malawi_hiv_program_reports 1.1.16 → 1.1.17
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- checksums.yaml +4 -4
- data/app/services/malawi_hiv_program_reports/cohort/disaggregated.rb +57 -47
- data/app/services/malawi_hiv_program_reports/moh/cumulative_cohort.rb +62 -1
- data/app/services/malawi_hiv_program_reports/pepfar/maternal_status.rb +103 -1
- data/app/services/malawi_hiv_program_reports/pepfar/tb_prev3.rb +214 -172
- data/app/services/malawi_hiv_program_reports/pepfar/tx_curr_mmd.rb +63 -25
- data/app/services/malawi_hiv_program_reports/pepfar/tx_ml.rb +137 -41
- data/app/services/malawi_hiv_program_reports/pepfar/tx_new.rb +51 -64
- data/app/services/malawi_hiv_program_reports/pepfar/tx_rtt.rb +91 -47
- data/app/services/malawi_hiv_program_reports/pepfar/tx_tb.rb +188 -135
- data/app/services/malawi_hiv_program_reports/report_map.rb +1 -1
- data/lib/malawi_hiv_program_reports/version.rb +1 -1
- metadata +3 -3
@@ -19,36 +19,48 @@ module MalawiHivProgramReports
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end
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def find_report
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drop_temporary_tables unless @location
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delete_patients_in_temp_table if @location
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create_temp_earliest_start_date unless temp_eartliest_start_date_exists?
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init_report
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build_cohort_tables
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process_tb_screening
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process_tb_confirmed_and_on_treatment
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process_patients_alive_and_on_art
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process_tb_screened
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process_tb_confirmed
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-
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flatten_the_report
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rescue StandardError => e
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Rails.logger.error("Error generating TxTb report: #{e.message}")
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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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def process_tb_data
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delete_patients_in_temp_table
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process_tb_screening
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process_tb_confirmed_and_on_treatment
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end
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private
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GENDER = %w[Male Female].freeze
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def init_report
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@report = initialize_report_structure
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addittional_groups
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end
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def initialize_report_structure
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pepfar_age_groups.each_with_object({}) do |age_group, report|
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report[age_group] ||= {}
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report[age_group][gender] = initialize_gender_metrics
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report[age_group] = GENDER.each_with_object({}) do |gender, age_group_report|
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age_group_report[gender] = initialize_gender_metrics
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end
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end
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end
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def addittional_groups
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@report['All'] = {}
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%w[Male FP FNP FBf].each do |key|
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@report['All'][key] = initialize_gender_metrics
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end
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end
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def initialize_gender_metrics
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{
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tx_curr: [],
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@@ -64,85 +76,114 @@ module MalawiHivProgramReports
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}
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end
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def
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def flatten_the_report
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result = []
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@report.each do |age_group, age_group_report|
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next if age_group == 'Unknown'
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age_group_report.each_key do |gender|
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next if gender == 'Unknown'
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result << process_age_group_report(age_group, gender, age_group_report[gender])
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end
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end
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new_group = pepfar_age_groups.map { |age_group| age_group }
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new_group << 'All'
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gender_scores = { 'Female' => 0, 'Male' => 1, 'FNP' => 3, 'FP' => 2, 'FBf' => 4 }
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result_scores = result.sort_by do |item|
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gender_score = gender_scores[item[:gender]] || 999
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age_group_score = new_group.index(item[:age_group]) || 999
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[gender_score, age_group_score]
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end
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# remove all unknown age groups
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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 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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**age_group_report
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}
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end
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def delete_patients_in_temp_table
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if ActiveRecord::Base.connection.table_exists?('cdr_tb_screened')
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execute_action("DELETE FROM cdr_tb_screened WHERE site_id = #{@location}")
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end
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return unless ActiveRecord::Base.connection.table_exists?('cdr_tb_confirmed_and_on_treatment')
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execute_action("DELETE FROM cdr_tb_confirmed_and_on_treatment WHERE site_id = #{@location}")
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end
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def build_cohort_tables
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return unless rebuild_outcome || @occupation.present?
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MalawiHivProgramReports::Moh::CumulativeCohort.new(
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start_date
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end_date
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start_date:,
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end_date:,
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locations: [@location.to_s],
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rebuild: rebuild_outcome
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).find_report
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end
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def process_tb_screening
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execute_action(create_temp_tb_screened_query)
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execute_action(insert_temp_tb_screened_query)
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end
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def
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def tb_status_results
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@tb_status_results ||= [::ConceptName.find_by_name('TB Suspected').concept_id,
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::ConceptName.find_by_name('TB NOT suspected').concept_id].join(',')
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end
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def tb_status
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@tb_status ||= ::ConceptName.find_by_name('TB status').concept_id
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end
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def tb_screening_method
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@tb_screening_method ||= ::ConceptName.find_by_name('TB screening method used').concept_id
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end
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def tb_treatment_start_date
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@tb_treatment_start_date ||= ::ConceptName.find_by_name('TB treatment start date').concept_id
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end
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def confirmed_tb_on_treatment
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@confirmed_tb_on_treatment ||= ::ConceptName.find_by_name('Confirmed TB on treatment').concept_id
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end
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def insert_temp_tb_screened_query
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<<~SQL
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INSERT INTO
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INSERT INTO cdr_tb_screened #{current_partition}
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SELECT
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tesd.patient_id,
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#{@location} AS site_id,
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LEFT(tesd.gender, 1) AS gender,
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MAX(o.obs_datetime) AS screened_date,
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tesd.earliest_start_date as enrollment_date,
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disaggregated_age_group(tesd.birthdate, DATE('#{end_date.to_date}')) AS age_group,
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cn.name AS tb_status,
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GROUP_CONCAT(DISTINCT vcn.name) AS screening_methods
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INNER JOIN cdr_temp_cohort_members tesd ON tesd.patient_id = o.person_id
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#{site_manager(operator: 'AND', column: 'tesd.site_id', location: @location)}
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WHERE o.concept_id = #{::ConceptName.find_by_name('TB status').concept_id}
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AND o.value_coded IN (SELECT concept_id FROM concept_name WHERE name IN ('TB Suspected', 'TB NOT suspected') AND voided = 0)
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AND o.voided = 0 AND o.obs_datetime BETWEEN '#{start_date}' AND '#{end_date}'
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GROUP BY o.person_id
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) current_obs ON current_obs.person_id = o.person_id AND current_obs.obs_datetime = o.obs_datetime
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FROM cdr_temp_cohort_members #{current_partition} tesd
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INNER JOIN obs #{current_partition} o ON o.person_id = tesd.patient_id
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AND o.voided = 0 AND o.concept_id = #{tb_status}
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AND o.obs_datetime BETWEEN '#{start_date}' AND '#{end_date}'
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AND o.value_coded IN (#{tb_status_results})
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INNER JOIN concept_name cn ON cn.concept_id = o.value_coded AND cn.voided = 0
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LEFT JOIN obs #{current_partition}
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LEFT JOIN obs #{current_partition} acurr ON acurr.person_id = o.person_id
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AND acurr.voided = 0 AND acurr.concept_id = #{tb_status}
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AND acurr.obs_datetime > o.obs_datetime
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AND acurr.obs_datetime BETWEEN '#{start_date}' AND '#{end_date}'
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AND acurr.value_coded IN (#{tb_status_results})
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LEFT JOIN obs #{current_partition} screen_method ON screen_method.concept_id = #{tb_screening_method}
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AND screen_method.voided = 0
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AND screen_method.person_id = o.person_id
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AND DATE(screen_method.obs_datetime) = DATE(
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AND DATE(screen_method.obs_datetime) = DATE(o.obs_datetime)
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LEFT JOIN concept_name vcn ON vcn.concept_id = screen_method.value_coded AND vcn.voided = 0 AND vcn.name IN ('CXR', 'MWRD')
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WHERE
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AND o.obs_datetime BETWEEN '#{start_date}' AND '#{end_date}'
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GROUP BY o.person_id
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WHERE acurr.person_id IS NULL
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GROUP BY tesd.patient_id
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ON DUPLICATE KEY UPDATE gender = VALUES(gender), screened_date = VALUES(screened_date), age_group = VALUES(age_group), tb_status = VALUES(tb_status), screening_methods = VALUES(screening_methods)
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SQL
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end
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@@ -152,72 +193,45 @@ module MalawiHivProgramReports
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def create_temp_earliest_start_date
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MalawiHivProgramReports::Moh::CumulativeCohort.new(
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start_date
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end_date
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start_date:,
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end_date:,
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locations: [@location],
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rebuild: rebuild_outcome
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).find_report
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end
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def process_tb_confirmed_and_on_treatment
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execute_action(create_temp_tb_confirmed_query)
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execute_action(insert_temp_tb_confirmed_query)
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end
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def create_temp_tb_confirmed_query
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<<~SQL
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CREATE TABLE IF NOT EXISTS temp_tb_confirmed_and_on_treatment(
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patient_id INT(11) NOT NULL,
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gender VARCHAR(255) NULL,
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age_group VARCHAR(255) NOT NULL,
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tb_confirmed_date DATE NULL,
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has_tb_confirmed_date BOOLEAN NOT NULL,
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enrollment_date DATE NULL,
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prev_reading DATE,
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site_id INT(11) DEFAULT 1,
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PRIMARY KEY (patient_id, site_id)
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)
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SQL
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end
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def insert_temp_tb_confirmed_query
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<<~SQL
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INSERT INTO
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INSERT INTO cdr_tb_confirmed_and_on_treatment #{current_partition}
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SELECT
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o.person_id as patient_id,
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#{@location} AS site_id,
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LEFT(tesd.gender, 1) AS gender,
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disaggregated_age_group(tesd.birthdate, DATE('#{end_date.to_date}')) AS age_group,
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COALESCE(MIN(tcd.value_datetime),MIN(o.obs_datetime)) AS tb_confirmed_date,
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CASE
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WHEN COUNT(tcd.value_datetime) > 0 THEN TRUE
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ELSE FALSE
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END AS has_tb_confirmed_date,
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tesd.earliest_start_date as enrollment_date,
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prev.
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#{@location ? ", #{@location}" : ''} AS site_id
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COALESCE(MIN(prev_tcd.value_datetime),MIN(prev.obs_datetime)) AS prev_reading
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FROM obs #{current_partition} o
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INNER JOIN cdr_temp_cohort_members tesd ON tesd.patient_id = o.person_id
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#{
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LEFT JOIN obs #{current_partition}
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LEFT JOIN obs #{current_partition} tcd ON tcd.concept_id = #{::ConceptName.find_by_name('TB treatment start date').concept_id}
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AND tcd.voided = 0 AND tcd.person_id = o.person_id
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WHERE o.concept_id = #{::ConceptName.find_by_name('TB status').concept_id}
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AND o.value_coded = #{::ConceptName.find_by_name('Confirmed TB on treatment').concept_id}
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INNER JOIN cdr_temp_cohort_members #{current_partition} tesd ON tesd.patient_id = o.person_id
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LEFT JOIN obs #{current_partition} tcd ON tcd.concept_id = #{tb_treatment_start_date}
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AND tcd.voided = 0 AND tcd.person_id = o.person_id
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LEFT JOIN obs #{current_partition} prev ON prev.person_id = o.person_id AND prev.voided = 0
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AND prev.concept_id = #{tb_status} AND prev.value_coded = #{confirmed_tb_on_treatment}
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AND prev.obs_datetime < '#{start_date}'
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LEFT JOIN obs #{current_partition} prev_tcd ON prev_tcd.person_id = o.person_id AND prev_tcd.voided = 0
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AND prev_tcd.concept_id = #{tb_treatment_start_date} AND prev_tcd.obs_datetime < '#{start_date}'
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WHERE o.concept_id = #{tb_status}
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AND o.value_coded = #{confirmed_tb_on_treatment}
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AND o.voided = 0
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AND o.obs_datetime
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GROUP BY o.person_id
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) prev ON prev.person_id = o.person_id
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WHERE o.concept_id = #{::ConceptName.find_by_name('TB status').concept_id}
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AND o.value_coded = #{::ConceptName.find_by_name('Confirmed TB on treatment').concept_id}
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AND o.voided = 0
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AND o.obs_datetime BETWEEN '#{start_date}' AND '#{end_date}'
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AND o.obs_datetime BETWEEN '#{start_date}' AND '#{end_date}'
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GROUP BY o.person_id
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SQL
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end
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@@ -225,8 +239,28 @@ module MalawiHivProgramReports
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def process_patients_alive_and_on_art
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find_patients_alive_and_on_art.each do |patient|
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next unless pepfar_age_groups.include?(patient['age_group'])
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next unless GENDER.include?(patient['gender'])
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-
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process_aggreggation_rows(patient['age_group'], patient['gender'], :tx_curr, patient['patient_id'],
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patient['maternal_status'])
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end
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end
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def process_aggreggation_rows(age_group, gender, indicator, patient_id, maternal_status)
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@report[age_group][gender][indicator] << patient_id
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if gender == 'Male'
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@report['All']['Male'][indicator] << patient_id
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return
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end
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+
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case maternal_status
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when 'FP'
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@report['All']['FP'][indicator] << patient_id
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when 'FBf'
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@report['All']['FBf'][indicator] << patient_id
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else
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|
+
@report['All']['FNP'][indicator] << patient_id
|
230
264
|
end
|
231
265
|
end
|
232
266
|
|
@@ -236,11 +270,15 @@ module MalawiHivProgramReports
|
|
236
270
|
|
237
271
|
def create_patients_alive_and_on_art_query
|
238
272
|
<<~SQL
|
239
|
-
SELECT tpo.patient_id,
|
273
|
+
SELECT tpo.patient_id, CASE tesd.gender
|
274
|
+
WHEN 'M' THEN 'Male'
|
275
|
+
WHEN 'F' THEN 'Female'
|
276
|
+
ELSE 'Unknown'
|
277
|
+
END gender, ms.maternal_status,
|
278
|
+
disaggregated_age_group(tesd.birthdate, DATE('#{end_date.to_date}')) age_group
|
240
279
|
FROM cdr_temp_patient_outcomes #{current_partition} tpo
|
241
|
-
INNER JOIN cdr_temp_cohort_members tesd ON tesd.patient_id = tpo.patient_id
|
242
|
-
#{
|
243
|
-
#{site_manager(operator: 'AND', column: 'tpo.site_id', location: @location)}
|
280
|
+
INNER JOIN cdr_temp_cohort_members #{current_partition} tesd ON tesd.patient_id = tpo.patient_id
|
281
|
+
LEFT JOIN cdr_temp_maternal_status #{current_partition} ms ON ms.patient_id = tpo.patient_id
|
244
282
|
WHERE tpo.cum_outcome = 'On antiretrovirals'
|
245
283
|
SQL
|
246
284
|
end
|
@@ -253,14 +291,15 @@ module MalawiHivProgramReports
|
|
253
291
|
age_group = patient['age_group']
|
254
292
|
next unless pepfar_age_groups.include?(age_group)
|
255
293
|
|
256
|
-
gender = patient['gender']
|
257
|
-
metrics = @report[age_group][gender]
|
294
|
+
gender = patient['gender']
|
258
295
|
enrollment_date = patient['enrollment_date']
|
259
296
|
tb_status = patient['tb_status'].downcase
|
260
|
-
|
297
|
+
methods = patient['screening_methods']&.split(',')&.map(&:downcase)
|
261
298
|
patient_id = patient['patient_id']
|
262
|
-
|
263
|
-
|
299
|
+
maternal_status = patient['maternal_status']
|
300
|
+
|
301
|
+
process_method(methods:, age_group:, gender:, patient_id:, maternal_status:)
|
302
|
+
process_screening_results(enrollment_date:, tb_status:, age_group:, gender:, patient_id:, maternal_status:)
|
264
303
|
end
|
265
304
|
end
|
266
305
|
|
@@ -269,34 +308,38 @@ module MalawiHivProgramReports
|
|
269
308
|
age_group = patient['age_group']
|
270
309
|
next unless pepfar_age_groups.include?(age_group)
|
271
310
|
|
272
|
-
gender = patient['gender']
|
273
|
-
metrics = @report[age_group][gender]
|
311
|
+
gender = patient['gender']
|
274
312
|
enrollment_date = patient['enrollment_date']
|
275
313
|
|
276
314
|
if new_on_art(enrollment_date)
|
277
|
-
|
315
|
+
process_aggreggation_rows(age_group, gender, :started_tb_new, patient['patient_id'], patient['maternal_status'])
|
278
316
|
else
|
279
|
-
|
317
|
+
process_aggreggation_rows(age_group, gender, :started_tb_prev, patient['patient_id'], patient['maternal_status'])
|
280
318
|
end
|
281
319
|
end
|
282
320
|
end
|
283
321
|
|
284
|
-
def process_screening_results(
|
322
|
+
def process_screening_results(enrollment_date:, tb_status:, **kwargs)
|
285
323
|
if new_on_art(enrollment_date)
|
286
|
-
|
324
|
+
indicator = :sceen_pos_new if ['tb suspected', 'sup', 'confirmed tb not on treatment', 'norx',
|
287
325
|
'confirmed tb on treatment', 'rx'].include?(tb_status)
|
288
|
-
|
326
|
+
indicator = :sceen_neg_new if ['tb not suspected', 'nosup'].include?(tb_status)
|
289
327
|
else
|
290
|
-
|
328
|
+
indicator = :sceen_pos_prev if ['tb suspected', 'sup', 'confirmed tb not on treatment',
|
291
329
|
'norx'].include?(tb_status)
|
292
|
-
|
330
|
+
indicator = :sceen_neg_prev if ['tb not suspected', 'nosup'].include?(tb_status)
|
293
331
|
end
|
332
|
+
return unless indicator
|
333
|
+
|
334
|
+
process_aggreggation_rows(kwargs[:age_group], kwargs[:gender], indicator, kwargs[:patient_id], kwargs[:maternal_status])
|
294
335
|
end
|
295
336
|
|
296
|
-
def process_method(
|
297
|
-
|
298
|
-
|
299
|
-
|
337
|
+
def process_method(methods:, **kwargs)
|
338
|
+
indicator = :symptom_screen_alone if methods.blank?
|
339
|
+
indicator = :cxr_screen if methods&.include?('cxr') && !methods&.include?('mwrd')
|
340
|
+
indicator = :mwrd_screen if methods&.include?('mwrd')
|
341
|
+
|
342
|
+
process_aggreggation_rows(kwargs[:age_group], kwargs[:gender], indicator, kwargs[:patient_id], kwargs[:maternal_status])
|
300
343
|
end
|
301
344
|
|
302
345
|
# rubocop:enable Metrics/AbcSize
|
@@ -324,18 +367,28 @@ module MalawiHivProgramReports
|
|
324
367
|
|
325
368
|
def find_tb_screened_data_query
|
326
369
|
<<~SQL
|
327
|
-
SELECT tbs.patient_id, tbs.enrollment_date,
|
328
|
-
|
329
|
-
|
370
|
+
SELECT tbs.patient_id, tbs.enrollment_date,
|
371
|
+
CASE tbs.gender
|
372
|
+
WHEN 'M' THEN 'Male'
|
373
|
+
WHEN 'F' THEN 'Female'
|
374
|
+
ELSE 'Unknown'
|
375
|
+
END gender, ms.maternal_status,
|
376
|
+
tbs.age_group, tbs.tb_status, tbs.screened_date, tbs.screening_methods
|
377
|
+
FROM cdr_tb_screened #{current_partition} tbs
|
378
|
+
LEFT JOIN cdr_temp_maternal_status #{current_partition} ms ON ms.patient_id = tbs.patient_id
|
330
379
|
SQL
|
331
380
|
end
|
332
381
|
|
333
382
|
def find_tb_confirmed_data_query
|
334
383
|
<<~SQL
|
335
|
-
SELECT t.patient_id, t.gender
|
336
|
-
|
384
|
+
SELECT t.patient_id, CASE t.gender
|
385
|
+
WHEN 'M' THEN 'Male'
|
386
|
+
WHEN 'F' THEN 'Female'
|
387
|
+
ELSE 'Unknown'
|
388
|
+
END gender, ms.maternal_status, t.age_group, t.enrollment_date, t.tb_confirmed_date
|
389
|
+
FROM cdr_tb_confirmed_and_on_treatment #{current_partition} t
|
390
|
+
LEFT JOIN cdr_temp_maternal_status #{current_partition} ms ON ms.patient_id = t.patient_id
|
337
391
|
WHERE t.tb_confirmed_date > '#{start_date}'
|
338
|
-
#{site_manager(operator: 'AND', column: 't.site_id', location: @location)}
|
339
392
|
AND (t.has_tb_confirmed_date = TRUE OR t.prev_reading IS NULL OR TIMESTAMPDIFF(MONTH,t.prev_reading, t.tb_confirmed_date) > 6)
|
340
393
|
SQL
|
341
394
|
end
|
@@ -35,7 +35,7 @@ module MalawiHivProgramReports
|
|
35
35
|
'VL_DUE' => MalawiHivProgramReports::Clinic::PatientsDueForViralLoad,
|
36
36
|
'DEFAULTER_LIST' => MalawiHivProgramReports::Pepfar::DefaulterList,
|
37
37
|
'VL_DISAGGREGATED' => MalawiHivProgramReports::Clinic::ViralLoadDisaggregated,
|
38
|
-
'TB_PREV' => MalawiHivProgramReports::Pepfar::
|
38
|
+
'TB_PREV' => MalawiHivProgramReports::Pepfar::TbPrev3,
|
39
39
|
'OUTCOME_LIST' => MalawiHivProgramReports::Clinic::OutcomeList,
|
40
40
|
'VIRAL_LOAD' => MalawiHivProgramReports::Clinic::ViralLoad,
|
41
41
|
'VIRAL_LOAD_COVERAGE' => MalawiHivProgramReports::Pepfar::ViralLoadCoverage2,
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: malawi_hiv_program_reports
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.1.
|
4
|
+
version: 1.1.17
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Roy Chanunkha
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2024-
|
11
|
+
date: 2024-09-25 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rails
|
@@ -191,7 +191,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
191
191
|
- !ruby/object:Gem::Version
|
192
192
|
version: '0'
|
193
193
|
requirements: []
|
194
|
-
rubygems_version: 3.5.
|
194
|
+
rubygems_version: 3.5.17
|
195
195
|
signing_key:
|
196
196
|
specification_version: 4
|
197
197
|
summary: Malawi HIV PROGRAM Reports for Ruby on Rails
|