malawi_hiv_program_reports 1.0.26 → 1.1.0
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 +12 -9
- data/app/services/malawi_hiv_program_reports/pepfar/tx_ml.rb +41 -40
- data/app/services/malawi_hiv_program_reports/pepfar/tx_new.rb +48 -47
- data/app/services/malawi_hiv_program_reports/pepfar/tx_rtt.rb +133 -133
- data/lib/malawi_hiv_program_reports/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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metadata.gz:
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data.tar.gz:
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metadata.gz: 9c6bffbef9d85fec441ab368a631e8e730446a87ed8722d2a60d348c68ecf969
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data.tar.gz: dfd3ba0bfe3a2fc65ca948d3dd2bee21c9f8bb4f7c42ade37623f46c6fb8aefb
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metadata.gz:
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metadata.gz: 9a0217e328962a1734f08e22d28df28624f0a6eff6ca02e1eb32f021e0397758ab58bca452ddada4ccf662cac36b862952c880b98e3c08e500e4160db51af968
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data.tar.gz: c6f54d2927268c90cf1e5b87ea621eb68aa5cea3d6f17095f382f7c7f91bdd0f4360a9ab4e00f8be536414a498c2dd1b3d01d8a7f88e01425dbb0e0292309a1c
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@@ -78,14 +78,17 @@ module MalawiHivProgramReports
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def process_data(location)
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start_time = Time.now
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if rebuild
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cdr_other_patient_types location
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external_clients location
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transfer_ins location
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min_drug_orders location
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potential_cohort_members location
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reason_for_starting_art location
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cohort_members location
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end
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outcome = MalawiHivProgramReports::Moh::CumulativeOutcome.new(end_date:, location:, definition:, rebuild:,
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start_date:)
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rebuild ? outcome.find_report : outcome.update_outcomes_by_definition
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end_time = Time.now
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time_taken = ((end_time - start_time) / 60).round(2)
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end
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clear_cohort_status
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end
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def clear_cohort_status
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if locations.empty?
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ActiveRecord::Base.connection.execute('TRUNCATE TABLE cdr_temp_cohort_status')
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def find_report
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if rebuild
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cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date
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cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date: start_date.to_date, end_date: end_date.to_date, definition: 'pepfar',
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locations: location.to_s, rebuild: true.to_s)
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cohort.find_report
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end
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process_data
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patient_id = pat['patient_id'].to_i
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outcome = pat['outcome']
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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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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 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 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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report = init_report
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addittional_groups report
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cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date
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cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date: start_date.to_date, end_date: end_date.to_date, definition: 'pepfar',
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locations: location.to_s, rebuild: true.to_s)
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cohort.find_report
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end
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process_data report
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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],
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cd4_greater_than_equal_to_200: age_group_report[:cd4_greater_than_equal_to_200],
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cd4_unknown_or_not_done: age_group_report[:cd4_unknown_or_not_done],
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transfer_in: age_group_report[:transfer_in]
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}
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end
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# rubocop:enable Metrics/AbcSize
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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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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
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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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19
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+
def find_report
|
|
20
|
+
if rebuild
|
|
21
|
+
cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date: start_date.to_date, end_date: end_date.to_date, definition: 'pepfar',
|
|
22
|
+
locations: location.to_s, rebuild: true.to_s)
|
|
23
|
+
cohort.find_report
|
|
25
24
|
end
|
|
25
|
+
process_report
|
|
26
|
+
end
|
|
26
27
|
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
process_report
|
|
33
|
-
rescue StandardError => e
|
|
34
|
-
Rails.logger.error "Error running TX_RTT Report: #{e}"
|
|
35
|
-
Rails.logger.error e.backtrace.join("\n")
|
|
36
|
-
raise e
|
|
28
|
+
def data
|
|
29
|
+
if rebuild
|
|
30
|
+
cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date: start_date.to_date, end_date: end_date.to_date, definition: 'pepfar',
|
|
31
|
+
locations: location.to_s, rebuild: true.to_s)
|
|
32
|
+
cohort.find_report
|
|
37
33
|
end
|
|
34
|
+
process_report
|
|
35
|
+
rescue StandardError => e
|
|
36
|
+
Rails.logger.error "Error running TX_RTT Report: #{e}"
|
|
37
|
+
Rails.logger.error e.backtrace.join("\n")
|
|
38
|
+
raise e
|
|
39
|
+
end
|
|
38
40
|
|
|
39
|
-
|
|
41
|
+
private
|
|
40
42
|
|
|
41
|
-
|
|
43
|
+
GENDER = %w[M F].freeze
|
|
42
44
|
|
|
43
|
-
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
end
|
|
45
|
+
def init_report
|
|
46
|
+
pepfar_age_groups.each_with_object({}) do |age_group, age_group_report|
|
|
47
|
+
age_group_report[age_group] = GENDER.each_with_object({}) do |gender, gender_report|
|
|
48
|
+
gender_report[gender] = indicators
|
|
48
49
|
end
|
|
49
50
|
end
|
|
51
|
+
end
|
|
50
52
|
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
|
|
53
|
+
def process_report
|
|
54
|
+
report = init_report
|
|
55
|
+
process_data report
|
|
56
|
+
flatten_the_report report
|
|
57
|
+
end
|
|
56
58
|
|
|
57
|
-
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
|
|
61
|
-
|
|
62
|
-
|
|
63
|
-
|
|
59
|
+
def process_data(report)
|
|
60
|
+
fetch_data.each do |row|
|
|
61
|
+
age_group = row['age_group']
|
|
62
|
+
gender = row['gender']
|
|
63
|
+
months = row['months']
|
|
64
|
+
patient_id = row['patient_id']
|
|
65
|
+
cd4_cat = row['cd4_count_group']
|
|
64
66
|
|
|
65
|
-
|
|
66
|
-
|
|
67
|
+
next unless GENDER.include?(gender)
|
|
68
|
+
next unless pepfar_age_groups.include?(age_group)
|
|
67
69
|
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
end
|
|
70
|
+
cat = report[age_group][gender]
|
|
71
|
+
process_months(cat, months, patient_id)
|
|
72
|
+
process_cd4(cat, months, patient_id, cd4_cat)
|
|
72
73
|
end
|
|
74
|
+
end
|
|
73
75
|
|
|
74
|
-
|
|
75
|
-
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
return report[:returned_greater_than_3_months_and_less_than_6_months] << patient_id
|
|
79
|
-
end
|
|
76
|
+
def process_months(report, months, patient_id)
|
|
77
|
+
return report[:returned_less_than_3_months] << patient_id if months.blank?
|
|
78
|
+
return report[:returned_less_than_3_months] << patient_id if months < 3
|
|
79
|
+
return report[:returned_greater_than_3_months_and_less_than_6_months] << patient_id if months >= 3 && months < 6
|
|
80
80
|
|
|
81
|
-
|
|
81
|
+
report[:returned_greater_than_or_equal_to_6_months] << patient_id if months >= 6
|
|
82
|
+
end
|
|
83
|
+
|
|
84
|
+
def process_cd4(report, months, patient_id, cd4_cat)
|
|
85
|
+
if cd4_cat == 'unknown_cd4_count' && (months.blank? || months <= 2)
|
|
86
|
+
report[:not_eligible_for_cd4] << patient_id
|
|
87
|
+
return
|
|
82
88
|
end
|
|
83
89
|
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
report[:not_eligible_for_cd4] << patient_id
|
|
87
|
-
return
|
|
88
|
-
end
|
|
90
|
+
report[cd4_cat.to_sym] << patient_id
|
|
91
|
+
end
|
|
89
92
|
|
|
90
|
-
|
|
91
|
-
|
|
93
|
+
def indicators
|
|
94
|
+
{
|
|
95
|
+
cd4_less_than_200: [],
|
|
96
|
+
cd4_greater_than_or_equal_to_200: [],
|
|
97
|
+
unknown_cd4_count: [],
|
|
98
|
+
not_eligible_for_cd4: [],
|
|
99
|
+
returned_less_than_3_months: [],
|
|
100
|
+
returned_greater_than_3_months_and_less_than_6_months: [],
|
|
101
|
+
returned_greater_than_or_equal_to_6_months: []
|
|
102
|
+
}
|
|
103
|
+
end
|
|
92
104
|
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
|
|
102
|
-
|
|
103
|
-
|
|
105
|
+
def process_age_group_report(age_group, gender, age_group_report)
|
|
106
|
+
{
|
|
107
|
+
age_group:,
|
|
108
|
+
gender:,
|
|
109
|
+
cd4_less_than_200: age_group_report[:cd4_less_than_200],
|
|
110
|
+
cd4_greater_than_or_equal_to_200: age_group_report[:cd4_greater_than_or_equal_to_200],
|
|
111
|
+
unknown_cd4_count: age_group_report[:unknown_cd4_count],
|
|
112
|
+
not_eligible_for_cd4: age_group_report[:not_eligible_for_cd4],
|
|
113
|
+
returned_less_than_3_months: age_group_report[:returned_less_than_3_months],
|
|
114
|
+
returned_greater_than_3_months_and_less_than_6_months: age_group_report[:returned_greater_than_3_months_and_less_than_6_months],
|
|
115
|
+
returned_greater_than_or_equal_to_6_months: age_group_report[:returned_greater_than_or_equal_to_6_months]
|
|
116
|
+
}
|
|
117
|
+
end
|
|
104
118
|
|
|
105
|
-
|
|
106
|
-
|
|
107
|
-
|
|
108
|
-
|
|
109
|
-
|
|
110
|
-
cd4_greater_than_or_equal_to_200: age_group_report[:cd4_greater_than_or_equal_to_200],
|
|
111
|
-
unknown_cd4_count: age_group_report[:unknown_cd4_count],
|
|
112
|
-
not_eligible_for_cd4: age_group_report[:not_eligible_for_cd4],
|
|
113
|
-
returned_less_than_3_months: age_group_report[:returned_less_than_3_months],
|
|
114
|
-
returned_greater_than_3_months_and_less_than_6_months: age_group_report[:returned_greater_than_3_months_and_less_than_6_months],
|
|
115
|
-
returned_greater_than_or_equal_to_6_months: age_group_report[:returned_greater_than_or_equal_to_6_months]
|
|
116
|
-
}
|
|
119
|
+
def flatten_the_report(report)
|
|
120
|
+
result = []
|
|
121
|
+
report.each do |age_group, age_group_report|
|
|
122
|
+
result << process_age_group_report(age_group, 'M', age_group_report['M'])
|
|
123
|
+
result << process_age_group_report(age_group, 'F', age_group_report['F'])
|
|
117
124
|
end
|
|
118
|
-
|
|
119
|
-
|
|
120
|
-
|
|
121
|
-
|
|
122
|
-
result << process_age_group_report(age_group, 'M', age_group_report['M'])
|
|
123
|
-
result << process_age_group_report(age_group, 'F', age_group_report['F'])
|
|
124
|
-
end
|
|
125
|
-
sorted_results = result.sort_by do |item|
|
|
126
|
-
gender_score = item[:gender] == 'Female' ? 0 : 1
|
|
127
|
-
age_group_score = pepfar_age_groups.index(item[:age_group])
|
|
128
|
-
[gender_score, age_group_score]
|
|
129
|
-
end
|
|
130
|
-
# sort by gender, start all females and push all males to the end
|
|
131
|
-
sorted_results.sort_by { |h| [h[:gender] == 'F' ? 0 : 1] }
|
|
125
|
+
sorted_results = result.sort_by do |item|
|
|
126
|
+
gender_score = item[:gender] == 'Female' ? 0 : 1
|
|
127
|
+
age_group_score = pepfar_age_groups.index(item[:age_group])
|
|
128
|
+
[gender_score, age_group_score]
|
|
132
129
|
end
|
|
130
|
+
# sort by gender, start all females and push all males to the end
|
|
131
|
+
sorted_results.sort_by { |h| [h[:gender] == 'F' ? 0 : 1] }
|
|
132
|
+
end
|
|
133
133
|
|
|
134
|
-
|
|
135
|
-
|
|
136
|
-
|
|
137
|
-
|
|
138
|
-
|
|
139
|
-
|
|
140
|
-
|
|
141
|
-
|
|
142
|
-
|
|
143
|
-
|
|
144
|
-
|
|
145
|
-
|
|
146
|
-
|
|
147
|
-
|
|
148
|
-
|
|
149
|
-
|
|
150
|
-
|
|
151
|
-
|
|
152
|
-
|
|
153
|
-
|
|
154
|
-
|
|
155
|
-
|
|
156
|
-
|
|
157
|
-
|
|
158
|
-
|
|
159
|
-
|
|
160
|
-
end
|
|
134
|
+
def fetch_data
|
|
135
|
+
ActiveRecord::Base.connection.select_all <<~SQL
|
|
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
|
|
159
|
+
SQL
|
|
161
160
|
end
|
|
162
161
|
end
|
|
163
|
-
end
|
|
162
|
+
end
|
|
163
|
+
end
|