malawi_hiv_program_reports 1.0.1 → 1.0.2

data/app/services/malawi_hiv_program_reports/clinic/vl_collection.rb

@@ -0,0 +1,48 @@
+# frozen_string_literal: true
+
+# Report for Showing all HIV Viral Load Tests Done Or Sample Collected per the specified period
+module MalawiHivProgramReports
+  module Clinic
+    class VlCollection
+      include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
+      def initialize(start_date:, end_date:, **kwargs)
+        @start_date = start_date.to_date.beginning_of_day
+        @end_date = end_date.to_date.end_of_day
+        @occupation = kwargs[:occupation]
+      end
+
+      def find_report
+        data
+      end
+
+      private
+
+      def data
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT
+            o.person_id AS patient_id,
+            pn.given_name,
+            pn.family_name,
+            p.gender,
+            p.birthdate,
+            i.identifier AS identifier,
+            DATE(ord.start_date) AS order_date
+          FROM obs o
+          INNER JOIN orders ord ON ord.order_id = o.order_id AND ord.voided = 0
+          INNER JOIN person p ON p.person_id = o.person_id AND p.voided = 0
+          INNER JOIN person_name pn ON pn.person_id = p.person_id AND pn.voided = 0
+          LEFT JOIN patient_identifier i ON i.patient_id = p.person_id AND i.voided = 0 AND i.identifier_type = #{indetifier_type}
+          LEFT JOIN (#{current_occupation_query}) AS a ON a.person_id = p.person_id
+          WHERE o.concept_id = 9737 -- Test Type
+          AND o.value_coded = 856 -- Viral Load
+          AND o.obs_datetime BETWEEN '#{@start_date}' AND '#{@end_date}'
+          AND o.voided = 0 #{%w[Military Civilian].include?(@occupation) ? 'AND' : ''} #{occupation_filter(occupation: @occupation, field_name: 'value', table_name: 'a', include_clause: false)}
+        SQL
+      end
+
+      def indetifier_type
+        @indetifier_type ||= ::PatientIdentifierType.find_by_name!(::GlobalPropertyService.use_filing_numbers? ? 'Filing Number' : 'ARV Number').id
+      end
+    end
+  end
+end

data/app/services/malawi_hiv_program_reports/cohort/outcomes.rb

@@ -0,0 +1,338 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Cohort
+    class Outcomes
+      include MalawiHivProgramReports::Adapters::Moh::Custom
+      include MalawiHivProgramReports::Utils::ModelUtils
+      attr_reader :end_date
+
+      def initialize(end_date:, definition: 'moh', location: nil)
+        definition = definition.downcase
+        raise ::ArgumentError, "Invalid outcomes definition: #{definition}" unless %w[moh pepfar].include?(definition)
+
+        @adapter = ActiveRecord::Base.connection.adapter_name.downcase
+        @end_date = end_date.to_date
+        @definition = definition
+        @location = location
+      end
+
+      def update_cummulative_outcomes
+        initialize_table
+
+        # HIC SUNT DRACONIS: The order of the operations below matters,
+        # do not change it unless you know what you are doing!!!
+        load_patients_who_died
+        load_patients_who_stopped_treatment
+        load_patients_on_pre_art
+        load_patients_without_state
+        load_patients_without_drug_orders
+        load_patients_on_treatment
+        load_defaulters
+      end
+
+      private
+
+      def arv_drugs_concept_set
+        @arv_drugs_concept_set ||= ::ConceptSet.where(set: concept_name('Antiretroviral drugs').concept)
+                                               .select(:concept_id)
+      end
+
+      def drug_order_type
+        @drug_order_type ||= order_type('Drug order')
+      end
+
+      def program_states(*names)
+        ::ProgramWorkflowState.joins(:program_workflow)
+                              .joins(:concept)
+                              .merge(::ProgramWorkflow.where(program: hiv_program))
+                              .merge(::Concept.joins(:concept_names)
+                                          .merge(::ConceptName.where(name: names)))
+                              .select(:program_workflow_state_id)
+      end
+
+      def hiv_program
+        @hiv_program ||= program('HIV Program')
+      end
+
+      def initialize_table
+        ActiveRecord::Base.connection.execute <<~SQL
+          DROP TABLE IF EXISTS temp_patient_outcomes
+        SQL
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          CREATE TABLE temp_patient_outcomes (
+            patient_id INT NOT NULL,
+            cum_outcome VARCHAR(120) NOT NULL,
+            outcome_date DATE DEFAULT NULL,
+            site_id INT NOT NULL,
+            PRIMARY KEY (patient_id, site_id)
+          )
+        SQL
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          CREATE INDEX tpo_outcomes ON temp_patient_outcomes (patient_id, cum_outcome, outcome_date, site_id)
+        SQL
+      end
+
+      # Loads all patiens with an outcome of died as of given date
+      # into the temp_patient_outcomes table.
+      def load_patients_who_died
+        date = ActiveRecord::Base.connection.quote(end_date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_outcomes
+          SELECT patients.patient_id, 'Patient died', MIN(patient_state.start_date), #{@location}
+          FROM temp_earliest_start_date AS patients
+          INNER JOIN patient_program
+            ON patient_program.patient_id = patients.patient_id
+            AND patient_program.program_id = #{hiv_program.program_id}
+            AND patient_program.voided = 0 #{site_manager(operator: 'AND', column: 'patient_program.site_id', location: @location)}
+          INNER JOIN patient_state
+            ON patient_state.patient_program_id = patient_program.patient_program_id
+            AND patient_state.state = (#{program_states('Patient died').limit(1).to_sql})
+            AND patient_state.start_date < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
+            AND patient_state.voided = 0 #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+          WHERE patients.date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'patients.site_id', location: @location)}
+          GROUP BY patients.patient_id
+        SQL
+      end
+
+      # Loads all patients with an outcome of transferred out or
+      # treatment stopped into temp_patient_outcomes table.
+      def load_patients_who_stopped_treatment
+        date = ActiveRecord::Base.connection.quote(end_date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_outcomes
+          SELECT patients.patient_id,
+                 (
+                   SELECT name FROM concept_name
+                   WHERE concept_id = (
+                   SELECT concept_id FROM program_workflow_state
+                   WHERE program_workflow_state_id = patient_state.state
+                   LIMIT 1
+                   )
+                 ) AS cum_outcome,
+                 patient_state.start_date, #{@location}
+          FROM temp_earliest_start_date AS patients
+          INNER JOIN patient_program
+            ON patient_program.patient_id = patients.patient_id
+            AND patient_program.program_id = #{hiv_program.program_id}
+            AND patient_program.voided = 0 #{site_manager(operator: 'AND', column: 'patient_program.site_id', location: @location)}
+          INNER JOIN patient_state
+            ON patient_state.patient_program_id = patient_program.patient_program_id
+            AND patient_state.state IN (#{program_states('Patient transferred out', 'Treatment stopped').to_sql})
+            AND patient_state.start_date < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
+            AND (patient_state.end_date >= #{date} OR patient_state.end_date IS NULL)
+            AND patient_state.voided = 0 #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+          INNER JOIN (
+            SELECT patient_program_id, MAX(start_date) AS start_date
+            FROM patient_state
+            WHERE patient_state.start_date < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
+              AND patient_state.voided = 0 #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+            GROUP BY patient_program_id
+          ) AS max_patient_state
+            ON max_patient_state.patient_program_id = patient_state.patient_program_id
+            AND max_patient_state.start_date = patient_state.start_date #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+          WHERE patients.date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'patients.site_id', location: @location)}
+            AND patients.patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
+          GROUP BY patients.patient_id #{@adapter == 'mysql2' ? '' : ',patient_state.state, patient_state.start_date'}
+        SQL
+      end
+
+      # Load all patients on Pre-ART.
+      def load_patients_on_pre_art
+        date = ActiveRecord::Base.connection.quote(end_date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_outcomes
+          SELECT patients.patient_id,
+                CASE
+                  WHEN #{current_defaulter_function('patients.patient_id')} = 1 THEN 'Defaulted'
+                  ELSE 'Pre-ART (Continue)'
+                END AS cum_outcome,
+                patient_state.start_date, #{@location}
+          FROM temp_earliest_start_date AS patients
+          INNER JOIN patient_program
+            ON patient_program.patient_id = patients.patient_id
+            AND patient_program.program_id = #{hiv_program.program_id}
+            AND patient_program.voided = 0 #{site_manager(operator: 'AND', column: 'patient_program.site_id', location: @location)}
+          INNER JOIN patient_state
+            ON patient_state.patient_program_id = patient_program.patient_program_id
+            AND patient_state.state = (#{program_states('Pre-ART (Continue)').limit(1).to_sql})
+            AND patient_state.start_date < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
+            AND (patient_state.end_date >= #{date} OR patient_state.end_date IS NULL)
+            AND patient_state.voided = 0 #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+          INNER JOIN (
+            SELECT patient_program_id, MAX(start_date) AS start_date
+            FROM patient_state
+            WHERE patient_state.start_date < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
+              AND patient_state.voided = 0 #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+            GROUP BY patient_program_id
+          ) AS max_patient_state
+            ON max_patient_state.patient_program_id = patient_state.patient_program_id
+            AND max_patient_state.start_date = patient_state.start_date #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+          WHERE patients.date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'patients.site_id', location: @location)}
+            AND patients.patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
+          GROUP BY patients.patient_id #{@adapter == 'mysql2' ? '' : ',patient_state.start_date'}
+        SQL
+      end
+
+      # Load all patients without a state
+      def load_patients_without_state
+        date = ActiveRecord::Base.connection.quote(end_date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_outcomes
+          SELECT patients.patient_id,
+                 CASE
+                    WHEN #{current_defaulter_function('patients.patient_id')} = 1 THEN 'Defaulted'
+                    ELSE 'Unknown'
+                  END AS cum_outcome,
+                 NULL, #{@location} as site_id
+          FROM temp_earliest_start_date AS patients
+          INNER JOIN patient_program
+            ON patient_program.patient_id = patients.patient_id
+            AND patient_program.program_id = #{hiv_program.program_id}
+            AND patient_program.voided = 0 #{site_manager(operator: 'AND', column: 'patient_program.site_id', location: @location)}
+          WHERE patients.date_enrolled <= #{date}
+            AND patient_program.patient_program_id NOT IN (
+              SELECT patient_program_id
+              FROM patient_state
+              WHERE start_date < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
+                AND voided = 0 #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+            )
+            AND patients.patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'patient_program.site_id', location: @location)} )
+          GROUP BY patients.patient_id
+        SQL
+      end
+
+      # Load all patients without drug orders or have drug orders
+      # without a quantity.
+      def load_patients_without_drug_orders
+        date = ActiveRecord::Base.connection.quote(end_date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_outcomes
+          SELECT patients.patient_id,
+                 'Unknown',
+                 NULL, #{@location}
+          FROM temp_earliest_start_date AS patients
+          WHERE date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'patients.site_id', location: @location)}
+            AND patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
+            AND patient_id NOT IN (
+              SELECT patient_id
+              FROM orders
+              LEFT JOIN drug_order ON orders.order_id = drug_order.order_id #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)}
+              WHERE start_date < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
+                AND quantity > 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
+                AND order_type_id = #{drug_order_type.order_type_id}
+                AND concept_id IN (#{arv_drugs_concept_set.to_sql})
+            )
+        SQL
+      end
+
+      # Loads all patients who are on treatment
+      def load_patients_on_treatment
+        date = ActiveRecord::Base.connection.quote(end_date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_outcomes
+          SELECT patients.patient_id, 'On antiretrovirals', patient_state.start_date, #{@location}
+          FROM temp_earliest_start_date AS patients
+          INNER JOIN patient_program
+            ON patient_program.patient_id = patients.patient_id
+            AND patient_program.program_id = #{hiv_program.program_id}
+            AND patient_program.voided = 0 #{site_manager(operator: 'AND', column: 'patient_program.site_id', location: @location)}
+          /* Get patients' `on ARV` states that are before given date */
+          INNER JOIN patient_state
+            ON patient_state.patient_program_id = patient_program.patient_program_id
+            AND patient_state.state = (#{program_states('On antiretrovirals').limit(1).to_sql})
+            AND patient_state.start_date < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
+            AND (patient_state.end_date >= #{date} OR patient_state.end_date IS NULL)
+            AND patient_state.voided = 0 #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+          /* Select only the most recent state out of those retrieved above */
+          INNER JOIN (
+            SELECT patient_program_id, MAX(start_date) AS start_date
+            FROM patient_state
+            WHERE patient_state.start_date < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
+              AND patient_state.voided = 0 #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+            GROUP BY patient_program_id
+          ) AS max_patient_state
+            ON max_patient_state.patient_program_id = patient_state.patient_program_id
+            AND max_patient_state.start_date = patient_state.start_date #{site_manager(operator: 'AND', column: 'patient_state.site_id', location: @location)}
+          /* HACK: Ensure that the states captured above do correspond have corresponding
+                   ARV dispensations. In other words filter out any `on ARVs` states whose
+                   dispensation's may have been voided or states that were created manually
+                   without any drugs being dispensed.  */
+          INNER JOIN (
+            SELECT orders.patient_id, MIN(orders.auto_expire_date) AS auto_expire_date
+            FROM orders
+            INNER JOIN drug_order ON orders.order_id = drug_order.order_id #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)}
+            INNER JOIN (
+              SELECT patient_id, MAX(start_date) AS start_date
+              FROM orders
+              INNER JOIN drug_order ON orders.order_id = drug_order.order_id #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)} AND drug_order.quantity > 0
+              WHERE order_type_id = #{drug_order_type.order_type_id}
+                AND concept_id IN (#{arv_drugs_concept_set.to_sql})
+                AND orders.start_date < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
+                AND voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
+                AND patient_id IN (SELECT patient_id FROM temp_earliest_start_date #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
+                AND patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
+              GROUP BY patient_id
+            ) AS max_drug_orders
+              ON max_drug_orders.patient_id = orders.patient_id
+              AND max_drug_orders.start_date = orders.start_date #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
+            WHERE order_type_id = #{drug_order_type.order_type_id}
+              AND concept_id IN (#{arv_drugs_concept_set.to_sql})
+              AND orders.start_date < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
+              AND quantity > 0
+              AND voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
+              AND orders.patient_id IN (SELECT patient_id FROM temp_earliest_start_date #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)})
+              AND orders.patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)})
+            GROUP BY orders.patient_id
+          ) AS first_order_to_expire
+            ON (first_order_to_expire.auto_expire_date >= #{date} OR #{timestampdiff_manager(date1: 'DATE(first_order_to_expire.auto_expire_date)', date2: date, interval: 'DAY')} <= #{@definition == 'pepfar' ? 28 : 56})
+            AND first_order_to_expire.patient_id = patient_program.patient_id #{site_manager(operator: 'AND', column: 'patient_program.site_id', location: @location)}
+          WHERE patients.date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'patients.site_id', location: @location)}
+            AND patients.patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
+          GROUP BY patients.patient_id #{@adapter == 'mysql2' ? '' : ',patient_state.start_date'}
+        SQL
+      end
+
+      # Load defaulters
+      def load_defaulters
+        date = ActiveRecord::Base.connection.quote(end_date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_outcomes
+          SELECT patient_id, #{patient_outcome_function('patient_id')}, NULL, #{@location}
+          FROM temp_earliest_start_date
+          WHERE date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
+            AND patient_id NOT IN (SELECT patient_id FROM temp_patient_outcomes #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)} )
+        SQL
+      end
+
+      def current_defaulter_function(sql_column)
+        defaulter_function = @definition == 'moh' ? 'current_defaulter' : 'current_pepfar_defaulter'
+        quoted_end_date = ActiveRecord::Base.connection.quote(end_date)
+        parameters = "#{sql_column}, #{quoted_end_date}, #{@location}"
+        function_manager(function: defaulter_function, location: @location, args: parameters)
+      rescue StandardError => e
+        Rails.logger.error "Error: #{e.message}"
+        raise "Invalid outcomes definition: #{@definition}"
+      end
+
+      def patient_outcome_function(sql_column)
+        outcome_function = @definition == 'moh' ? 'patient_outcome' : 'pepfar_patient_outcome'
+        quoted_end_date = ActiveRecord::Base.connection.quote(end_date)
+        parameters = "#{sql_column}, #{quoted_end_date}, #{@location}"
+        function_manager(function: outcome_function, location: @location, args: parameters)
+      rescue StandardError => e
+        Rails.logger.error "Error: #{e.message}"
+        raise "Invalid outcomes definition: #{@definition}"
+      end
+    end
+  end
+end

data/app/services/malawi_hiv_program_reports/cohort/regimens.rb

@@ -0,0 +1,69 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Cohort
+    class Regimens
+      include MalawiHivProgramReports::Utils::ModelUtils
+      include MalawiHivProgramReports::Adapters::Moh::Custom
+
+      def patient_regimens(date, location)
+        @location = location
+        @adapter = ActiveRecord::Base.connection.adapter_name.downcase
+        date = ActiveRecord::Base.connection.quote(date)
+
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT prescriptions.patient_id,
+                 regimens.name AS regimen_category,
+                 prescriptions.drugs,
+                 prescriptions.prescription_date
+          FROM (
+            SELECT orders.patient_id,
+                  #{@adapter == 'mysql2' ? 'GROUP_CONCAT(DISTINCT drug_order.drug_inventory_id ORDER BY drug_order.drug_inventory_id ASC) AS drugs,' : "(SELECT STRING_AGG(drug_inventory_id::VARCHAR, ',') FROM (SELECT DISTINCT drug_order.drug_inventory_id FROM drug_order ORDER BY drug_order.drug_inventory_id ASC) AS subquery) AS drugs,"}
+                   recent_prescription.prescription_date
+            FROM temp_patient_outcomes AS outcomes
+            INNER JOIN orders
+              ON orders.patient_id = outcomes.patient_id
+              AND orders.concept_id IN (#{arv_drugs_concept_set.to_sql})
+              AND orders.voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
+            INNER JOIN drug_order
+              ON drug_order.order_id = orders.order_id AND drug_order.quantity > 0 #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)}
+            /* Only select drugs prescribed on the last prescription day */
+            INNER JOIN (
+              SELECT patient_id, DATE(MAX(start_date)) AS prescription_date
+              FROM orders
+              INNER JOIN drug_order
+                ON drug_order.order_id = orders.order_id
+                AND drug_order.quantity > 0 #{site_manager(operator: 'AND', column: 'drug_order.site_id', location: @location)}
+              WHERE orders.voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
+                AND orders.concept_id IN (#{arv_drugs_concept_set.to_sql})
+                AND orders.start_date < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
+                AND orders.patient_id IN (
+                  SELECT patient_id FROM temp_patient_outcomes WHERE cum_outcome = 'On antiretrovirals' #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
+                )
+              GROUP BY orders.patient_id
+            ) AS recent_prescription
+              ON recent_prescription.patient_id = orders.patient_id
+              AND orders.start_date
+                BETWEEN recent_prescription.prescription_date
+                AND #{interval_manager(date: 'recent_prescription.prescription_date', value: 1, interval: 'DAY', operator: '+')}
+            GROUP BY orders.patient_id #{@adapter == 'mysql2' ? '' : ', recent_prescription.prescription_date'}
+          ) AS prescriptions
+          LEFT JOIN (
+            SELECT #{@adapter == 'mysql2' ? 'GROUP_CONCAT(drug.drug_id ORDER BY drug.drug_id ASC) AS drugs,' : "(SELECT STRING_AGG(drug_id::VARCHAR, ',') FROM (SELECT drug.drug_id FROM drug ORDER BY drug.drug_id ASC) AS subquery) AS drugs,"}
+                  regimen_name.name AS name
+            FROM moh_regimen_combination AS combo
+              INNER JOIN moh_regimen_combination_drug AS drug USING (regimen_combination_id)
+              INNER JOIN moh_regimen_name AS regimen_name USING (regimen_name_id)
+            GROUP BY combo.regimen_combination_id, regimen_name.name#{' '}
+          ) AS regimens
+            ON regimens.drugs = prescriptions.drugs
+        SQL
+      end
+
+      def arv_drugs_concept_set
+        @arv_drugs_concept_set ||= ::ConceptSet.where(set: concept_name('Antiretroviral drugs'))
+                                               .select(:concept_id)
+      end
+    end
+  end
+end

data/app/services/malawi_hiv_program_reports/cohort/side_effects.rb

@@ -0,0 +1,141 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Cohort
+    class SideEffects
+      include MalawiHivProgramReports::Utils::ModelUtils
+      include MalawiHivProgramReports::Adapters::Moh::Custom
+
+      def update_side_effects(date, location)
+        @location = location
+        @adapter = ActiveRecord::Base.connection.adapter_name.downcase
+        initialize_table
+
+        load_patients_with_side_effects(date)
+        load_patients_without_side_effects(date)
+        load_patients_missing_side_effects(date)
+      end
+
+      def initialize_table
+        ActiveRecord::Base.connection.execute <<~SQL
+          DROP TABLE IF EXISTS temp_patient_side_effects
+        SQL
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          CREATE TABLE temp_patient_side_effects (
+            patient_id INT PRIMARY KEY,
+            has_se VARCHAR(120) NOT NULL,
+            site_id INT DEFAULT NULL
+          )
+        SQL
+        ActiveRecord::Base.connection.execute 'CREATE INDEX tpse_site_id ON temp_patient_side_effects(site_id)'
+        ActiveRecord::Base.connection.execute 'CREATE INDEX idx_se ON temp_patient_side_effects(has_se)'
+        ActiveRecord::Base.connection.execute <<~SQL
+          CREATE INDEX idx_side_effects ON temp_patient_side_effects (patient_id, has_se, site_id)
+        SQL
+      end
+
+      def load_patients_with_side_effects(date)
+        date = ActiveRecord::Base.connection.quote(date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_side_effects(patient_id, has_se, site_id)
+          SELECT patients.patient_id, 'Yes', #{@location}
+          FROM temp_earliest_start_date AS patients
+          INNER JOIN temp_patient_outcomes
+            ON temp_patient_outcomes.patient_id = patients.patient_id
+            AND LOWER(temp_patient_outcomes.cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'temp_patient_outcomes.site_id', location: @location)}
+          INNER JOIN obs AS side_effects_group
+            ON side_effects_group.person_id = patients.patient_id
+            AND side_effects_group.concept_id = #{art_side_effects.concept_id}
+            AND side_effects_group.voided = 0 #{site_manager(operator: 'AND', column: 'side_effects_group.site_id', location: @location)}
+          /* Limit check to last visit before #{date} */
+          INNER JOIN (
+            SELECT person_id, MAX(obs_datetime) AS obs_datetime FROM obs
+            WHERE concept_id = #{art_side_effects.concept_id}
+              /* Side effects on initial visit are treated as contra-indications */
+              AND obs_datetime < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
+              AND voided = 0 #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}
+              AND person_id IN (SELECT patient_id FROM temp_patient_outcomes WHERE LOWER(cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'site_id', location: @location)})
+            GROUP BY person_id
+          ) AS last_visit
+            ON last_visit.person_id = side_effects_group.person_id
+            AND last_visit.obs_datetime = side_effects_group.obs_datetime
+            AND last_visit.obs_datetime >= #{interval_manager(date: 'patients.date_enrolled', value: 1, interval: 'DAY', operator: '+')}
+          INNER JOIN obs AS side_effects
+            ON side_effects.person_id = patients.patient_id
+            AND side_effects_group.obs_id = side_effects.obs_group_id
+            AND side_effects.value_coded = #{yes.concept_id}
+            AND side_effects.voided = 0 #{site_manager(operator: 'AND', column: 'side_effects.site_id', location: @location)}
+          WHERE patients.date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'patients.site_id', location: @location)}
+          GROUP BY patients.patient_id
+        SQL
+      end
+
+      def load_patients_without_side_effects(date)
+        date = ActiveRecord::Base.connection.quote(date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_side_effects
+          SELECT patients.patient_id, 'No', #{@location}
+          FROM temp_earliest_start_date AS patients
+          INNER JOIN temp_patient_outcomes
+            ON temp_patient_outcomes.patient_id = patients.patient_id
+            AND LOWER(temp_patient_outcomes.cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'temp_patient_outcomes.site_id', location: @location)}
+          INNER JOIN obs AS side_effects_group
+            ON side_effects_group.person_id = patients.patient_id
+            AND side_effects_group.concept_id = #{art_side_effects.concept_id}
+            AND side_effects_group.voided = 0 #{site_manager(operator: 'AND', column: 'side_effects_group.site_id', location: @location)}
+          /* Limit check to last visit before #{date} */
+          INNER JOIN (
+            SELECT person_id, MAX(obs_datetime) AS obs_datetime FROM obs
+            WHERE concept_id = #{art_side_effects.concept_id}
+              /* Side effects on initial visit are treated as contra-indications */
+              AND obs_datetime < #{interval_manager(date:, value: 1, interval: 'DAY', operator: '+')}
+              AND voided = 0 #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
+              AND person_id IN (
+                SELECT patient_id FROM temp_patient_outcomes WHERE LOWER(cum_outcome) = LOWER('On antiretrovirals') #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
+              )
+            GROUP BY person_id
+          ) AS last_visit
+            ON last_visit.person_id = side_effects_group.person_id
+            AND last_visit.obs_datetime = side_effects_group.obs_datetime
+            AND last_visit.obs_datetime >= #{interval_manager(date: 'patients.date_enrolled', value: 1, interval: 'DAY', operator: '+')}
+          INNER JOIN obs AS side_effects
+            ON side_effects.person_id = patients.patient_id
+            AND side_effects_group.obs_id = side_effects.obs_group_id
+            AND side_effects.value_coded = #{no.concept_id}
+            AND side_effects.voided = 0 #{site_manager(operator: 'AND', column: 'side_effects.site_id', location: @location)}
+          WHERE patients.date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'patients.site_id', location: @location)}
+            AND patients.patient_id NOT IN (
+              SELECT patient_id FROM temp_patient_side_effects WHERE has_se = 'Yes' #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
+            )
+          GROUP BY patients.patient_id
+        SQL
+      end
+
+      def load_patients_missing_side_effects(date)
+        date = ActiveRecord::Base.connection.quote(date)
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO temp_patient_side_effects
+          SELECT patient_id, 'Unknown', #{@location} FROM temp_earliest_start_date
+          WHERE date_enrolled <= #{date} #{site_manager(operator: 'AND', column: 'site_id', location: @location)}
+            AND patient_id NOT IN (SELECT patient_id FROM temp_patient_side_effects #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)})
+        SQL
+      end
+
+      def yes
+        @yes ||= concept_name('Yes')
+      end
+
+      def no
+        @no ||= concept_name('No')
+      end
+
+      def art_side_effects
+        @art_side_effects ||= concept_name('Malawi ART Side Effects')
+      end
+    end
+  end
+end