malawi_hiv_program_reports 1.0.27 → 1.1.0
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- 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 +4 -4
- data/lib/malawi_hiv_program_reports/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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---
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SHA256:
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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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SHA512:
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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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-
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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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@@ -18,7 +18,8 @@ module MalawiHivProgramReports
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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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@@ -32,10 +33,10 @@ module MalawiHivProgramReports
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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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@@ -70,49 +71,49 @@ module MalawiHivProgramReports
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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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@@ -22,7 +22,8 @@ module MalawiHivProgramReports
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report = init_report
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addittional_groups 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 report
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@@ -120,10 +121,10 @@ module MalawiHivProgramReports
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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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@@ -151,48 +152,48 @@ module MalawiHivProgramReports
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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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198
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end
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# rubocop:enable Metrics/ClassLength
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@@ -18,8 +18,8 @@ module MalawiHivProgramReports
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18
18
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|
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19
19
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def find_report
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|
20
20
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if rebuild
|
|
21
|
-
cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date
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22
|
-
locations: location.to_s, rebuild: true)
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21
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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_report
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@@ -27,8 +27,8 @@ module MalawiHivProgramReports
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|
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27
27
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28
28
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def data
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29
29
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if rebuild
|
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30
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-
cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date
|
|
31
|
-
locations: location.to_s, rebuild: true)
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30
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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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31
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+
locations: location.to_s, rebuild: true.to_s)
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|
32
32
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cohort.find_report
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|
33
33
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end
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34
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process_report
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