malawi_hiv_program_reports 1.0.24 → 1.0.26

data/app/services/malawi_hiv_program_reports/pepfar/tx_ml.rb

@@ -3,7 +3,7 @@
 module MalawiHivProgramReports
   module Pepfar
     class TxMl
-      attr_reader :start_date, :end_date, :location
+      attr_reader :start_date, :end_date, :location, :rebuild
 
       include Utils
       include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
@@ -12,69 +12,30 @@ module MalawiHivProgramReports
       def initialize(start_date:, end_date:, **kwargs)
         @start_date = start_date.to_date.strftime('%Y-%m-%d 00:00:00')
         @end_date = end_date.to_date.strftime('%Y-%m-%d 23:59:59')
-        @occupation = kwargs[:occupation]
         @location = kwargs[:location]
-        @adapter = ActiveRecord::Base.connection.adapter_name.downcase
+        @rebuild = kwargs[:rebuild]&.casecmp?('true')
       end
 
       def find_report
-        tx_ml
+        if rebuild
+          cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date:, end_date:, definition: 'pepfar', locations: location.to_s, rebuild: true)
+          cohort.find_report
+        end
+        process_data
       end
 
       private
 
-      def tx_ml
+      def process_data
         data = {}
-        tx_curr = potential_tx_ml_clients
-        tx_new  = new_potential_tx_ml_clients
-        patient_ids = []
-        earliest_start_dates = {}
-
-        (tx_curr || []).each do |pat|
-          patient_id = pat['patient_id'].to_i
-          patient_ids << patient_id
-          earliest_start_dates[patient_id] = begin
-            pat['earliest_start_date'].to_date
-          rescue StandardError
-            pat['date_enrolled'].to_date
-          end
-        end
-
-        (tx_new || []).each do |pat|
+        (process_tx_ml_clients || []).each do |pat|
           patient_id = pat['patient_id'].to_i
-          patient_ids << patient_id
-          patient_ids = patient_ids.uniq
-          earliest_start_dates[patient_id] = begin
-            pat['earliest_start_date'].to_date
-          rescue StandardError
-            pat['date_enrolled'].to_date
-          end
-          patient_ids << pat['patient_id']
-          patient_ids = patient_ids.uniq
-        end
-
-        return [] if patient_ids.blank?
-
-        filtered_patients = ActiveRecord::Base.connection.select_all <<~SQL
-          SELECT
-            p.person_id patient_id, birthdate, gender,
-            #{function_manager(function: 'pepfar_patient_outcome', location: @location, args: "p.person_id::int, '#{end_date.to_date}'::date, #{@location}::int")} outcome,
-            #{function_manager(function: 'disaggregated_age_group', location: @location, args: "p.birthdate::date, '#{end_date.to_date}::date'")} age_group
-          FROM person #{current_partition} p
-          WHERE #{in_manager(column: 'p.person_id', values: patient_ids)}
-          GROUP BY p.person_id #{group_by_columns('p.birthdate, p.gender')}
-        SQL
-
-        (filtered_patients || []).each do |pat|
           outcome = pat['outcome']
-          next if outcome == 'On antiretrovirals'
-
-          patient_id = pat['patient_id'].to_i
           gender = begin
-            pat['gender'].first.upcase
-          rescue StandardError
-            'Unknown'
-          end
+                     pat['gender'].first.upcase
+                   rescue StandardError
+                     'Unknown'
+                   end
           age_group = pat['age_group']
 
           if data[age_group].blank?
@@ -86,7 +47,7 @@ module MalawiHivProgramReports
 
           case outcome
           when 'Defaulted'
-            def_months = defaulter_period(patient_id, earliest_start_dates[patient_id])
+            def_months = pat['months'].to_i
             if def_months < 3
               data[age_group][gender][1] << patient_id
             elsif def_months <= 5
@@ -104,70 +65,54 @@ module MalawiHivProgramReports
         rescue StandardError => e
           Rails.logger.error(e.message)
         end
-
         data
       end
 
-      def potential_tx_ml_clients
-        ActiveRecord::Base.connection.select_all <<~SQL
-          SELECT
-            p.patient_id AS patient_id,
-            pe.birthdate,
-            pe.gender,
-            #{function_manager(function: 'patient_date_enrolled', location: @location, args: "p.patient_id::int, #{@location}::int")} AS date_enrolled,
-            #{function_manager(function: 'date_antiretrovirals_started', location: @location, args: "p.patient_id::int, MIN(s.start_date)::date, #{@location}::int")} AS earliest_start_date
-          FROM patient_program #{current_partition} p
-            INNER JOIN person #{current_partition} pe ON pe.person_id = p.patient_id AND pe.voided = 0
-            INNER JOIN patient_state #{current_partition} s ON p.patient_program_id = s.patient_program_id AND s.voided = 0 AND s.state = 7
-            LEFT JOIN (#{current_occupation_query}) a ON a.person_id = p.patient_id
-            WHERE p.program_id = 1 #{%w[Military Civilian].include?(@occupation) ? 'AND' : ''} #{occupation_filter(occupation: @occupation, field_name: 'value', table_name: 'a', include_clause: false)}
-              AND DATE(s.start_date) < '#{start_date.to_date}'
-              AND #{function_manager(function: 'pepfar_patient_outcome', location: @location, args: "p.patient_id::int, '#{start_date.to_date}'::date, #{@location}::int")} = 'On antiretrovirals'
-              AND pe.person_id NOT IN (#{drug_refills_and_external_consultation_list})
-            GROUP BY p.patient_id
-            HAVING date_enrolled IS NOT NULL AND DATE(date_enrolled) < '#{start_date.to_date}';
-        SQL
+      def tx_ml_clients
+        <<~SQL
+            SELECT
+              e.patient_id,
+              e.birthdate,
+              e.gender,
+              e.date_enrolled,
+              e.earliest_start_date,
+              o.outcome_date,
+              TIMESTAMPDIFF(MONTH, DATE(e.earliest_start_date), DATE(o.outcome_date)) months,
+              disaggregated_age_group(e.birthdate, DATE('#{end_date}')) age_group,
+              o.cum_outcome outcome
+            FROM cdr_temp_cohort_members #{current_partition} e
+            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')
+            WHERE e.patient_id IN (SELECT patient_id FROM cdr_temp_patient_outcomes_start #{current_partition} WHERE cum_outcome = 'On antiretrovirals')
+              AND DATE(e.date_enrolled) < '#{start_date.to_date}'
+            GROUP BY e.patient_id
+          SQL
       end
 
-      def new_potential_tx_ml_clients
-        ActiveRecord::Base.connection.select_all <<~SQL
-          SELECT
-            p.patient_id AS patient_id,
-            pe.birthdate,
-            pe.gender,
-            #{function_manager(function: 'patient_date_enrolled', location: @location, args: "p.patient_id::int, #{@location}::int")} AS date_enrolled,
-            #{function_manager(function: 'date_antiretrovirals_started', location: @location, args: "p.patient_id::int, MIN(s.start_date)::date, #{@location}::int")} AS earliest_start_date
-          FROM patient_program #{current_partition} p
-            INNER JOIN person #{current_partition} pe ON pe.person_id = p.patient_id AND pe.voided = 0
-            INNER JOIN patient_state #{current_partition} s ON p.patient_program_id = s.patient_program_id AND s.voided = 0 AND s.state = 7
-            LEFT JOIN (#{current_occupation_query}) a ON a.person_id = p.patient_id
-            WHERE p.program_id = 1 #{%w[Military Civilian].include?(@occupation) ? 'AND' : ''} #{occupation_filter(occupation: @occupation, field_name: 'value', table_name: 'a', include_clause: false)}
-              AND DATE(s.start_date) BETWEEN DATE('#{start_date}') AND DATE('#{end_date}')
-              AND pe.person_id NOT IN (#{drug_refills_and_external_consultation_list})
-            GROUP BY p.patient_id
-            HAVING date_enrolled IS NOT NULL AND date_enrolled BETWEEN DATE('#{start_date}') AND DATE('#{end_date}');
-        SQL
+      def tx_ml_clients_new
+        <<~SQL
+            SELECT
+              e.patient_id,
+              e.birthdate,
+              e.gender,
+              e.date_enrolled,
+              e.earliest_start_date,
+              o.outcome_date,
+              TIMESTAMPDIFF(MONTH, DATE(e.earliest_start_date), DATE(o.outcome_date)) months,
+              disaggregated_age_group(e.birthdate, DATE('#{end_date}')) age_group,
+              o.cum_outcome outcome
+            FROM cdr_temp_cohort_members #{current_partition} e
+            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')
+            WHERE e.date_enrolled BETWEEN DATE('#{start_date}') AND DATE('#{end_date}')
+            GROUP BY e.patient_id
+          SQL
       end
 
-      def defaulter_period(patient_id, earliest_start_date)
-        defaulter_date = ActiveRecord::Base.connection.select_one <<~SQL
-          SELECT #{function_manager(function: 'current_pepfar_defaulter_date', location: @location, args: "#{patient_id}::int, '#{end_date}'::date, #{@location}::int")} def_date;
-        SQL
-
-        defaulter_date = begin
-          defaulter_date['def_date'].to_date
-        rescue StandardError
-          end_date.to_date
-        end
-
-        raise 'Defaulted outside the reporting period' if defaulter_date > end_date.to_date
-        raise 'Defaulted outside the reporting period' if defaulter_date < start_date.to_date
-
-        days_gone = ActiveRecord::Base.connection.select_one <<~SQL
-          SELECT TIMESTAMPDIFF(MONTH, DATE('#{earliest_start_date}'), DATE('#{defaulter_date}')) months;
-        SQL
-
-        days_gone['months'].to_i
+      def process_tx_ml_clients
+        ActiveRecord::Base.connection.select_all <<~SQL
+            (#{tx_ml_clients})
+            UNION
+            (#{tx_ml_clients_new})
+          SQL
       end
     end
   end

data/app/services/malawi_hiv_program_reports/pepfar/tx_new.rb

@@ -14,8 +14,7 @@ module MalawiHivProgramReports
       def initialize(start_date:, end_date:, **kwargs)
         @start_date = start_date.to_date.beginning_of_day.strftime('%Y-%m-%d %H:%M:%S')
         @end_date = end_date.to_date.end_of_day.strftime('%Y-%m-%d %H:%M:%S')
-        rebuild_string = kwargs[:rebuild]
-        @rebuild = rebuild_string.present? ? rebuild_string&.downcase == 'true' : false
+        @rebuild = kwargs[:rebuild]&.casecmp?('true')
         @location = kwargs[:location]
       end
 
@@ -23,8 +22,8 @@ module MalawiHivProgramReports
         report = init_report
         addittional_groups report
         if rebuild
-          MalawiHivProgramReports::Moh::CohortBuilder.new(location: @location).init_temporary_tables(start_date,
-                                                                                                     end_date, '')
+          cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date:, end_date:, definition: 'pepfar', locations: location.to_s, rebuild: true)
+          cohort.find_report
         end
         process_data report
         flatten_the_report report
@@ -64,8 +63,12 @@ module MalawiHivProgramReports
         end
       end
 
+      # rubocop:disable Metrics/AbcSize
+      # rubocop:disable Metrics/MethodLength
+      # rubocop:disable Metrics/PerceivedComplexity
+      # rubocop:disable Metrics/CyclomaticComplexity
       def process_data(report)
-        data.each do |row|
+        fetch_data.each do |row|
           age_group = row['age_group']
           gender = row['gender']
           date_enrolled = row['date_enrolled']
@@ -106,6 +109,8 @@ module MalawiHivProgramReports
           report['All']['FNP'][indicator.to_sym] << kwargs[:patient_id]
         end
       end
+      # rubocop:enable Metrics/PerceivedComplexity
+      # rubocop:enable Metrics/CyclomaticComplexity
 
       def process_age_group_report(age_group, gender, age_group_report)
         {
@@ -115,12 +120,14 @@ module MalawiHivProgramReports
                   else
                     (gender == 'M' ? 'Male' : gender)
                   end,
-          cd4_less_than_200: age_group_report[:cd4_less_than_200],
-          cd4_greater_than_equal_to_200: age_group_report[:cd4_greater_than_equal_to_200],
-          cd4_unknown_or_not_done: age_group_report[:cd4_unknown_or_not_done],
-          transfer_in: age_group_report[:transfer_in]
+          cd4_less_than_200: age_group_report['cd4_less_than_200'.to_sym],
+          cd4_greater_than_equal_to_200: age_group_report['cd4_greater_than_equal_to_200'.to_sym],
+          cd4_unknown_or_not_done: age_group_report['cd4_unknown_or_not_done'.to_sym],
+          transfer_in: age_group_report['transfer_in'.to_sym]
         }
       end
+      # rubocop:enable Metrics/AbcSize
+      # rubocop:enable Metrics/MethodLength
 
       def flatten_the_report(report)
         result = []
@@ -142,58 +149,50 @@ module MalawiHivProgramReports
         result_scores.reject { |item| item[:age_group].match?(/unknown/i) }
       end
 
-      def data
+      def fetch_data
         ActiveRecord::Base.connection.select_all <<~SQL
-          SELECT
-            pp.patient_id,
-            MIN(pp.gender) gender,
-            disaggregated_age_group(pp.birthdate, DATE('#{end_date}')) age_group,
-            CASE
-              WHEN o.value_numeric < 200 THEN 'cd4_less_than_200'
-              WHEN o.value_numeric = 200 AND o.value_modifier = '=' THEN 'cd4_greater_than_equal_to_200'
-              WHEN o.value_numeric = 200 AND o.value_modifier = '<' THEN 'cd4_less_than_200'
-              WHEN o.value_numeric = 200 AND o.value_modifier = '>' THEN 'cd4_greater_than_equal_to_200'
-              WHEN o.value_numeric > 200 THEN 'cd4_greater_than_equal_to_200'
-              ELSE 'cd4_unknown_or_not_done'
-            END cd4_count_group,
-            CASE
-              WHEN transfer_in.value_coded IS NOT NULL THEN 0
-              ELSE 1
-            END new_patient,
-            pp.date_enrolled,
-            pp.earliest_start_date,
-            preg_or_breast.name AS maternal_status,
-            DATE(MIN(pregnant_or_breastfeeding.obs_datetime)) AS maternal_status_date
-          FROM cdr_temp_cohort_members pp
-          INNER JOIN person #{current_partition} pe ON pe.person_id = pp.patient_id AND pe.voided = 0
-          #{site_manager(operator: 'AND', column: 'pp.site_id', location: @location)}
-          LEFT JOIN (
-            SELECT max(o.obs_datetime) AS obs_datetime, o.person_id
-            FROM obs #{current_partition} o
-            INNER JOIN concept_name cn ON cn.concept_id = o.concept_id AND cn.name = 'CD4 count' AND cn.voided = 0
-            INNER JOIN patient_program #{current_partition} pp ON pp.patient_id = o.person_id
-                AND pp.program_id = #{program('HIV PROGRAM').id}
-                AND pp.voided = 0
-            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}')
-            WHERE o.concept_id = #{concept_name('CD4 count').concept_id} AND o.voided = 0
-            AND o.obs_datetime <= '#{end_date}' AND o.obs_datetime >= '#{start_date}'
-            GROUP BY o.person_id
-          ) current_cd4 ON current_cd4.person_id = pp.patient_id
-          LEFT JOIN obs #{current_partition} o ON o.person_id = pp.patient_id AND o.concept_id = #{concept_name('CD4 count').concept_id} AND o.voided = 0 AND o.obs_datetime = current_cd4.obs_datetime
-          LEFT JOIN obs #{current_partition} transfer_in ON transfer_in.person_id = pp.patient_id
-            AND transfer_in.concept_id = #{concept_name('Ever registered at ART clinic').concept_id}
-            AND transfer_in.voided = 0
-            AND transfer_in.value_coded = #{concept_name('Yes').concept_id}
-            AND transfer_in.obs_datetime <= '#{end_date}'
-            AND transfer_in.obs_datetime >= '#{start_date}'
-          LEFT JOIN obs #{current_partition} pregnant_or_breastfeeding ON pregnant_or_breastfeeding.person_id = pp.patient_id
-            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)
-            AND pregnant_or_breastfeeding.voided = 0
-            AND pregnant_or_breastfeeding.value_coded = #{concept_name('Yes').concept_id}
+            SELECT
+              e.patient_id,
+              e.gender,
+              disaggregated_age_group(e.birthdate, DATE('#{end_date}')) age_group,
+              CASE
+                WHEN o.value_numeric < 200 THEN 'cd4_less_than_200'
+                WHEN o.value_numeric = 200 AND o.value_modifier = '=' THEN 'cd4_greater_than_equal_to_200'
+                WHEN o.value_numeric = 200 AND o.value_modifier = '<' THEN 'cd4_less_than_200'
+                WHEN o.value_numeric = 200 AND o.value_modifier = '>' THEN 'cd4_greater_than_equal_to_200'
+                WHEN o.value_numeric > 200 THEN 'cd4_greater_than_equal_to_200'
+                ELSE 'cd4_unknown_or_not_done'
+              END cd4_count_group,
+              CASE
+                WHEN e.recorded_start_date IS NULL THEN 1
+                ELSE 0
+              END new_patient,
+              e.date_enrolled,
+              e.earliest_start_date,
+              preg_or_breast.name AS maternal_status,
+              DATE(MIN(pregnant_or_breastfeeding.obs_datetime)) AS maternal_status_date
+            FROM cdr_temp_cohort_members #{current_partition} e
+            LEFT JOIN (
+              SELECT max(o.obs_datetime) AS obs_datetime, o.person_id
+              FROM obs #{current_partition} o
+              INNER JOIN concept_name cn ON cn.concept_id = o.concept_id AND cn.name = 'CD4 count' AND cn.voided = 0
+              INNER JOIN patient_program #{current_partition} pp ON pp.patient_id = o.person_id
+                  AND pp.program_id = #{program('HIV PROGRAM').id}
+                  AND pp.voided = 0
+              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}')
+              WHERE o.concept_id = #{concept_name('CD4 count').concept_id} AND o.voided = 0
+              AND o.obs_datetime <= '#{end_date}' AND o.obs_datetime >= '#{start_date}'
+              GROUP BY o.person_id
+            ) current_cd4 ON current_cd4.person_id = e.patient_id
+            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
+            LEFT JOIN obs #{current_partition} pregnant_or_breastfeeding ON pregnant_or_breastfeeding.person_id = e.patient_id
+              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)
+              AND pregnant_or_breastfeeding.voided = 0
+              AND pregnant_or_breastfeeding.value_coded = #{concept_name('Yes').concept_id}
             LEFT JOIN concept_name preg_or_breast ON preg_or_breast.concept_id = pregnant_or_breastfeeding.concept_id AND preg_or_breast.voided = 0
-          WHERE pp.date_enrolled <= '#{end_date}' AND pp.date_enrolled >= '#{start_date}'
-          GROUP BY pp.patient_id
-        SQL
+            WHERE e.date_enrolled <= '#{end_date}' AND e.date_enrolled >= '#{start_date}'
+            GROUP BY e.patient_id
+          SQL
       end
     end
     # rubocop:enable Metrics/ClassLength

data/app/services/malawi_hiv_program_reports/pepfar/tx_rtt.rb

@@ -7,20 +7,28 @@ module MalawiHivProgramReports
         include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
         include MalawiHivProgramReports::Adapters::Moh::Custom
         include MalawiHivProgramReports::Utils::ModelUtils
-        attr_reader :start_date, :end_date, :location
+        attr_reader :start_date, :end_date, :location, :rebuild
 
         def initialize(start_date:, end_date:, **kwargs)
           @start_date = ActiveRecord::Base.connection.quote(start_date.to_date.beginning_of_day.strftime('%Y-%m-%d %H:%M:%S'))
           @end_date = ActiveRecord::Base.connection.quote(end_date.to_date.end_of_day.strftime('%Y-%m-%d %H:%M:%S'))
-          @occupation = kwargs[:occupation]
+          @rebuild = kwargs[:rebuild]&.casecmp?(true)
           @location = kwargs[:location]
         end
 
         def find_report
+          if rebuild
+            cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date:, end_date:, definition: 'pepfar', locations: location.to_s, rebuild: true)
+            cohort.find_report
+          end
           process_report
         end
 
         def data
+          if rebuild
+            cohort = MalawiHivProgramReports::Moh::CumulativeCohort.new(start_date:, end_date:, definition: 'pepfar', locations: location.to_s, rebuild: true)
+            cohort.find_report
+          end
           process_report
         rescue StandardError => e
           Rails.logger.error "Error running TX_RTT Report: #{e}"
@@ -47,7 +55,7 @@ module MalawiHivProgramReports
         end
 
         def process_data(report)
-          tx_rtt.each do |row|
+          fetch_data.each do |row|
             age_group = row['age_group']
             gender = row['gender']
             months = row['months']
@@ -64,14 +72,17 @@ module MalawiHivProgramReports
         end
 
         def process_months(report, months, patient_id)
-          report[:returned_less_than_3_months] << patient_id if months.blank?
-          report[:returned_less_than_3_months] << patient_id if months < 3
-          report[:returned_greater_than_3_months_and_less_than_6_months] << patient_id if months >= 3 && months < 6
+          return report[:returned_less_than_3_months] << patient_id if months.blank?
+          return report[:returned_less_than_3_months] << patient_id if months < 3
+          if months >= 3 && months < 6
+            return report[:returned_greater_than_3_months_and_less_than_6_months] << patient_id
+          end
+
           report[:returned_greater_than_or_equal_to_6_months] << patient_id if months >= 6
         end
 
         def process_cd4(report, months, patient_id, cd4_cat)
-          if cd4_cat == 'unknown_cd4_count' && months <= 2
+          if cd4_cat == 'unknown_cd4_count' && (months.blank? || months <= 2)
             report[:not_eligible_for_cd4] << patient_id
             return
           end
@@ -120,160 +131,31 @@ module MalawiHivProgramReports
           sorted_results.sort_by { |h| [h[:gender] == 'F' ? 0 : 1] }
         end
 
-        def tx_rtt
+        def fetch_data
           ActiveRecord::Base.connection.select_all <<~SQL
-            SELECT patient_program.patient_id,
-            #{function_manager(function: 'disaggregated_age_group', location: @location, args: "person.birthdate::date, #{@end_date}::date")} AS age_group,
-            person.gender,
-            IF(
-              patient_state_at_start_of_quarter.state = 6, 'Treatment stopped',
-              IF(
-                patient_state_at_start_of_quarter.state = 12, 'Defaulted',
-                #{function_manager(function: 'pepfar_patient_outcome', location: @location, args: "patient_program.patient_id, (DATE(#{@start_date}) - INTERVAL 1 DAY), #{@location}")}
-              )
-            ) AS initial_outcome,
-            IF(
-              patient_state_at_start_of_quarter.state = 6,
-              patient_state_at_start_of_quarter.start_date,
-              IF(
-                patient_state_at_start_of_quarter.state = 12,
-                patient_state_at_start_of_quarter.start_date,
-                #{function_manager(function: 'current_pepfar_defaulter_date', location: @location, args: "patient_program.patient_id, (DATE(#{@start_date}) - INTERVAL 1 DAY), #{@location}")} 
-                )) AS initial_outcome_date,
-              IF(
-                patients_with_orders_at_end_of_quarter.patient_id IS NOT NULL,  'On antiretrovirals',
-                IF(
-                  #{function_manager(function: 'current_pepfar_defaulter', location: @location, args: "patient_program.patient_id, #{@end_date}, #{@location}")} = 0,
-                  'On antiretrovirals','Defaulted'
-              )
-            ) AS final_outcome,
-            TIMESTAMPDIFF(MONTH, IF(
-              patient_state_at_start_of_quarter.state = 6,
-              patient_state_at_start_of_quarter.start_date,
-              IF(
-                patient_state_at_start_of_quarter.state = 12,
-                patient_state_at_start_of_quarter.start_date,
-                #{function_manager(function: 'current_pepfar_defaulter_date', location: @location, args: "patient_program.patient_id, (DATE(#{@start_date}) - INTERVAL 1 DAY), #{@location}")})
-            ), patients_who_received_art_in_quarter.start_date) AS months,
-                CASE
-                    WHEN cd4_result.value_numeric < 200 THEN 'cd4_less_than_200'
-                    WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '=' THEN 'cd4_greater_than_or_equal_to_200'
-                    WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '<' THEN 'cd4_less_than_200'
-                    WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '>' THEN 'cd4_greater_than_or_equal_to_200'
-                    WHEN cd4_result.value_numeric > 200 THEN 'cd4_greater_than_or_equal_to_200'
-                    ELSE 'unknown_cd4_count'
-                END cd4_count_group
-            FROM patient_program #{current_partition}
-            INNER JOIN person #{current_partition} ON person.person_id = patient_program.patient_id
-            /* Select patients that were on treatment before start of reporting period */
-            INNER JOIN patient_state #{current_partition} AS patient_ever_on_treatment
-              ON patient_ever_on_treatment.patient_program_id = patient_program.patient_program_id
-              AND patient_ever_on_treatment.state = 7
-              AND patient_ever_on_treatment.start_date < DATE(#{start_date})
-              AND patient_ever_on_treatment.voided = 0
-            /* Get patient's state at the start of the quarter. */
-            INNER JOIN (
-              SELECT patient_program_id, MAX(patient_state.date_created) AS date_created
-              FROM patient_state #{current_partition}
-              INNER JOIN patient_program #{current_partition} USING (patient_program_id)
-              WHERE patient_state.voided = 0
-                AND patient_program.voided = 0
-                AND patient_program.program_id = 1
-                AND patient_state.start_date < DATE(#{start_date}) + INTERVAL 1 DAY
-              GROUP BY patient_program_id
-            ) AS date_of_last_patient_state_before_quarter
-              ON date_of_last_patient_state_before_quarter.patient_program_id = patient_program.patient_program_id
-            LEFT JOIN patient_state #{current_partition} AS patient_state_at_start_of_quarter
-              ON patient_state_at_start_of_quarter.patient_program_id = date_of_last_patient_state_before_quarter.patient_program_id
-              AND patient_state_at_start_of_quarter.date_created = date_of_last_patient_state_before_quarter.date_created
-              AND patient_state_at_start_of_quarter.state IN (6, 12) /* 2: TO, 6: Tx Stopped, 12: Defaulted */
-            /* Select patients who received ART within the reporting period. */
-            INNER JOIN (
-              SELECT DISTINCT encounter.patient_id, orders.start_date
-              FROM encounter #{current_partition}
-              INNER JOIN orders #{current_partition}
-                ON orders.encounter_id = encounter.encounter_id
-                AND DATE(orders.start_date) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
-                AND orders.voided = 0
-              INNER JOIN drug_order #{current_partition}
-                ON drug_order.order_id = orders.order_id
-                AND drug_order.quantity > 0
-                AND drug_order.drug_inventory_id IN (SELECT DISTINCT drug_id FROM arv_drug)
-              WHERE encounter.voided = 0
-                AND encounter.program_id = 1
-                AND DATE(encounter.encounter_datetime) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
-            ) AS patients_who_received_art_in_quarter
-              ON patients_who_received_art_in_quarter.patient_id = patient_program.patient_id
-            /* Ensure that patients are on ART at the end of the quarter */
-            INNER JOIN (
-              SELECT patient_program_id, MAX(patient_state.date_created) AS date_created
-              FROM patient_state #{current_partition}
-              INNER JOIN patient_program #{current_partition} USING (patient_program_id)
-              WHERE patient_state.voided = 0
-                AND patient_program.voided = 0
-                AND patient_program.program_id = 1
-                AND patient_state.start_date < DATE(#{end_date}) + INTERVAL 1 DAY
-              GROUP BY patient_program_id
-            ) AS date_of_last_patient_state_in_quarter
-              ON date_of_last_patient_state_in_quarter.patient_program_id = patient_program.patient_program_id
-
-              /*Not sure why Walter had this section in but I believe its not neccessary*/
-              /*INNER JOIN patient_state AS patient_state_at_end_of_quarter
-              ON patient_state_at_end_of_quarter.patient_program_id = patient_program.patient_program_id
-              AND patient_state_at_end_of_quarter.date_created = date_of_last_patient_state_before_quarter.date_created
-              AND patient_state_at_end_of_quarter.state = 7*/
-
-            /* Select patient who had orders in the last 30 days of the reporting period.
-               This is to be used as a quick filter for patients who are definitely
-               'On ART' by the end of the reporting period. The rest will be filtered by
-               the current_defaulter function. */
-            LEFT JOIN (
-              SELECT DISTINCT encounter.patient_id
-              FROM encounter #{current_partition}
-              INNER JOIN orders #{current_partition}
-                ON orders.encounter_id = encounter.encounter_id
-                AND orders.voided = 0
-                AND DATE(orders.start_date) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
-                AND DATE(orders.auto_expire_date) >= (DATE(#{end_date}) - INTERVAL 30 DAY)
-              INNER JOIN drug_order #{current_partition}
-                ON drug_order.order_id = orders.order_id
-                AND drug_order.quantity > 0
-                AND drug_order.drug_inventory_id IN (SELECT DISTINCT drug_id FROM arv_drug)
-              WHERE encounter.program_id = 1
-                AND DATE(encounter.encounter_datetime) BETWEEN DATE(#{start_date}) AND DATE(#{end_date})
-                AND encounter.voided = 0
-            ) AS patients_with_orders_at_end_of_quarter
-              ON patients_with_orders_at_end_of_quarter.patient_id = patient_program.patient_id
-            LEFT JOIN (
-                SELECT max(o.obs_datetime) AS obs_datetime, o.person_id
-                FROM obs #{current_partition} o
-                INNER JOIN concept_name cn ON cn.concept_id = o.concept_id AND cn.name = 'CD4 count'
-                WHERE o.concept_id = #{concept_name('CD4 count').concept_id} AND o.voided = 0
-                AND o.obs_datetime <= #{end_date} AND o.obs_datetime >= #{start_date}
-                GROUP BY o.person_id
-            ) current_cd4 ON current_cd4.person_id = patient_program.patient_id
-            LEFT JOIN obs #{current_partition} cd4_result ON cd4_result.person_id = patient_program.patient_id AND cd4_result.concept_id = #{concept_name('CD4 count').concept_id} AND cd4_result.voided = 0
-            #  Not sure why we are matching the two dates but the result was excluding cd4 results for patients.
-            # AND cd4_result.obs_datetime = current_cd4.obs_datetime
-            LEFT JOIN (#{current_occupation_query}) a ON a.person_id = patient_program.patient_id
-            WHERE patient_program.program_id = 1 #{%w[Military Civilian].include?(@occupation) ? 'AND' : ''} #{occupation_filter(occupation: @occupation, field_name: 'value', table_name: 'a', include_clause: false)}
-              /* Ensure that the patients retrieved, did not receive ART within 28 days
-                 before the start of the reporting period */
-              AND patient_program.patient_id NOT IN (
-                SELECT DISTINCT orders.patient_id
-                FROM orders #{current_partition}
-                INNER JOIN drug_order #{current_partition} USING (order_id)
-                INNER JOIN arv_drug ON arv_drug.drug_id = drug_inventory_id
-                INNER JOIN patient_program #{current_partition}
-                  ON patient_program.patient_id = orders.patient_id
-                  AND patient_program.program_id = 1
-                WHERE ((DATE(orders.start_date )BETWEEN (DATE(#{start_date}) - INTERVAL 30 DAY) AND DATE(#{start_date}))
-                       OR (DATE(orders.auto_expire_date) BETWEEN (DATE(#{start_date}) - INTERVAL 30 DAY) AND DATE(#{start_date})))
-                  AND orders.voided = 0
-              )
-            GROUP BY patient_program.patient_id
-            HAVING initial_outcome IN ('Defaulted', 'Treatment stopped')
-               AND final_outcome = 'On antiretrovirals';
+            SELECT
+              e.patient_id,
+              disaggregated_age_group(e.birthdate, #{end_date}) AS age_group,
+              e.gender,
+              s.cum_outcome initial_outcome,
+              o.cum_outcome final_outcome,
+              TIMESTAMPDIFF(MONTH, COALESCE(s.outcome_date, c.outcome_date), ord.min_order_date) months,
+              CASE
+                WHEN cd4_result.value_numeric < 200 THEN 'cd4_less_than_200'
+                WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '=' THEN 'cd4_greater_than_or_equal_to_200'
+                WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '<' THEN 'cd4_less_than_200'
+                WHEN cd4_result.value_numeric = 200 AND cd4_result.value_modifier = '>' THEN 'cd4_greater_than_or_equal_to_200'
+                WHEN cd4_result.value_numeric > 200 THEN 'cd4_greater_than_or_equal_to_200'
+                ELSE 'unknown_cd4_count'
+              END cd4_count_group
+            FROM cdr_temp_cohort_members #{current_partition} e
+            INNER JOIN cdr_temp_patient_outcomes #{current_partition} o ON o.patient_id = e.patient_id AND o.cum_outcome = 'On antiretrovirals'
+            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')
+            INNER JOIN cdr_temp_current_state_start #{current_partition} c ON c.patient_id = e.patient_id
+            INNER JOIN cdr_temp_max_drug_orders #{current_partition} ord ON ord.patient_id = e.patient_id
+            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
+            WHERE e.date_enrolled < #{start_date}
+            GROUP BY e.patient_id
           SQL
         end
       end

data/lib/malawi_hiv_program_reports/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module MalawiHivProgramReports
-  VERSION = '1.0.24'
+  VERSION = '1.0.26'
 end