malawi_hiv_program_reports 1.0.1 → 1.0.2
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- checksums.yaml +4 -4
- data/app/services/malawi_hiv_program_reports/README.md +16 -0
- data/app/services/malawi_hiv_program_reports/adapters/moh/custom.rb +199 -0
- data/app/services/malawi_hiv_program_reports/archiving_candidates.rb +130 -0
- data/app/services/malawi_hiv_program_reports/arv_refill_periods.rb +311 -0
- data/app/services/malawi_hiv_program_reports/clinic/README.md +5 -0
- data/app/services/malawi_hiv_program_reports/clinic/appointments_report.rb +317 -0
- data/app/services/malawi_hiv_program_reports/clinic/discrepancy_report.rb +42 -0
- data/app/services/malawi_hiv_program_reports/clinic/docs/hypertension_report.md +31 -0
- data/app/services/malawi_hiv_program_reports/clinic/drug_dispensations.rb +48 -0
- data/app/services/malawi_hiv_program_reports/clinic/external_consultation_clients.rb +69 -0
- data/app/services/malawi_hiv_program_reports/clinic/hypertension_report.rb +223 -0
- data/app/services/malawi_hiv_program_reports/clinic/ipt_coverage.rb +112 -0
- data/app/services/malawi_hiv_program_reports/clinic/ipt_report.rb +69 -0
- data/app/services/malawi_hiv_program_reports/clinic/lims_results.rb +55 -0
- data/app/services/malawi_hiv_program_reports/clinic/outcome_list.rb +127 -0
- data/app/services/malawi_hiv_program_reports/clinic/patients_alive_and_on_treatment.rb +57 -0
- data/app/services/malawi_hiv_program_reports/clinic/patients_due_for_viral_load.rb +39 -0
- data/app/services/malawi_hiv_program_reports/clinic/patients_on_antiretrovirals.rb +44 -0
- data/app/services/malawi_hiv_program_reports/clinic/patients_on_dtg.rb +36 -0
- data/app/services/malawi_hiv_program_reports/clinic/patients_on_treatment.rb +42 -0
- data/app/services/malawi_hiv_program_reports/clinic/patients_with_outdated_demographics.rb +173 -0
- data/app/services/malawi_hiv_program_reports/clinic/pregnant_patients.rb +91 -0
- data/app/services/malawi_hiv_program_reports/clinic/regimen_dispensation_data.rb +282 -0
- data/app/services/malawi_hiv_program_reports/clinic/regimen_switch.rb +456 -0
- data/app/services/malawi_hiv_program_reports/clinic/regimens_and_formulations.rb +182 -0
- data/app/services/malawi_hiv_program_reports/clinic/regimens_by_weight_and_gender.rb +108 -0
- data/app/services/malawi_hiv_program_reports/clinic/retention.rb +246 -0
- data/app/services/malawi_hiv_program_reports/clinic/stock_card_report.rb +65 -0
- data/app/services/malawi_hiv_program_reports/clinic/tpt_outcome.rb +494 -0
- data/app/services/malawi_hiv_program_reports/clinic/tx_rtt.rb +169 -0
- data/app/services/malawi_hiv_program_reports/clinic/viral_load.rb +292 -0
- data/app/services/malawi_hiv_program_reports/clinic/viral_load_disaggregated.rb +97 -0
- data/app/services/malawi_hiv_program_reports/clinic/viral_load_results.rb +175 -0
- data/app/services/malawi_hiv_program_reports/clinic/visits_report.rb +113 -0
- data/app/services/malawi_hiv_program_reports/clinic/vl_collection.rb +48 -0
- data/app/services/malawi_hiv_program_reports/cohort/outcomes.rb +338 -0
- data/app/services/malawi_hiv_program_reports/cohort/regimens.rb +69 -0
- data/app/services/malawi_hiv_program_reports/cohort/side_effects.rb +141 -0
- data/app/services/malawi_hiv_program_reports/cohort/tpt.rb +172 -0
- data/app/services/malawi_hiv_program_reports/moh/cohort.rb +278 -0
- data/app/services/malawi_hiv_program_reports/moh/cohort_builder.rb +2340 -0
- data/app/services/malawi_hiv_program_reports/moh/cohort_disaggregated.rb +608 -0
- data/app/services/malawi_hiv_program_reports/moh/cohort_disaggregated_additions.rb +208 -0
- data/app/services/malawi_hiv_program_reports/moh/cohort_disaggregated_builder.rb +526 -0
- data/app/services/malawi_hiv_program_reports/moh/cohort_struct.rb +219 -0
- data/app/services/malawi_hiv_program_reports/moh/cohort_survival_analysis.rb +203 -0
- data/app/services/malawi_hiv_program_reports/moh/moh_tpt.rb +223 -0
- data/app/services/malawi_hiv_program_reports/moh/tpt_newly_initiated.rb +235 -0
- data/app/services/malawi_hiv_program_reports/pepfar/defaulter_list.rb +25 -0
- data/app/services/malawi_hiv_program_reports/pepfar/maternal_status.rb +29 -0
- data/app/services/malawi_hiv_program_reports/pepfar/patient_start_vl.rb +45 -0
- data/app/services/malawi_hiv_program_reports/pepfar/regimen_switch.rb +479 -0
- data/app/services/malawi_hiv_program_reports/pepfar/sc_arvdisp.rb +174 -0
- data/app/services/malawi_hiv_program_reports/pepfar/sc_curr.rb +98 -0
- data/app/services/malawi_hiv_program_reports/pepfar/tb_prev.rb +163 -0
- data/app/services/malawi_hiv_program_reports/pepfar/tb_prev2.rb +222 -0
- data/app/services/malawi_hiv_program_reports/pepfar/tb_prev3.rb +421 -0
- data/app/services/malawi_hiv_program_reports/pepfar/tpt_status.rb +181 -0
- data/app/services/malawi_hiv_program_reports/pepfar/tx_ml.rb +181 -0
- data/app/services/malawi_hiv_program_reports/pepfar/tx_new.rb +202 -0
- data/app/services/malawi_hiv_program_reports/pepfar/tx_rtt.rb +288 -0
- data/app/services/malawi_hiv_program_reports/pepfar/tx_tb.rb +283 -0
- data/app/services/malawi_hiv_program_reports/pepfar/utils.rb +141 -0
- data/app/services/malawi_hiv_program_reports/pepfar/viral_load_coverage.rb +414 -0
- data/app/services/malawi_hiv_program_reports/pepfar/viral_load_coverage2.rb +433 -0
- data/app/services/malawi_hiv_program_reports/report_map.rb +56 -0
- data/app/services/malawi_hiv_program_reports/utils/README.md +8 -0
- data/app/services/malawi_hiv_program_reports/utils/common_sql_query_utils.rb +60 -0
- data/app/services/malawi_hiv_program_reports/utils/concurrency_utils.rb +53 -0
- data/app/services/malawi_hiv_program_reports/utils/docs/common_sql_query_utils.md +53 -0
- data/app/services/malawi_hiv_program_reports/utils/model_utils.rb +66 -0
- data/app/services/malawi_hiv_program_reports/utils/parameter_utils.rb +32 -0
- data/app/services/malawi_hiv_program_reports/utils/time_utils.rb +52 -0
- data/lib/malawi_hiv_program_reports/version.rb +1 -1
- metadata +74 -1
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# frozen_string_literal: true
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module MalawiHivProgramReports
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module Pepfar
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##
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# Patients who started TPT just before the start of the current
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# and have finished within the current reporting period.
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class TbPrev3
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attr_reader :start_date, :end_date, :check_date, :cut_off_point, :occupation, :location
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include MalawiHivProgramReports::Adapters::Moh::Custom
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include Utils
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include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
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def initialize(start_date:, end_date:, **kwargs)
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@start_date = ActiveRecord::Base.connection.quote(start_date)
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@check_date = start_date.to_date - 6.months
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@cut_off_point = start_date.to_date
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@end_date = ActiveRecord::Base.connection.quote(end_date)
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@occupation = kwargs[:occupation]
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@location = kwargs[:location]
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end
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def find_report
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report = init_report
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patients = group_patients_by_tpt_course(patients_on_tpt)
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load_patients_into_report(report, patients.six_h, '6H') do |patient|
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# 6H has a constant dosage of 1 pill per day
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patient_completed_tpt?(patient, '6H')
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end
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load_patients_into_report(report, patients.three_hp, '3HP') do |patient|
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# 3HP daily dosages vary by patient weight can't use easily use pills
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# to determine course completion
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patient_completed_tpt?(patient, '3HP')
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end
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report
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end
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def fetch_individual_report(patient_id)
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individual_tpt_report(patient_id)
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end
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private
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def init_report
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pepfar_age_groups.each_with_object({}) do |age_group, report|
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report[age_group] = %w[M F Unknown].each_with_object({}) do |gender, gender_sub_report|
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gender_sub_report[gender] = %w[6H 3HP].each_with_object({}) do |tpt, tpt_sub_report|
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tpt_sub_report[tpt] = {
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started_new_on_art: [],
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started_previously_on_art: [],
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completed_new_on_art: [],
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completed_previously_on_art: []
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}
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end
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end
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end
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end
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def load_patients_into_report(report, patients, tpt, &patient_has_completed_tpt)
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patients.each do |patient|
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next if patient['transfer_in'] == 1 && !patient_has_completed_tpt[patient]
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age_group = patient['age_group']
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gender = patient['gender']&.first&.upcase || 'Unknown'
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tpt_states = find_patient_tpt_state(patient, &patient_has_completed_tpt)
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tpt_states.each do |tpt_state|
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report[age_group][gender][tpt][tpt_state] << patient
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end
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end
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end
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def find_patient_tpt_state(patient, &patient_has_completed_tpt)
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if patient_has_completed_tpt[patient]
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return %i[completed_new_on_art] if patient_new_on_art?(patient) && patient['transfer_in'] == 1
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return %i[started_new_on_art completed_new_on_art] if patient_new_on_art?(patient)
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return %i[completed_previously_on_art] if patient['transfer_in'] == 1
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return %i[started_previously_on_art completed_previously_on_art]
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end
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return %i[started_new_on_art] if patient_new_on_art?(patient)
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%i[started_previously_on_art]
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end
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def patient_new_on_art?(patient)
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tpt_initiation_date = patient['tpt_initiation_date'].to_date
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art_start_date = patient['art_start_date'].to_date
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(tpt_initiation_date >= art_start_date) && (tpt_initiation_date < art_start_date + 180.days)
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end
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def patients_on_tpt
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clients = fetch_patients_on_tpt.to_a
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results = []
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clients.each do |client|
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next if client['tpt_initiation_date'].to_date > cut_off_point
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result = individual_tpt_report(client['patient_id'])
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next if result.blank?
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next if result['tpt_initiation_date'].to_date < check_date
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client['tpt_initiation_date'] = result['tpt_initiation_date']
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client['total_pills_taken'] = result['total_pills_taken']
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client['months_on_tpt'] = result['months_on_tpt']
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client['total_days_on_medication'] = result['total_days_on_medication']
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client['drug_concepts'] = result['drug_concepts']
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client['transfer_in'] = result['transfer_in']
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results << client
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end
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results
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end
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def fetch_patients_on_tpt
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ActiveRecord::Base.connection.select_all <<~SQL
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SELECT person.person_id AS patient_id,
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patient_identifier.identifier AS arv_number,
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DATE(MIN(orders.start_date)) AS tpt_initiation_date,
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#{function_manager(function: 'date_antiretrovirals_started', location: @location, args: "person.person_id::int, MIN(denominator_patient.start_date)::date, #{@location}::int")} AS art_start_date,
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#{function_manager(function: 'patient_outcome', location: @location, args: "person.person_id::int, #{@end_date}::date, #{@location}::int")} AS outcome,
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person.gender,
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person.birthdate,
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#{function_manager(function: 'disaggregated_age_group', location: @location, args: "person.birthdate::date, #{@end_date}::date")} AS age_group
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FROM person
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LEFT JOIN patient_identifier
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ON patient_identifier.patient_id = person.person_id
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AND patient_identifier.voided = 0
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AND #{in_manager(column: 'patient_identifier.identifier_type', values: "(SELECT patient_identifier_type_id FROM patient_identifier_type WHERE name = 'ARV Number')")}
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#{site_manager(operator: 'AND', column: 'patient_identifier.site_id', location: @location)}
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LEFT JOIN (#{current_occupation_query}) AS current_occupation ON current_occupation.person_id = person.person_id
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#{site_manager(operator: 'AND', column: 'current_occupation.site_id', location: @location)}
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INNER JOIN(
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SELECT denominator_encounter.patient_id AS patient_id, patient_state.start_date AS start_date
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FROM person
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INNER JOIN patient_program
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ON patient_program.patient_id = person.person_id
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AND #{in_manager(column: 'patient_program.program_id', values: "(SELECT program_id FROM program WHERE name = 'HIV PROGRAM')")}
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AND patient_program.voided = 0
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INNER JOIN patient_state
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ON patient_state.patient_program_id = patient_program.patient_program_id
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AND patient_state.state = 7 /* State: 7 == On antiretrovirals */
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AND patient_state.start_date < DATE(#{start_date})
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AND patient_state.voided = 0
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INNER JOIN encounter AS denominator_encounter
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ON denominator_encounter.patient_id = patient_program.patient_id
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AND #{in_manager(column: 'denominator_encounter.program_id', values: "(SELECT program_id FROM program WHERE name = 'HIV PROGRAM')")}
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AND #{in_manager(column: 'denominator_encounter.encounter_type', values: "(SELECT encounter_type_id FROM encounter_type WHERE name = 'Treatment')")}
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AND denominator_encounter.encounter_datetime >= #{interval_manager(date: start_date, value: 6, interval: 'MONTH', operator: '-')}
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AND denominator_encounter.encounter_datetime <= DATE(#{start_date})
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AND denominator_encounter.voided = 0
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#{site_manager(operator: 'AND', column: 'patient_program.site_id', location: @location)}
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GROUP BY denominator_encounter.patient_id, patient_state.start_date
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) AS denominator_patient ON denominator_patient.patient_id = person.person_id
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INNER JOIN encounter AS prescription_encounter
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ON prescription_encounter.patient_id = denominator_patient.patient_id
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AND prescription_encounter.program_id = 1
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AND #{in_manager(column: 'prescription_encounter.encounter_type', values: "(SELECT encounter_type_id FROM encounter_type WHERE name = 'Treatment')")}
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AND prescription_encounter.encounter_datetime >= #{interval_manager(date: start_date, value: 6, interval: 'MONTH', operator: '-')}
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AND prescription_encounter.encounter_datetime <= DATE(#{end_date})
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AND prescription_encounter.voided = 0
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INNER JOIN orders
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ON orders.encounter_id = prescription_encounter.encounter_id
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AND #{in_manager(column: 'orders.order_type_id', values: "(SELECT order_type_id FROM order_type WHERE name = 'Drug order')")}
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AND orders.start_date >= #{interval_manager(date: start_date, value: 6, interval: 'MONTH', operator: '-')}
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AND orders.start_date <= CAST(#{end_date} as DATE)
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AND orders.voided = 0
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INNER JOIN concept_name
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ON concept_name.concept_id = orders.concept_id
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AND #{in_manager(column: 'concept_name.name', values: "'Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine'" )}
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INNER JOIN drug_order
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ON drug_order.order_id = orders.order_id
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AND drug_order.quantity > 0
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WHERE person.voided = 0 #{%w[Military Civilian].include?(@occupation) ? 'AND' : ''} #{occupation_filter(occupation: @occupation, field_name: 'value', table_name: 'current_occupation', include_clause: false)}
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#{site_manager(operator: 'AND', column: 'person.site_id', location: @location)}
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AND person.person_id NOT IN (
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/* External consultations */
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SELECT DISTINCT registration_encounter.patient_id
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FROM patient_program pp
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INNER JOIN program p ON p.program_id = pp.program_id AND p.name = 'HIV PROGRAM' AND p.retired = 0
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INNER JOIN encounter AS registration_encounter
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ON registration_encounter.patient_id = pp.patient_id
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AND registration_encounter.program_id = pp.program_id
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AND registration_encounter.encounter_datetime < #{interval_manager(date: end_date, value: 1, interval: 'MONTH', operator: '+')}
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AND registration_encounter.voided = 0
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INNER JOIN (
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SELECT MAX(encounter.encounter_datetime) AS encounter_datetime, encounter.patient_id
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FROM encounter
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INNER JOIN encounter_type
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ON encounter_type.encounter_type_id = encounter.encounter_type
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AND encounter_type.name = 'Registration'
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INNER JOIN program
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ON program.program_id = encounter.program_id
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AND program.name = 'HIV PROGRAM'
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WHERE encounter.encounter_datetime < CAST(#{end_date} AS DATE) AND encounter.voided = 0
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GROUP BY encounter.patient_id
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) AS max_registration_encounter
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ON max_registration_encounter.patient_id = registration_encounter.patient_id
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AND max_registration_encounter.encounter_datetime = registration_encounter.encounter_datetime
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INNER JOIN obs AS patient_type_obs
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ON patient_type_obs.encounter_id = registration_encounter.encounter_id
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AND #{in_manager(column: 'patient_type_obs.concept_id', values: "(SELECT concept_id FROM concept_name WHERE name = 'Type of patient' AND voided = 0)")}
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AND #{in_manager(column: 'patient_type_obs.value_coded', values: "(SELECT concept_id FROM concept_name WHERE name IN ('Drug refill', 'External consultation') AND voided = 0)")}
|
211
|
+
AND patient_type_obs.voided = 0
|
212
|
+
WHERE pp.voided = 0
|
213
|
+
)
|
214
|
+
GROUP BY person.person_id #{group_by_columns('patient_identifier.identifier, person.gender, person.birthdate, denominator_patient.start_date')}
|
215
|
+
SQL
|
216
|
+
end
|
217
|
+
|
218
|
+
def individual_tpt_report(patient_id)
|
219
|
+
result = process_current_tpt_course_date(patient_id)
|
220
|
+
c_start_date = ActiveRecord::Base.connection.quote(result[:start_date])
|
221
|
+
c_end_date = ActiveRecord::Base.connection.quote(client_tpt_end_date(patient_id, c_start_date))
|
222
|
+
ActiveRecord::Base.connection.select_one <<-SQL
|
223
|
+
SELECT
|
224
|
+
CASE
|
225
|
+
WHEN tpt_transfer_in_obs.value_datetime IS NULL THEN DATE(MIN(o.start_date))
|
226
|
+
WHEN tpt_transfer_in_obs.value_datetime > MIN(o.start_date) THEN DATE(MIN(o.start_date))
|
227
|
+
ELSE DATE(tpt_transfer_in_obs.value_datetime)
|
228
|
+
END AS tpt_initiation_date,
|
229
|
+
COUNT(DISTINCT(DATE(o.start_date))) AS months_on_tpt,
|
230
|
+
SUM(dor.quantity) + SUM(CASE WHEN tpt_transfer_in_obs.value_numeric IS NOT NULL THEN tpt_transfer_in_obs.value_numeric ELSE 0 END) AS total_pills_taken,
|
231
|
+
SUM(DATEDIFF(o.auto_expire_date, o.start_date)) + SUM(CASE WHEN tpt_transfer_in_obs.value_datetime IS NOT NULL THEN DATEDIFF(tpt_transfer_in_obs.obs_datetime, tpt_transfer_in_obs.value_datetime) ElSE 0 END) AS total_days_on_medication,
|
232
|
+
GROUP_CONCAT(DISTINCT o.concept_id SEPARATOR ',') AS drug_concepts,
|
233
|
+
CASE
|
234
|
+
WHEN tpt_transfer_in_obs.value_numeric IS NOT NULL THEN 1
|
235
|
+
ELSE 0
|
236
|
+
END AS transfer_in,
|
237
|
+
MAX(o.start_date) AS last_dispensed_date,
|
238
|
+
MAX(o.auto_expire_date) AS auto_expire_date
|
239
|
+
FROM orders o
|
240
|
+
INNER JOIN concept_name cn
|
241
|
+
ON cn.concept_id = o.concept_id
|
242
|
+
AND cn.name IN ('Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine')
|
243
|
+
#{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
|
244
|
+
LEFT JOIN obs tpt_transfer_in_obs
|
245
|
+
ON tpt_transfer_in_obs.person_id = o.patient_id
|
246
|
+
AND tpt_transfer_in_obs.concept_id = #{::ConceptName.find_by_name('TPT Drugs Received').concept_id}
|
247
|
+
AND tpt_transfer_in_obs.voided = 0
|
248
|
+
#{site_manager(operator: 'AND', column: 'tpt_transfer_in_obs.site_id', location: @location)}
|
249
|
+
AND tpt_transfer_in_obs.value_drug IN (SELECT drug_id FROM drug WHERE concept_id IN (SELECT concept_id FROM concept_name WHERE name IN ('Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine')))
|
250
|
+
INNER JOIN drug_order dor
|
251
|
+
ON dor.order_id = o.order_id
|
252
|
+
AND dor.quantity > 0
|
253
|
+
WHERE DATE(o.start_date) BETWEEN DATE(#{c_start_date}) AND DATE(#{c_end_date})
|
254
|
+
AND o.order_type_id IN (SELECT order_type_id FROM order_type WHERE name = 'Drug order')
|
255
|
+
AND o.voided = 0
|
256
|
+
AND o.patient_id = #{patient_id}
|
257
|
+
GROUP BY o.patient_id
|
258
|
+
SQL
|
259
|
+
end
|
260
|
+
|
261
|
+
def process_current_tpt_course_date(patient_id)
|
262
|
+
result = client_tpt_dates(patient_id)
|
263
|
+
return { start_date: '1900-01-01', end_date: } if result.blank?
|
264
|
+
|
265
|
+
sorted_result = result.sort { |a, b| a['start_date'].to_date <=> b['start_date'].to_date }.reverse
|
266
|
+
return_date = { start_date: sorted_result.last['start_date'], end_date: }
|
267
|
+
|
268
|
+
course_interruption = result.first['course'] == '3HP' ? 1 : 2
|
269
|
+
# loop through the result array and find the first gap in the dates that equals the course interruption
|
270
|
+
sorted_result.each_with_index do |row, index|
|
271
|
+
next if index.zero?
|
272
|
+
|
273
|
+
diff = ActiveRecord::Base.connection.select_one("SELECT TIMESTAMPDIFF(MONTH,DATE('#{row['end_date']}'), DATE('#{sorted_result[index - 1]['start_date']}')) as months")['months']
|
274
|
+
|
275
|
+
if diff.to_i >= course_interruption
|
276
|
+
return_date = { start_date: sorted_result[index - 1]['start_date'], end_date: }
|
277
|
+
break
|
278
|
+
end
|
279
|
+
end
|
280
|
+
return_date
|
281
|
+
end
|
282
|
+
|
283
|
+
def client_tpt_dates(patient_id)
|
284
|
+
ActiveRecord::Base.connection.select_all <<~SQL
|
285
|
+
(
|
286
|
+
SELECT
|
287
|
+
DATE(o.value_datetime) AS start_date,
|
288
|
+
DATE(o.obs_datetime) AS end_date,
|
289
|
+
CASE
|
290
|
+
WHEN count(distinct(o.value_drug)) > 1 THEN '3HP'
|
291
|
+
WHEN o.value_drug = #{isoniazid_rifapentine_drug.drug_id} THEN '3HP'
|
292
|
+
ELSE '6H'
|
293
|
+
END AS course
|
294
|
+
FROM obs o
|
295
|
+
WHERE o.concept_id = #{::ConceptName.find_by_name('TPT Drugs Received').concept_id}
|
296
|
+
AND o.voided = 0
|
297
|
+
#{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
|
298
|
+
AND o.value_drug IN (SELECT drug_id FROM drug WHERE concept_id IN (SELECT concept_id FROM concept_name WHERE name IN ('Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine')))
|
299
|
+
AND o.person_id = #{patient_id}
|
300
|
+
AND o.value_numeric IS NOT NULL
|
301
|
+
AND DATE(o.obs_datetime) <= DATE(#{start_date})
|
302
|
+
GROUP BY DATE(o.obs_datetime)
|
303
|
+
ORDER BY DATE(o.obs_datetime) DESC
|
304
|
+
)
|
305
|
+
UNION
|
306
|
+
(
|
307
|
+
SELECT
|
308
|
+
DATE(o.start_date) AS start_date,
|
309
|
+
DATE(o.auto_expire_date) AS end_date,
|
310
|
+
CASE
|
311
|
+
WHEN count(distinct(o.concept_id)) > 1 THEN '3HP'
|
312
|
+
WHEN o.concept_id = #{isoniazid_rifapentine_concept.concept_id} THEN '3HP'
|
313
|
+
ELSE '6H'
|
314
|
+
END AS course
|
315
|
+
FROM orders o
|
316
|
+
INNER JOIN encounter e ON e.encounter_id = o.encounter_id AND e.voided = 0 AND e.program_id = 1 /* HIV PROGRAM */
|
317
|
+
INNER JOIN drug_order dor ON dor.order_id = o.order_id AND dor.quantity > 0
|
318
|
+
WHERE o.order_type_id IN (SELECT order_type_id FROM order_type WHERE name = 'Drug order')
|
319
|
+
AND o.voided = 0
|
320
|
+
#{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
|
321
|
+
AND o.concept_id IN (#{::ConceptName.where(name: ['Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine']).select(:concept_id).to_sql})
|
322
|
+
AND o.patient_id = #{patient_id}
|
323
|
+
AND o.auto_expire_date IS NOT NULL
|
324
|
+
AND DATE(o.start_date) <= DATE(#{start_date})
|
325
|
+
GROUP BY DATE(o.start_date)
|
326
|
+
ORDER BY DATE(o.start_date) DESC
|
327
|
+
)
|
328
|
+
SQL
|
329
|
+
end
|
330
|
+
|
331
|
+
def client_tpt_end_date(patient_id, start_date)
|
332
|
+
# Get patient tpt dispensations dates after the start date and before the end date
|
333
|
+
result = ActiveRecord::Base.connection.select_all <<~SQL
|
334
|
+
(
|
335
|
+
SELECT
|
336
|
+
DATE(o.value_datetime) AS start_date,
|
337
|
+
DATE(MAX(o.obs_datetime)) AS end_date,
|
338
|
+
CASE
|
339
|
+
WHEN count(distinct(o.value_drug)) > 1 THEN '3HP'
|
340
|
+
WHEN o.value_drug = #{isoniazid_rifapentine_drug.drug_id} THEN '3HP'
|
341
|
+
ELSE '6H'
|
342
|
+
END AS course
|
343
|
+
FROM obs o
|
344
|
+
WHERE o.concept_id = #{::ConceptName.find_by_name('TPT Drugs Received').concept_id}
|
345
|
+
AND o.voided = 0
|
346
|
+
#{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
|
347
|
+
AND o.value_drug IN (SELECT drug_id FROM drug WHERE concept_id IN (SELECT concept_id FROM concept_name WHERE name IN ('Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine')))
|
348
|
+
AND o.person_id = #{patient_id}
|
349
|
+
AND o.value_numeric IS NOT NULL
|
350
|
+
AND DATE(o.obs_datetime) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
|
351
|
+
GROUP BY DATE(o.obs_datetime)
|
352
|
+
ORDER BY DATE(o.obs_datetime) DESC
|
353
|
+
)
|
354
|
+
UNION
|
355
|
+
(
|
356
|
+
SELECT
|
357
|
+
DATE(o.start_date) AS start_date,
|
358
|
+
DATE(MAX(o.auto_expire_date)) AS end_date,
|
359
|
+
CASE
|
360
|
+
WHEN count(distinct(o.concept_id)) > 1 THEN '3HP'
|
361
|
+
WHEN o.concept_id = #{isoniazid_rifapentine_concept.concept_id} THEN '3HP'
|
362
|
+
ELSE '6H'
|
363
|
+
END AS course
|
364
|
+
FROM orders o
|
365
|
+
INNER JOIN encounter e ON e.encounter_id = o.encounter_id AND e.voided = 0 AND e.program_id = 1 /* HIV PROGRAM */
|
366
|
+
INNER JOIN drug_order dor ON dor.order_id = o.order_id AND dor.quantity > 0
|
367
|
+
WHERE o.order_type_id IN (SELECT order_type_id FROM order_type WHERE name = 'Drug order')
|
368
|
+
AND o.voided = 0
|
369
|
+
#{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
|
370
|
+
AND o.concept_id IN (#{::ConceptName.where(name: ['Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine']).select(:concept_id).to_sql})
|
371
|
+
AND o.patient_id = #{patient_id}
|
372
|
+
AND o.auto_expire_date IS NOT NULL
|
373
|
+
AND DATE(o.start_date) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
|
374
|
+
GROUP BY DATE(o.start_date)
|
375
|
+
ORDER BY DATE(o.start_date) DESC
|
376
|
+
)
|
377
|
+
SQL
|
378
|
+
|
379
|
+
return end_date if result.blank?
|
380
|
+
|
381
|
+
sorted_result = result.sort { |a, b| a['start_date'].to_date <=> b['start_date'].to_date }
|
382
|
+
return_date = sorted_result.last['end_date']
|
383
|
+
course_interruption = result.first['course'] == '3HP' ? 1 : 2
|
384
|
+
# use a for loop to check if there is a course interruption
|
385
|
+
sorted_result.each_with_index do |row, i|
|
386
|
+
next if i.zero?
|
387
|
+
|
388
|
+
if row['course'] != sorted_result[i - 1]['course']
|
389
|
+
return_date = sorted_result[i - 1]['end_date']
|
390
|
+
break
|
391
|
+
end
|
392
|
+
diff = ActiveRecord::Base.connection.select_one("SELECT TIMESTAMPDIFF(MONTH,DATE('#{sorted_result[i - 1]['end_date']}'),DATE('#{row['start_date']}')) as months")['months']
|
393
|
+
if diff.to_i >= course_interruption
|
394
|
+
return_date = sorted_result[i - 1]['end_date']
|
395
|
+
break
|
396
|
+
end
|
397
|
+
end
|
398
|
+
return_date
|
399
|
+
end
|
400
|
+
|
401
|
+
##
|
402
|
+
# Groups patients into their TPT categories (ie 6H and 3HP) based on their drugs
|
403
|
+
#
|
404
|
+
# Returns an object with a three_hp and six_h methods, each of which
|
405
|
+
# is an array of patients for that category.
|
406
|
+
def group_patients_by_tpt_course(patients)
|
407
|
+
patients.each_with_object(OpenStruct.new(six_h: [], three_hp: [])) do |patient, categories|
|
408
|
+
if patient_on_3hp?(patient)
|
409
|
+
categories.three_hp << patient
|
410
|
+
else
|
411
|
+
categories.six_h << patient
|
412
|
+
end
|
413
|
+
end
|
414
|
+
end
|
415
|
+
|
416
|
+
def isoniazid_rifapentine_drug
|
417
|
+
@isoniazid_rifapentine_drug ||= ::Drug.find_by!(concept_id: isoniazid_rifapentine_concept.concept_id)
|
418
|
+
end
|
419
|
+
end
|
420
|
+
end
|
421
|
+
end
|
@@ -0,0 +1,181 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
module MalawiHivProgramReports
|
4
|
+
module Pepfar
|
5
|
+
# This class is used to generate the TPT Status report for an ART patient
|
6
|
+
class TptStatus
|
7
|
+
attr_reader :start_date, :end_date, :patient_id
|
8
|
+
|
9
|
+
include Utils
|
10
|
+
|
11
|
+
def initialize(start_date:, end_date:, **kwargs)
|
12
|
+
@start_date = start_date
|
13
|
+
@end_date = end_date
|
14
|
+
@patient_id = kwargs[:patient_id]
|
15
|
+
@tpt_status = {}
|
16
|
+
end
|
17
|
+
|
18
|
+
def find_report
|
19
|
+
patient_tpt_status
|
20
|
+
rescue StandardError => e
|
21
|
+
Rails.logger.error("Error generating TPT Status report for patient #{patient_id}: #{e.message}")
|
22
|
+
Rails.logger.error(e.backtrace.join("\n"))
|
23
|
+
raise e
|
24
|
+
end
|
25
|
+
|
26
|
+
private
|
27
|
+
|
28
|
+
def patient_tpt_status
|
29
|
+
return tb_treatment_status if patient_on_tb_treatment?(patient_id)
|
30
|
+
return completed_tpt_status if patient_history_on_completed_tpt
|
31
|
+
|
32
|
+
patient = TbPrev3.new(start_date:, end_date:).fetch_individual_report(patient_id)
|
33
|
+
return default_status if patient.blank?
|
34
|
+
|
35
|
+
tpt_status_based_on_patient(patient)
|
36
|
+
end
|
37
|
+
|
38
|
+
def tb_treatment_status
|
39
|
+
{
|
40
|
+
tpt: nil,
|
41
|
+
completed: false,
|
42
|
+
tb_treatment: true,
|
43
|
+
tpt_init_date: nil,
|
44
|
+
tpt_complete_date: nil,
|
45
|
+
eligible: {
|
46
|
+
'3HP': false,
|
47
|
+
'6H': false
|
48
|
+
}
|
49
|
+
}
|
50
|
+
end
|
51
|
+
|
52
|
+
def completed_tpt_status
|
53
|
+
tpt = patient_history_on_completed_tpt.include?('IPT') ? '6H' : '3HP'
|
54
|
+
{ tpt:, completed: true, tb_treatment: false, tpt_init_date: nil, tpt_complete_date: nil, tpt_end_date: nil,
|
55
|
+
eligible: {
|
56
|
+
'3HP': false,
|
57
|
+
'6H': false
|
58
|
+
} }
|
59
|
+
end
|
60
|
+
|
61
|
+
def default_status
|
62
|
+
patient = ::Patient.find(patient_id)
|
63
|
+
art_start_date = patient.art_start_date
|
64
|
+
{ tpt: nil, completed: false, tb_treatment: false, tpt_init_date: nil, tpt_complete_date: nil, tpt_end_date: nil,
|
65
|
+
eligible: {
|
66
|
+
'3HP': art_start_date ? difference_in_months(end_date.to_date, art_start_date.to_date) < 3 : true,
|
67
|
+
'6H': art_start_date ? difference_in_months(end_date.to_date, art_start_date.to_date) < 3 : true
|
68
|
+
} }
|
69
|
+
end
|
70
|
+
|
71
|
+
def tpt_status_based_on_patient(patient)
|
72
|
+
tpt = determine_tpt(patient)
|
73
|
+
completed = patient_has_totally_completed_tpt?(patient, tpt)
|
74
|
+
tpt_init_date = patient['tpt_initiation_date']
|
75
|
+
tpt_current_expiry_date = patient['auto_expire_date']&.to_date
|
76
|
+
diff_in_months = difference_in_months(end_date.to_date, tpt_current_expiry_date)
|
77
|
+
art_start_date = ::Patient.find(patient_id).art_start_date
|
78
|
+
tpt_complete_date = completed ? patient['auto_expire_date']&.to_date : nil
|
79
|
+
tpt_end_date = calculate_tpt_end_date(tpt, tpt_init_date)
|
80
|
+
tpt_name = determine_tpt_name(tpt, patient)
|
81
|
+
arv_drug_runout_date = patient_arv_drug_runout_date
|
82
|
+
|
83
|
+
@tpt_status.merge!({ tpt: tpt_name, completed:, tb_treatment: false,
|
84
|
+
tpt_init_date:, tpt_complete_date:,
|
85
|
+
tpt_end_date:, art_start_date:,
|
86
|
+
art_drug_auto_expire_date: arv_drug_runout_date })
|
87
|
+
determine_eligibility(tpt, diff_in_months, art_start_date, arv_drug_runout_date)
|
88
|
+
end
|
89
|
+
|
90
|
+
def determine_tpt(patient)
|
91
|
+
patient_on_3hp?(patient) ? '3HP' : '6H'
|
92
|
+
end
|
93
|
+
|
94
|
+
def determine_tpt_name(tpt, patient)
|
95
|
+
if tpt == '6H'
|
96
|
+
'IPT'
|
97
|
+
else
|
98
|
+
(patient['drug_concepts'].split(',').length > 1 ? '3HP (RFP + INH)' : 'INH 300 / RFP 300 (3HP)')
|
99
|
+
end
|
100
|
+
end
|
101
|
+
|
102
|
+
def calculate_tpt_end_date(tpt, tpt_init_date)
|
103
|
+
tpt == '6H' ? tpt_init_date + 6.months : tpt_init_date + 3.months
|
104
|
+
end
|
105
|
+
|
106
|
+
def determine_eligibility(tpt, diff_in_months, art_start_date, arv_drug_runout_date)
|
107
|
+
three_hp_eligible = false
|
108
|
+
six_h_eligible = false
|
109
|
+
tpt_init_date = @tpt_status[:tpt_init_date]
|
110
|
+
tpt_end_date = @tpt_status[:tpt_end_date]
|
111
|
+
case tpt
|
112
|
+
when '3HP'
|
113
|
+
# 3HP is taken 1 dose per week
|
114
|
+
# if client misses dose for less than a month, they are eligible
|
115
|
+
# if client misses more than a month:
|
116
|
+
# check if they have been on ART for less than 3 months, they are eligible
|
117
|
+
# if they have been on ART continuosly for more than 3 months, they are not eligible
|
118
|
+
three_hp_eligible = true if diff_in_months <= 1
|
119
|
+
if diff_in_months > 1 && (arv_drug_runout_date && difference_in_months(arv_drug_runout_date.to_date,
|
120
|
+
art_start_date.to_date) < 3)
|
121
|
+
# Patient defaulted for ART and TPT and was on ART for less than 3 months: patient TPT status is reset
|
122
|
+
three_hp_eligible = true
|
123
|
+
six_h_eligible = true
|
124
|
+
tpt_end_date = nil
|
125
|
+
tpt_init_date = nil
|
126
|
+
@tpt_status[:tpt] = nil
|
127
|
+
end
|
128
|
+
when '6H'
|
129
|
+
# 6H is taken 1 dose per day
|
130
|
+
# if client misses dose for less than 2 months, they are eligible
|
131
|
+
# if client misses more than a month:
|
132
|
+
# check if they have been on ART for less than 3 months, they are eligible
|
133
|
+
# if they have been on ART continuosly for more than 3 months, they are not eligible
|
134
|
+
six_h_eligible = true if diff_in_months <= 2
|
135
|
+
if diff_in_months > 2 && (arv_drug_runout_date && difference_in_months(arv_drug_runout_date.to_date,
|
136
|
+
art_start_date.to_date) < 3)
|
137
|
+
# Patient defaulted for ART and TPT and was on ART for less than 3 months: patient TPT status is reset
|
138
|
+
three_hp_eligible = true
|
139
|
+
six_h_eligible = true
|
140
|
+
tpt_end_date = nil
|
141
|
+
tpt_init_date = nil
|
142
|
+
@tpt_status[:tpt] = nil
|
143
|
+
end
|
144
|
+
end
|
145
|
+
@tpt_status.merge!({
|
146
|
+
tpt_init_date:,
|
147
|
+
tpt_end_date:,
|
148
|
+
eligible: {
|
149
|
+
'3HP': three_hp_eligible,
|
150
|
+
'6H': six_h_eligible
|
151
|
+
}
|
152
|
+
})
|
153
|
+
end
|
154
|
+
|
155
|
+
def patient_has_totally_completed_tpt?(patient, tpt)
|
156
|
+
if tpt == '3HP'
|
157
|
+
init_date = patient['tpt_initiation_date'].to_date
|
158
|
+
end_date = patient['auto_expire_date'].to_date
|
159
|
+
days_on_medication = (end_date - init_date).to_i
|
160
|
+
days_on_medication >= 80
|
161
|
+
else
|
162
|
+
patient['total_days_on_medication'].to_i >= 176
|
163
|
+
end
|
164
|
+
end
|
165
|
+
|
166
|
+
def patient_arv_drug_runout_date
|
167
|
+
::Patient.find(patient_id).last_arv_drug_expire_date
|
168
|
+
end
|
169
|
+
|
170
|
+
def patient_history_on_completed_tpt
|
171
|
+
@patient_history_on_completed_tpt ||= ::Observation.where(person_id: patient_id,
|
172
|
+
concept_id: ::ConceptName.find_by_name('Previous TB treatment history').concept_id)
|
173
|
+
.where("value_text LIKE '%complete%' AND obs_datetime < DATE('#{end_date}') + INTERVAL 1 DAY")&.first&.value_text
|
174
|
+
end
|
175
|
+
|
176
|
+
def difference_in_months(date1, date2)
|
177
|
+
((date1.year * 12) + date1.month) - ((date2.year * 12) + date2.month)
|
178
|
+
end
|
179
|
+
end
|
180
|
+
end
|
181
|
+
end
|