malawi_hiv_program_reports 1.0.26 → 1.0.27
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checksums.yaml
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metadata.gz: 8b8fed6ebe30ff7bc1f0573f0b560d33796ee13af2ff4de885c694dd023fbfc7
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data.tar.gz: 59b5f6b719c14f0eb297ee1ff9e8aabf54e69ffa7ab97cda0f803aa4414f1a01
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metadata.gz: 47261e1116d8d96465267866238b02402bddc68c6ff4385590fdf1e3347abebdbbe003250b313a993ae443cff4d9803d408f95a7199e14e4569c3aa335ce3ff8
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data.tar.gz: a32981a2ab869c4bd28de08625eca90cd3b93bdb267604bc3ebbf9197cb5489dd59728406c035529c513f55832bba41c296e0df10adabeeba6c1039256652582
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# frozen_string_literal: true
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module MalawiHivProgramReports
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module Pepfar
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class TxRtt
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include Utils
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include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
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include MalawiHivProgramReports::Adapters::Moh::Custom
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include MalawiHivProgramReports::Utils::ModelUtils
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attr_reader :start_date, :end_date, :location, :rebuild
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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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@end_date = ActiveRecord::Base.connection.quote(end_date.to_date.end_of_day.strftime('%Y-%m-%d %H:%M:%S'))
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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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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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@end_date = ActiveRecord::Base.connection.quote(end_date.to_date.end_of_day.strftime('%Y-%m-%d %H:%M:%S'))
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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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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_report
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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',
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locations: location.to_s, rebuild: true)
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cohort.find_report
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end
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process_report
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end
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process_report
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rescue StandardError => e
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Rails.logger.error "Error running TX_RTT Report: #{e}"
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Rails.logger.error e.backtrace.join("\n")
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raise e
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def data
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if rebuild
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cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date:, end_date:, definition: 'pepfar',
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locations: location.to_s, rebuild: true)
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cohort.find_report
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end
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process_report
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rescue StandardError => e
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Rails.logger.error "Error running TX_RTT Report: #{e}"
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Rails.logger.error e.backtrace.join("\n")
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raise e
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end
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private
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GENDER = %w[M F].freeze
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end
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def init_report
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pepfar_age_groups.each_with_object({}) do |age_group, age_group_report|
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age_group_report[age_group] = GENDER.each_with_object({}) do |gender, gender_report|
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gender_report[gender] = indicators
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end
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end
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end
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def process_report
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report = init_report
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process_data report
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flatten_the_report report
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end
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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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months = row['months']
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patient_id = row['patient_id']
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cd4_cat = row['cd4_count_group']
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next unless GENDER.include?(gender)
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next unless pepfar_age_groups.include?(age_group)
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end
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cat = report[age_group][gender]
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process_months(cat, months, patient_id)
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process_cd4(cat, months, patient_id, cd4_cat)
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end
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end
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return report[:returned_greater_than_3_months_and_less_than_6_months] << patient_id
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end
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def process_months(report, months, patient_id)
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return report[:returned_less_than_3_months] << patient_id if months.blank?
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return report[:returned_less_than_3_months] << patient_id if months < 3
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return report[:returned_greater_than_3_months_and_less_than_6_months] << patient_id if months >= 3 && months < 6
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report[:returned_greater_than_or_equal_to_6_months] << patient_id if months >= 6
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end
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def process_cd4(report, months, patient_id, cd4_cat)
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if cd4_cat == 'unknown_cd4_count' && (months.blank? || months <= 2)
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report[:not_eligible_for_cd4] << patient_id
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return
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end
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report[:not_eligible_for_cd4] << patient_id
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return
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end
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report[cd4_cat.to_sym] << patient_id
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end
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def indicators
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{
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cd4_less_than_200: [],
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cd4_greater_than_or_equal_to_200: [],
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unknown_cd4_count: [],
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not_eligible_for_cd4: [],
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returned_less_than_3_months: [],
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returned_greater_than_3_months_and_less_than_6_months: [],
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returned_greater_than_or_equal_to_6_months: []
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}
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end
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def process_age_group_report(age_group, gender, age_group_report)
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{
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age_group:,
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gender:,
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cd4_less_than_200: age_group_report[:cd4_less_than_200],
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cd4_greater_than_or_equal_to_200: age_group_report[:cd4_greater_than_or_equal_to_200],
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unknown_cd4_count: age_group_report[:unknown_cd4_count],
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not_eligible_for_cd4: age_group_report[:not_eligible_for_cd4],
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returned_less_than_3_months: age_group_report[:returned_less_than_3_months],
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returned_greater_than_3_months_and_less_than_6_months: age_group_report[:returned_greater_than_3_months_and_less_than_6_months],
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returned_greater_than_or_equal_to_6_months: age_group_report[:returned_greater_than_or_equal_to_6_months]
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}
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end
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cd4_greater_than_or_equal_to_200: age_group_report[:cd4_greater_than_or_equal_to_200],
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unknown_cd4_count: age_group_report[:unknown_cd4_count],
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not_eligible_for_cd4: age_group_report[:not_eligible_for_cd4],
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returned_less_than_3_months: age_group_report[:returned_less_than_3_months],
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returned_greater_than_3_months_and_less_than_6_months: age_group_report[:returned_greater_than_3_months_and_less_than_6_months],
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returned_greater_than_or_equal_to_6_months: age_group_report[:returned_greater_than_or_equal_to_6_months]
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}
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def flatten_the_report(report)
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result = []
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report.each do |age_group, age_group_report|
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result << process_age_group_report(age_group, 'M', age_group_report['M'])
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result << process_age_group_report(age_group, 'F', age_group_report['F'])
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end
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result << process_age_group_report(age_group, 'M', age_group_report['M'])
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result << process_age_group_report(age_group, 'F', age_group_report['F'])
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end
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sorted_results = result.sort_by do |item|
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gender_score = item[:gender] == 'Female' ? 0 : 1
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age_group_score = pepfar_age_groups.index(item[:age_group])
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[gender_score, age_group_score]
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end
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# sort by gender, start all females and push all males to the end
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sorted_results.sort_by { |h| [h[:gender] == 'F' ? 0 : 1] }
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sorted_results = result.sort_by do |item|
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gender_score = item[:gender] == 'Female' ? 0 : 1
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age_group_score = pepfar_age_groups.index(item[:age_group])
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[gender_score, age_group_score]
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end
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# sort by gender, start all females and push all males to the end
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sorted_results.sort_by { |h| [h[:gender] == 'F' ? 0 : 1] }
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end
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end
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def fetch_data
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ActiveRecord::Base.connection.select_all <<~SQL
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SELECT
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e.patient_id,
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disaggregated_age_group(e.birthdate, #{end_date}) AS age_group,
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e.gender,
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s.cum_outcome initial_outcome,
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o.cum_outcome final_outcome,
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TIMESTAMPDIFF(MONTH, COALESCE(s.outcome_date, c.outcome_date), ord.min_order_date) months,
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CASE
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WHEN cd4_result.value_numeric < 200 THEN 'cd4_less_than_200'
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WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '=' THEN 'cd4_greater_than_or_equal_to_200'
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WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '<' THEN 'cd4_less_than_200'
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WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '>' THEN 'cd4_greater_than_or_equal_to_200'
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WHEN cd4_result.value_numeric > 200 THEN 'cd4_greater_than_or_equal_to_200'
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ELSE 'unknown_cd4_count'
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END cd4_count_group
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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 o.patient_id = e.patient_id AND o.cum_outcome = 'On antiretrovirals'
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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')
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INNER JOIN cdr_temp_current_state_start #{current_partition} c ON c.patient_id = e.patient_id
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INNER JOIN cdr_temp_max_drug_orders #{current_partition} ord ON ord.patient_id = e.patient_id
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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
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WHERE 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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end
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end
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end
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