discounted_prep_aggregate),
discontinuedPrepBase: this.cloneJsonSchema(discounted_prep_base)
});
break;
case 'gbvPrepAggregate':
resolve({
main: this.cloneJsonSchema(gbv_prep_aggregate),
gbvPrepBase: this.cloneJsonSchema(gbv_prep_base)
});
break;
case 'transactionalSexPrepAggregate':
resolve({
main: this.cloneJsonSchema(transactional_sex_prep_aggregate),
transactionalSexPrepBase: this.cloneJsonSchema(
transactional_sex_prep_base
)
});
break;
case 'recentSTIPrepAggregate':
resolve({
main: this.cloneJsonSchema(recent_sti_prep_aggregate),
recentSTIPrepBase: this.cloneJsonSchema(recent_sti_prep_base)
});
break;
case 'recurrentUseOfPepPrepAggregate':
resolve({
main: this.cloneJsonSchema(recurrent_use_of_pep_prep_aggregate),
recurrentUseOfPepPrepBase: this.cloneJsonSchema(
recurrent_use_of_pep_prep_base
)
});
break;
case 'inconsistentOrNoCondomUsePrepAggregate':
resolve({
main: this.cloneJsonSchema(
inconsistent_or_no_condom_use_prep_aggregate
),
inconsistentOrNoCondomUsePrepBase: this.cloneJsonSchema(
inconsistent_or_no_condom_use_prep_base
)
});
break;
case 'otherReasonsForPrepAggregate':
resolve({
main: this.cloneJsonSchema(other_reasons_prep_aggregate),
otherReasonsForPrepBase: this.cloneJsonSchema(
other_reasons_prep_base
)
});
break;
case 'sharedNeedlesPrepAggregate':
resolve({
main: this.cloneJsonSchema(shared_needles_prep_aggregate),
sharedNeedlesPrepBase: this.cloneJsonSchema(
shared_needles_prep_base
)
});
break;
case 'testedHIVPositivePrepAggregate':
resolve({
main: this.cloneJsonSchema(tested_hiv_positive_prep_aggregate),
testedHIVPositivePrepBase: this.cloneJsonSchema(
tested_hiv_positive_prep_base
)
});
break;
case 'lowRiskForHIVPrepAggregate':
resolve({
main: this.cloneJsonSchema(low_risk_for_hiv_prep_aggregate),
lowRiskForHIVPrepBase: this.cloneJsonSchema(
low_risk_for_hiv_prep_base
)
});
break;
case 'prepSideEffectsAggregate':
resolve({
main: this.cloneJsonSchema(prep_side_effects_prep_aggregate),
prepSideEffectsPrepBase: this.cloneJsonSchema(
prep_side_effects_prep_base
)
});
break;
case 'nonAdherencePrepAggregate':
resolve({
main: this.cloneJsonSchema(non_adherence_prep_aggregate),
nonAdherencePrepBase: this.cloneJsonSchema(non_adherence_prep_base)
});
break;
case 'viralSuppressionOfHIVPositivePartnerPrepAggregate':
resolve({
main: this.cloneJsonSchema(
viral_suppression_of_hiv_positive_partner_prep_aggregate
),
viralSuppressionOfHIVPositivePartnerPrepBase: this.cloneJsonSchema(
viral_suppression_of_hiv_positive_partner_prep_base
)
});
break;
case 'tooManyHIVTestsPrepAggregate':
resolve({
main: this.cloneJsonSchema(too_many_hiv_tests_prep_aggregate),
tooManyHIVTestsPrepBase: this.cloneJsonSchema(
too_many_hiv_tests_prep_base
)
});
break;
case 'partnerRefusalPrepAggregate':
resolve({
main: this.cloneJsonSchema(partner_refusal_prep_aggregate),
partnerRefusalPrepBase: this.cloneJsonSchema(
partner_refusal_prep_base
)
});
break;
case 'partnerViolencePrepAggregate':
resolve({
main: this.cloneJsonSchema(partner_violence_prep_aggregate),
partnerViolencePrepBase: this.cloneJsonSchema(
partner_violence_prep_base
)
});
break;
case 'diedPrepAggregate':
resolve({
main: this.cloneJsonSchema(died_prep_aggregate),
diedPrepBase: this.cloneJsonSchema(died_prep_base)
});
break;
case 'transferOutsPrepAggregate':
resolve({
main: this.cloneJsonSchema(transfer_outs_prep_aggregate),
transferOutsPrepBase: this.cloneJsonSchema(transfer_outs_prep_base)
});
break;
case 'missedDrugPickupsPrepAggregate':
resolve({
main: this.cloneJsonSchema(missed_drug_pickups_prep_aggregate),
missedDrugPickupsPrepBase: this.cloneJsonSchema(
missed_drug_pickups_prep_base
)
});
break;
case 'anyOtherReasonPrepAggregate':
resolve({
main: this.cloneJsonSchema(any_other_reason_prep_aggregate),
anyOtherReasonPrepBase: this.cloneJsonSchema(
any_other_reason_prep_base
)
});
break;
case 'covid-19-monthly-report':
resolve({
main: this.cloneJsonSchema(covid_19_monthly_report)
Expand Down
2 changes: 1 addition & 1 deletion app/reporting-framework/hiv/moh-731.report.js
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Expand Up @@ -15,7 +15,7 @@ export class Moh731Report extends MultiDatasetPatientlistReport {
}
params.hivMonthlyDatasetSource = 'etl.hiv_monthly_report_dataset_frozen'; // defaults to frozen
params.hivVlDataSource =
'(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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)';
'(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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)';
console.log('creating new moh 731 report service');
super(reportName, params);
}
Expand Down
2 changes: 1 addition & 1 deletion app/reporting-framework/json-reports/clinical-reminder-report.json
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Expand Up @@ -16,7 +16,7 @@
"alias": "t1"
},
{
"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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
"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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
"alias": "fli",
"join": {
"type": "LEFT",
Expand Down
18 changes: 17 additions & 1 deletion app/reporting-framework/json-reports/defaulter-list-base.json
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,15 @@
"alias": "de",
"join": {
"type": "LEFT",
"joinCondition": "de.encounter_id = fd.encounter_id"
"joinCondition": "de.encounter_id = fd.encounter_id "
}
},
{
"table": "(SELECT MAX(am.encounter_datetime) AS max_encounter_datetime, am.encounter_datetime, am.encounter_type, am.patient_id, fd.person_id , fd.rtc_date FROM etl.flat_defaulters fd INNER JOIN amrs.encounter am on (am.patient_id = fd.person_id) WHERE am.encounter_type = 21 group by am.patient_id)",
"alias": "am",
"join": {
"type": "INNER",
"joinCondition": "am.patient_id = fd.person_id"
}
},
{
Expand Down Expand Up @@ -82,6 +90,14 @@
"type": "simple_column",
"alias": "rtc_date",
"column": "DATE_FORMAT(fd.rtc_date,'%Y-%m-%d')"
},
{
"type": "derived_column",
"alias": "outreach_follow_up",
"expressionType": "simple_expression",
"expressionOptions": {
"expression": "case when max_encounter_datetime >= fd.rtc_date then 'Yes' else 'No' end"
}
}
],
"filters": {
Expand Down
2 changes: 1 addition & 1 deletion app/reporting-framework/json-reports/patient-list-template.json
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
"alias": "t1"
},
{
"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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
"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,max(encounter_id) as encounter_id 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.encounter_id = max_dates.encounter_id)",
"alias": "fli",
"join": {
"type": "LEFT",
Expand Down
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