malawi_hiv_program_reports 1.0.25 → 1.0.26
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/app/services/malawi_hiv_program_reports/moh/cumulative_cohort.rb +62 -55
- data/app/services/malawi_hiv_program_reports/moh/cumulative_outcome.rb +255 -212
- data/app/services/malawi_hiv_program_reports/pepfar/tx_ml.rb +55 -110
- data/app/services/malawi_hiv_program_reports/pepfar/tx_new.rb +58 -59
- data/app/services/malawi_hiv_program_reports/pepfar/tx_rtt.rb +42 -160
- data/lib/malawi_hiv_program_reports/version.rb +1 -1
- metadata +2 -2
@@ -3,7 +3,7 @@
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module MalawiHivProgramReports
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module Pepfar
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class TxMl
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attr_reader :start_date, :end_date, :location
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attr_reader :start_date, :end_date, :location, :rebuild
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include Utils
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include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
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@@ -12,69 +12,30 @@ module MalawiHivProgramReports
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def initialize(start_date:, end_date:, **kwargs)
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@start_date = start_date.to_date.strftime('%Y-%m-%d 00:00:00')
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@end_date = end_date.to_date.strftime('%Y-%m-%d 23:59:59')
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@occupation = kwargs[:occupation]
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@location = kwargs[:location]
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@
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@rebuild = kwargs[:rebuild]&.casecmp?('true')
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end
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def find_report
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if rebuild
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cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date:, end_date:, definition: 'pepfar', locations: location.to_s, rebuild: true)
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cohort.find_report
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end
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process_data
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end
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private
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def
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def process_data
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data = {}
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tx_new = new_potential_tx_ml_clients
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patient_ids = []
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earliest_start_dates = {}
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(tx_curr || []).each do |pat|
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patient_id = pat['patient_id'].to_i
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patient_ids << patient_id
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earliest_start_dates[patient_id] = begin
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pat['earliest_start_date'].to_date
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rescue StandardError
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pat['date_enrolled'].to_date
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end
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end
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(tx_new || []).each do |pat|
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(process_tx_ml_clients || []).each do |pat|
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patient_id = pat['patient_id'].to_i
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patient_ids << patient_id
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patient_ids = patient_ids.uniq
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earliest_start_dates[patient_id] = begin
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pat['earliest_start_date'].to_date
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rescue StandardError
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pat['date_enrolled'].to_date
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end
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patient_ids << pat['patient_id']
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patient_ids = patient_ids.uniq
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end
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return [] if patient_ids.blank?
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filtered_patients = ActiveRecord::Base.connection.select_all <<~SQL
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SELECT
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p.person_id patient_id, birthdate, gender,
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#{function_manager(function: 'pepfar_patient_outcome', location: @location, args: "p.person_id::int, '#{end_date.to_date}'::date, #{@location}::int")} outcome,
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#{function_manager(function: 'disaggregated_age_group', location: @location, args: "p.birthdate::date, '#{end_date.to_date}::date'")} age_group
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FROM person #{current_partition} p
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WHERE #{in_manager(column: 'p.person_id', values: patient_ids)}
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GROUP BY p.person_id #{group_by_columns('p.birthdate, p.gender')}
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SQL
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(filtered_patients || []).each do |pat|
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outcome = pat['outcome']
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next if outcome == 'On antiretrovirals'
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patient_id = pat['patient_id'].to_i
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gender = begin
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pat['gender'].first.upcase
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rescue StandardError
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'Unknown'
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end
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age_group = pat['age_group']
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if data[age_group].blank?
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@@ -86,7 +47,7 @@ module MalawiHivProgramReports
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case outcome
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when 'Defaulted'
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def_months =
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def_months = pat['months'].to_i
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if def_months < 3
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data[age_group][gender][1] << patient_id
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elsif def_months <= 5
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@@ -104,70 +65,54 @@ module MalawiHivProgramReports
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rescue StandardError => e
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Rails.logger.error(e.message)
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end
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-
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data
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end
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def
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AND
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GROUP BY
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SQL
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def tx_ml_clients
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<<~SQL
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SELECT
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e.patient_id,
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e.birthdate,
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e.gender,
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e.date_enrolled,
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e.earliest_start_date,
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o.outcome_date,
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TIMESTAMPDIFF(MONTH, DATE(e.earliest_start_date), DATE(o.outcome_date)) months,
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disaggregated_age_group(e.birthdate, DATE('#{end_date}')) age_group,
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o.cum_outcome outcome
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FROM cdr_temp_cohort_members #{current_partition} e
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INNER JOIN cdr_temp_patient_outcomes #{current_partition} o ON e.patient_id = o.patient_id AND o.cum_outcome IN ('Defaulted', 'Patient died', 'Treatment stopped', 'Patient transferred out')
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WHERE e.patient_id IN (SELECT patient_id FROM cdr_temp_patient_outcomes_start #{current_partition} WHERE cum_outcome = 'On antiretrovirals')
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AND DATE(e.date_enrolled) < '#{start_date.to_date}'
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GROUP BY e.patient_id
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SQL
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end
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def
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GROUP BY
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SQL
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def tx_ml_clients_new
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<<~SQL
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SELECT
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e.patient_id,
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e.birthdate,
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e.gender,
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e.date_enrolled,
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e.earliest_start_date,
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o.outcome_date,
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TIMESTAMPDIFF(MONTH, DATE(e.earliest_start_date), DATE(o.outcome_date)) months,
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disaggregated_age_group(e.birthdate, DATE('#{end_date}')) age_group,
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o.cum_outcome outcome
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FROM cdr_temp_cohort_members #{current_partition} e
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INNER JOIN cdr_temp_patient_outcomes #{current_partition} o ON e.patient_id = o.patient_id AND o.cum_outcome IN ('Defaulted', 'Patient died', 'Treatment stopped', 'Patient transferred out')
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WHERE e.date_enrolled BETWEEN DATE('#{start_date}') AND DATE('#{end_date}')
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GROUP BY e.patient_id
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SQL
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end
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def
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defaulter_date['def_date'].to_date
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rescue StandardError
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end_date.to_date
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end
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raise 'Defaulted outside the reporting period' if defaulter_date > end_date.to_date
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raise 'Defaulted outside the reporting period' if defaulter_date < start_date.to_date
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days_gone = ActiveRecord::Base.connection.select_one <<~SQL
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SELECT TIMESTAMPDIFF(MONTH, DATE('#{earliest_start_date}'), DATE('#{defaulter_date}')) months;
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SQL
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days_gone['months'].to_i
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def process_tx_ml_clients
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ActiveRecord::Base.connection.select_all <<~SQL
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(#{tx_ml_clients})
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UNION
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(#{tx_ml_clients_new})
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SQL
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end
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end
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end
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def initialize(start_date:, end_date:, **kwargs)
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@start_date = start_date.to_date.beginning_of_day.strftime('%Y-%m-%d %H:%M:%S')
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@end_date = end_date.to_date.end_of_day.strftime('%Y-%m-%d %H:%M:%S')
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@rebuild = rebuild_string.present? ? rebuild_string&.downcase == 'true' : false
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@rebuild = kwargs[:rebuild]&.casecmp?('true')
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@location = kwargs[:location]
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end
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report = init_report
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addittional_groups report
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if rebuild
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MalawiHivProgramReports::Moh::
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cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date:, end_date:, definition: 'pepfar', locations: location.to_s, rebuild: true)
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cohort.find_report
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end
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process_data report
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flatten_the_report report
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end
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end
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# rubocop:disable Metrics/AbcSize
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# rubocop:disable Metrics/MethodLength
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# rubocop:disable Metrics/PerceivedComplexity
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# rubocop:disable Metrics/CyclomaticComplexity
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def process_data(report)
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fetch_data.each do |row|
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age_group = row['age_group']
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gender = row['gender']
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date_enrolled = row['date_enrolled']
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report['All']['FNP'][indicator.to_sym] << kwargs[:patient_id]
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end
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end
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# rubocop:enable Metrics/PerceivedComplexity
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# rubocop:enable Metrics/CyclomaticComplexity
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def process_age_group_report(age_group, gender, age_group_report)
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{
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else
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(gender == 'M' ? 'Male' : gender)
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end,
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cd4_less_than_200: age_group_report[
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cd4_greater_than_equal_to_200: age_group_report[
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cd4_unknown_or_not_done: age_group_report[
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transfer_in: age_group_report[
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cd4_less_than_200: age_group_report['cd4_less_than_200'.to_sym],
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cd4_greater_than_equal_to_200: age_group_report['cd4_greater_than_equal_to_200'.to_sym],
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cd4_unknown_or_not_done: age_group_report['cd4_unknown_or_not_done'.to_sym],
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transfer_in: age_group_report['transfer_in'.to_sym]
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}
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end
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# rubocop:enable Metrics/AbcSize
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# rubocop:enable Metrics/MethodLength
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def flatten_the_report(report)
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result = []
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result_scores.reject { |item| item[:age_group].match?(/unknown/i) }
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end
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def
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def fetch_data
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ActiveRecord::Base.connection.select_all <<~SQL
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AND transfer_in.voided = 0
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AND transfer_in.value_coded = #{concept_name('Yes').concept_id}
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AND transfer_in.obs_datetime <= '#{end_date}'
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AND transfer_in.obs_datetime >= '#{start_date}'
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LEFT JOIN obs #{current_partition} pregnant_or_breastfeeding ON pregnant_or_breastfeeding.person_id = pp.patient_id
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AND pregnant_or_breastfeeding.concept_id IN (SELECT concept_id FROM concept_name WHERE name IN ('Breast feeding?', 'Breast feeding', 'Breastfeeding', 'Is patient pregnant?', 'patient pregnant') AND voided = 0)
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AND pregnant_or_breastfeeding.voided = 0
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AND pregnant_or_breastfeeding.value_coded = #{concept_name('Yes').concept_id}
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SELECT
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e.patient_id,
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e.gender,
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disaggregated_age_group(e.birthdate, DATE('#{end_date}')) age_group,
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CASE
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WHEN o.value_numeric < 200 THEN 'cd4_less_than_200'
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WHEN o.value_numeric = 200 AND o.value_modifier = '=' THEN 'cd4_greater_than_equal_to_200'
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WHEN o.value_numeric = 200 AND o.value_modifier = '<' THEN 'cd4_less_than_200'
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WHEN o.value_numeric = 200 AND o.value_modifier = '>' THEN 'cd4_greater_than_equal_to_200'
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WHEN o.value_numeric > 200 THEN 'cd4_greater_than_equal_to_200'
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ELSE 'cd4_unknown_or_not_done'
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END cd4_count_group,
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CASE
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WHEN e.recorded_start_date IS NULL THEN 1
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ELSE 0
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END new_patient,
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e.date_enrolled,
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e.earliest_start_date,
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preg_or_breast.name AS maternal_status,
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DATE(MIN(pregnant_or_breastfeeding.obs_datetime)) AS maternal_status_date
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FROM cdr_temp_cohort_members #{current_partition} e
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LEFT JOIN (
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SELECT max(o.obs_datetime) AS obs_datetime, o.person_id
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FROM obs #{current_partition} o
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INNER JOIN concept_name cn ON cn.concept_id = o.concept_id AND cn.name = 'CD4 count' AND cn.voided = 0
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INNER JOIN patient_program #{current_partition} pp ON pp.patient_id = o.person_id
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AND pp.program_id = #{program('HIV PROGRAM').id}
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AND pp.voided = 0
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INNER JOIN patient_state #{current_partition} ps ON ps.patient_program_id = pp.patient_program_id AND ps.voided = 0 AND ps.state = 7 AND ps.start_date <= DATE('#{end_date}')
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WHERE o.concept_id = #{concept_name('CD4 count').concept_id} AND o.voided = 0
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AND o.obs_datetime <= '#{end_date}' AND o.obs_datetime >= '#{start_date}'
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GROUP BY o.person_id
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) current_cd4 ON current_cd4.person_id = e.patient_id
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LEFT JOIN obs #{current_partition} o ON o.person_id = e.patient_id AND o.concept_id = #{concept_name('CD4 count').concept_id} AND o.voided = 0 AND o.obs_datetime = current_cd4.obs_datetime
|
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LEFT JOIN obs #{current_partition} pregnant_or_breastfeeding ON pregnant_or_breastfeeding.person_id = e.patient_id
|
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AND pregnant_or_breastfeeding.concept_id IN (SELECT concept_id FROM concept_name WHERE name IN ('Breast feeding?', 'Breast feeding', 'Breastfeeding', 'Is patient pregnant?', 'patient pregnant') AND voided = 0)
|
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AND pregnant_or_breastfeeding.voided = 0
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AND pregnant_or_breastfeeding.value_coded = #{concept_name('Yes').concept_id}
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LEFT JOIN concept_name preg_or_breast ON preg_or_breast.concept_id = pregnant_or_breastfeeding.concept_id AND preg_or_breast.voided = 0
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WHERE e.date_enrolled <= '#{end_date}' AND e.date_enrolled >= '#{start_date}'
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GROUP BY e.patient_id
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SQL
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end
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end
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# rubocop:enable Metrics/ClassLength
|
@@ -7,20 +7,28 @@ module MalawiHivProgramReports
|
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7
7
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include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
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8
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include MalawiHivProgramReports::Adapters::Moh::Custom
|
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9
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include MalawiHivProgramReports::Utils::ModelUtils
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10
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-
attr_reader :start_date, :end_date, :location
|
10
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+
attr_reader :start_date, :end_date, :location, :rebuild
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11
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12
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def initialize(start_date:, end_date:, **kwargs)
|
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@start_date = ActiveRecord::Base.connection.quote(start_date.to_date.beginning_of_day.strftime('%Y-%m-%d %H:%M:%S'))
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14
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@end_date = ActiveRecord::Base.connection.quote(end_date.to_date.end_of_day.strftime('%Y-%m-%d %H:%M:%S'))
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15
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-
@
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15
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+
@rebuild = kwargs[:rebuild]&.casecmp?(true)
|
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@location = kwargs[:location]
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end
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18
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19
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def find_report
|
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+
if rebuild
|
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+
cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date:, end_date:, definition: 'pepfar', locations: location.to_s, rebuild: true)
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+
cohort.find_report
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+
end
|
20
24
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process_report
|
21
25
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end
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26
|
|
23
27
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def data
|
28
|
+
if rebuild
|
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+
cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date:, end_date:, definition: 'pepfar', locations: location.to_s, rebuild: true)
|
30
|
+
cohort.find_report
|
31
|
+
end
|
24
32
|
process_report
|
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33
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rescue StandardError => e
|
26
34
|
Rails.logger.error "Error running TX_RTT Report: #{e}"
|
@@ -47,7 +55,7 @@ module MalawiHivProgramReports
|
|
47
55
|
end
|
48
56
|
|
49
57
|
def process_data(report)
|
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-
|
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|
+
fetch_data.each do |row|
|
51
59
|
age_group = row['age_group']
|
52
60
|
gender = row['gender']
|
53
61
|
months = row['months']
|
@@ -64,14 +72,17 @@ module MalawiHivProgramReports
|
|
64
72
|
end
|
65
73
|
|
66
74
|
def process_months(report, months, patient_id)
|
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|
-
report[:returned_less_than_3_months] << patient_id if months.blank?
|
68
|
-
report[:returned_less_than_3_months] << patient_id if months < 3
|
69
|
-
|
75
|
+
return report[:returned_less_than_3_months] << patient_id if months.blank?
|
76
|
+
return report[:returned_less_than_3_months] << patient_id if months < 3
|
77
|
+
if months >= 3 && months < 6
|
78
|
+
return report[:returned_greater_than_3_months_and_less_than_6_months] << patient_id
|
79
|
+
end
|
80
|
+
|
70
81
|
report[:returned_greater_than_or_equal_to_6_months] << patient_id if months >= 6
|
71
82
|
end
|
72
83
|
|
73
84
|
def process_cd4(report, months, patient_id, cd4_cat)
|
74
|
-
if cd4_cat == 'unknown_cd4_count' && months <= 2
|
85
|
+
if cd4_cat == 'unknown_cd4_count' && (months.blank? || months <= 2)
|
75
86
|
report[:not_eligible_for_cd4] << patient_id
|
76
87
|
return
|
77
88
|
end
|
@@ -120,160 +131,31 @@ module MalawiHivProgramReports
|
|
120
131
|
sorted_results.sort_by { |h| [h[:gender] == 'F' ? 0 : 1] }
|
121
132
|
end
|
122
133
|
|
123
|
-
def
|
134
|
+
def fetch_data
|
124
135
|
ActiveRecord::Base.connection.select_all <<~SQL
|
125
|
-
SELECT
|
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|
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|
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|
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|
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-
|
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-
|
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-
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-
|
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-
|
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|
-
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|
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-
|
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|
-
|
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|
-
|
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-
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-
|
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-
|
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|
-
|
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|
-
|
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|
-
|
147
|
-
|
148
|
-
)
|
149
|
-
) AS final_outcome,
|
150
|
-
TIMESTAMPDIFF(MONTH, IF(
|
151
|
-
patient_state_at_start_of_quarter.state = 6,
|
152
|
-
patient_state_at_start_of_quarter.start_date,
|
153
|
-
IF(
|
154
|
-
patient_state_at_start_of_quarter.state = 12,
|
155
|
-
patient_state_at_start_of_quarter.start_date,
|
156
|
-
#{function_manager(function: 'current_pepfar_defaulter_date', location: @location, args: "patient_program.patient_id, (DATE(#{@start_date}) - INTERVAL 1 DAY), #{@location}")})
|
157
|
-
), patients_who_received_art_in_quarter.start_date) AS months,
|
158
|
-
CASE
|
159
|
-
WHEN cd4_result.value_numeric < 200 THEN 'cd4_less_than_200'
|
160
|
-
WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '=' THEN 'cd4_greater_than_or_equal_to_200'
|
161
|
-
WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '<' THEN 'cd4_less_than_200'
|
162
|
-
WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '>' THEN 'cd4_greater_than_or_equal_to_200'
|
163
|
-
WHEN cd4_result.value_numeric > 200 THEN 'cd4_greater_than_or_equal_to_200'
|
164
|
-
ELSE 'unknown_cd4_count'
|
165
|
-
END cd4_count_group
|
166
|
-
FROM patient_program #{current_partition}
|
167
|
-
INNER JOIN person #{current_partition} ON person.person_id = patient_program.patient_id
|
168
|
-
/* Select patients that were on treatment before start of reporting period */
|
169
|
-
INNER JOIN patient_state #{current_partition} AS patient_ever_on_treatment
|
170
|
-
ON patient_ever_on_treatment.patient_program_id = patient_program.patient_program_id
|
171
|
-
AND patient_ever_on_treatment.state = 7
|
172
|
-
AND patient_ever_on_treatment.start_date < DATE(#{start_date})
|
173
|
-
AND patient_ever_on_treatment.voided = 0
|
174
|
-
/* Get patient's state at the start of the quarter. */
|
175
|
-
INNER JOIN (
|
176
|
-
SELECT patient_program_id, MAX(patient_state.date_created) AS date_created
|
177
|
-
FROM patient_state #{current_partition}
|
178
|
-
INNER JOIN patient_program #{current_partition} USING (patient_program_id)
|
179
|
-
WHERE patient_state.voided = 0
|
180
|
-
AND patient_program.voided = 0
|
181
|
-
AND patient_program.program_id = 1
|
182
|
-
AND patient_state.start_date < DATE(#{start_date}) + INTERVAL 1 DAY
|
183
|
-
GROUP BY patient_program_id
|
184
|
-
) AS date_of_last_patient_state_before_quarter
|
185
|
-
ON date_of_last_patient_state_before_quarter.patient_program_id = patient_program.patient_program_id
|
186
|
-
LEFT JOIN patient_state #{current_partition} AS patient_state_at_start_of_quarter
|
187
|
-
ON patient_state_at_start_of_quarter.patient_program_id = date_of_last_patient_state_before_quarter.patient_program_id
|
188
|
-
AND patient_state_at_start_of_quarter.date_created = date_of_last_patient_state_before_quarter.date_created
|
189
|
-
AND patient_state_at_start_of_quarter.state IN (6, 12) /* 2: TO, 6: Tx Stopped, 12: Defaulted */
|
190
|
-
/* Select patients who received ART within the reporting period. */
|
191
|
-
INNER JOIN (
|
192
|
-
SELECT DISTINCT encounter.patient_id, orders.start_date
|
193
|
-
FROM encounter #{current_partition}
|
194
|
-
INNER JOIN orders #{current_partition}
|
195
|
-
ON orders.encounter_id = encounter.encounter_id
|
196
|
-
AND DATE(orders.start_date) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
|
197
|
-
AND orders.voided = 0
|
198
|
-
INNER JOIN drug_order #{current_partition}
|
199
|
-
ON drug_order.order_id = orders.order_id
|
200
|
-
AND drug_order.quantity > 0
|
201
|
-
AND drug_order.drug_inventory_id IN (SELECT DISTINCT drug_id FROM arv_drug)
|
202
|
-
WHERE encounter.voided = 0
|
203
|
-
AND encounter.program_id = 1
|
204
|
-
AND DATE(encounter.encounter_datetime) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
|
205
|
-
) AS patients_who_received_art_in_quarter
|
206
|
-
ON patients_who_received_art_in_quarter.patient_id = patient_program.patient_id
|
207
|
-
/* Ensure that patients are on ART at the end of the quarter */
|
208
|
-
INNER JOIN (
|
209
|
-
SELECT patient_program_id, MAX(patient_state.date_created) AS date_created
|
210
|
-
FROM patient_state #{current_partition}
|
211
|
-
INNER JOIN patient_program #{current_partition} USING (patient_program_id)
|
212
|
-
WHERE patient_state.voided = 0
|
213
|
-
AND patient_program.voided = 0
|
214
|
-
AND patient_program.program_id = 1
|
215
|
-
AND patient_state.start_date < DATE(#{end_date}) + INTERVAL 1 DAY
|
216
|
-
GROUP BY patient_program_id
|
217
|
-
) AS date_of_last_patient_state_in_quarter
|
218
|
-
ON date_of_last_patient_state_in_quarter.patient_program_id = patient_program.patient_program_id
|
219
|
-
|
220
|
-
/*Not sure why Walter had this section in but I believe its not neccessary*/
|
221
|
-
/*INNER JOIN patient_state AS patient_state_at_end_of_quarter
|
222
|
-
ON patient_state_at_end_of_quarter.patient_program_id = patient_program.patient_program_id
|
223
|
-
AND patient_state_at_end_of_quarter.date_created = date_of_last_patient_state_before_quarter.date_created
|
224
|
-
AND patient_state_at_end_of_quarter.state = 7*/
|
225
|
-
|
226
|
-
/* Select patient who had orders in the last 30 days of the reporting period.
|
227
|
-
This is to be used as a quick filter for patients who are definitely
|
228
|
-
'On ART' by the end of the reporting period. The rest will be filtered by
|
229
|
-
the current_defaulter function. */
|
230
|
-
LEFT JOIN (
|
231
|
-
SELECT DISTINCT encounter.patient_id
|
232
|
-
FROM encounter #{current_partition}
|
233
|
-
INNER JOIN orders #{current_partition}
|
234
|
-
ON orders.encounter_id = encounter.encounter_id
|
235
|
-
AND orders.voided = 0
|
236
|
-
AND DATE(orders.start_date) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
|
237
|
-
AND DATE(orders.auto_expire_date) >= (DATE(#{end_date}) - INTERVAL 30 DAY)
|
238
|
-
INNER JOIN drug_order #{current_partition}
|
239
|
-
ON drug_order.order_id = orders.order_id
|
240
|
-
AND drug_order.quantity > 0
|
241
|
-
AND drug_order.drug_inventory_id IN (SELECT DISTINCT drug_id FROM arv_drug)
|
242
|
-
WHERE encounter.program_id = 1
|
243
|
-
AND DATE(encounter.encounter_datetime) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
|
244
|
-
AND encounter.voided = 0
|
245
|
-
) AS patients_with_orders_at_end_of_quarter
|
246
|
-
ON patients_with_orders_at_end_of_quarter.patient_id = patient_program.patient_id
|
247
|
-
LEFT JOIN (
|
248
|
-
SELECT max(o.obs_datetime) AS obs_datetime, o.person_id
|
249
|
-
FROM obs #{current_partition} o
|
250
|
-
INNER JOIN concept_name cn ON cn.concept_id = o.concept_id AND cn.name = 'CD4 count'
|
251
|
-
WHERE o.concept_id = #{concept_name('CD4 count').concept_id} AND o.voided = 0
|
252
|
-
AND o.obs_datetime <= #{end_date} AND o.obs_datetime >= #{start_date}
|
253
|
-
GROUP BY o.person_id
|
254
|
-
) current_cd4 ON current_cd4.person_id = patient_program.patient_id
|
255
|
-
LEFT JOIN obs #{current_partition} cd4_result ON cd4_result.person_id = patient_program.patient_id AND cd4_result.concept_id = #{concept_name('CD4 count').concept_id} AND cd4_result.voided = 0
|
256
|
-
# Not sure why we are matching the two dates but the result was excluding cd4 results for patients.
|
257
|
-
# AND cd4_result.obs_datetime = current_cd4.obs_datetime
|
258
|
-
LEFT JOIN (#{current_occupation_query}) a ON a.person_id = patient_program.patient_id
|
259
|
-
WHERE patient_program.program_id = 1 #{%w[Military Civilian].include?(@occupation) ? 'AND' : ''} #{occupation_filter(occupation: @occupation, field_name: 'value', table_name: 'a', include_clause: false)}
|
260
|
-
/* Ensure that the patients retrieved, did not receive ART within 28 days
|
261
|
-
before the start of the reporting period */
|
262
|
-
AND patient_program.patient_id NOT IN (
|
263
|
-
SELECT DISTINCT orders.patient_id
|
264
|
-
FROM orders #{current_partition}
|
265
|
-
INNER JOIN drug_order #{current_partition} USING (order_id)
|
266
|
-
INNER JOIN arv_drug ON arv_drug.drug_id = drug_inventory_id
|
267
|
-
INNER JOIN patient_program #{current_partition}
|
268
|
-
ON patient_program.patient_id = orders.patient_id
|
269
|
-
AND patient_program.program_id = 1
|
270
|
-
WHERE ((DATE(orders.start_date )BETWEEN (DATE(#{start_date}) - INTERVAL 30 DAY) AND DATE(#{start_date}))
|
271
|
-
OR (DATE(orders.auto_expire_date) BETWEEN (DATE(#{start_date}) - INTERVAL 30 DAY) AND DATE(#{start_date})))
|
272
|
-
AND orders.voided = 0
|
273
|
-
)
|
274
|
-
GROUP BY patient_program.patient_id
|
275
|
-
HAVING initial_outcome IN ('Defaulted', 'Treatment stopped')
|
276
|
-
AND final_outcome = 'On antiretrovirals';
|
136
|
+
SELECT
|
137
|
+
e.patient_id,
|
138
|
+
disaggregated_age_group(e.birthdate, #{end_date}) AS age_group,
|
139
|
+
e.gender,
|
140
|
+
s.cum_outcome initial_outcome,
|
141
|
+
o.cum_outcome final_outcome,
|
142
|
+
TIMESTAMPDIFF(MONTH, COALESCE(s.outcome_date, c.outcome_date), ord.min_order_date) months,
|
143
|
+
CASE
|
144
|
+
WHEN cd4_result.value_numeric < 200 THEN 'cd4_less_than_200'
|
145
|
+
WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '=' THEN 'cd4_greater_than_or_equal_to_200'
|
146
|
+
WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '<' THEN 'cd4_less_than_200'
|
147
|
+
WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '>' THEN 'cd4_greater_than_or_equal_to_200'
|
148
|
+
WHEN cd4_result.value_numeric > 200 THEN 'cd4_greater_than_or_equal_to_200'
|
149
|
+
ELSE 'unknown_cd4_count'
|
150
|
+
END cd4_count_group
|
151
|
+
FROM cdr_temp_cohort_members #{current_partition} e
|
152
|
+
INNER JOIN cdr_temp_patient_outcomes #{current_partition} o ON o.patient_id = e.patient_id AND o.cum_outcome = 'On antiretrovirals'
|
153
|
+
INNER JOIN cdr_temp_patient_outcomes_start #{current_partition} s ON s.patient_id = e.patient_id AND s.cum_outcome IN ('Defaulted', 'Treatment stopped')
|
154
|
+
INNER JOIN cdr_temp_current_state_start #{current_partition} c ON c.patient_id = e.patient_id
|
155
|
+
INNER JOIN cdr_temp_max_drug_orders #{current_partition} ord ON ord.patient_id = e.patient_id
|
156
|
+
LEFT JOIN obs #{current_partition} cd4_result ON cd4_result.person_id = e.patient_id AND cd4_result.concept_id = #{concept_name('CD4 count').concept_id} AND cd4_result.voided = 0
|
157
|
+
WHERE e.date_enrolled < #{start_date}
|
158
|
+
GROUP BY e.patient_id
|
277
159
|
SQL
|
278
160
|
end
|
279
161
|
end
|