malawi_hiv_program_reports 1.0.1 → 1.0.2

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

@@ -0,0 +1,108 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Clinic
+    class RegimensByWeightAndGender
+      include MalawiHivProgramReports::Utils::ConcurrencyUtils
+
+      attr_reader :start_date, :end_date
+
+      def initialize(start_date:, end_date:, **kwargs)
+        @start_date = start_date
+        @end_date = end_date
+        @rebuild_outcomes = true
+        @occupation = kwargs[:occupation]
+      end
+
+      def find_report
+        regimen_counts
+      end
+
+      private
+
+      WEIGHT_BANDS = [
+        [3, 3.9],
+        [4, 4.9],
+        [6, 9.9],
+        [10, 13.9],
+        [14, 19.9],
+        [20, 24.9],
+        [25, 29.9],
+        [30, 34.9],
+        [35, 39.9],
+        [40, 49.9],
+        [50, Float::INFINITY],
+        [nil, nil] # To capture all those missing weight
+      ].freeze
+
+      def regimen_counts
+        with_lock(Cohort::LOCK_FILE) do
+          PatientsAliveAndOnTreatment.new(start_date:, end_date:, occupation: @occupation)
+                                     .refresh_outcomes_table
+
+          WEIGHT_BANDS.map do |start_weight, end_weight|
+            {
+              weight: weight_band_to_string(start_weight, end_weight),
+              males: regimen_counts_by_weight_and_gender(start_weight, end_weight, 'M'),
+              females: regimen_counts_by_weight_and_gender(start_weight, end_weight, 'F'),
+              unknown_gender: regimen_counts_by_weight_and_gender(start_weight, end_weight, nil)
+            }
+          end
+        end
+      end
+
+      def weight_band_to_string(start_weight, end_weight)
+        if start_weight.nil? && end_weight.nil?
+          'Unknown'
+        elsif end_weight == Float::INFINITY
+          "#{start_weight} Kg +"
+        else
+          "#{start_weight} - #{end_weight} Kg"
+        end
+      end
+
+      # TODO: Refactor the queries in this module... Possibly
+      # prefer joins over the subqueries (ie if performance becomes an
+      # issue - it probably will eventually).
+
+      def regimen_counts_by_weight_and_gender(start_weight, end_weight, gender)
+        date = ActiveRecord::Base.connection.quote(end_date)
+
+        query = TempPatientOutcome.joins('INNER JOIN temp_earliest_start_date USING (patient_id)')
+                                  .select("patient_current_regimen(patient_id, #{date}) as regimen, count(*) AS count")
+                                  .where(patient_id: patients_in_weight_band(start_weight, end_weight))
+                                  .where(cum_outcome: 'On Antiretrovirals')
+                                  .group(:regimen)
+
+        query = gender ? query.where('gender LIKE ?', "#{gender}%") : query.where('gender IS NULL')
+
+        query.collect { |obs| { obs.regimen => obs.count } }
+      end
+
+      def patients_in_weight_band(start_weight, end_weight)
+        if start_weight.nil? && end_weight.nil?
+          # If no weight is provided then this must be all patients without a weight observation
+          return ::PatientProgram.select(:patient_id)
+                                 .where(program_id: ::ArtService::Constants::PROGRAM_ID)
+                                 .where.not(patient_id: patients_with_known_weight.select(:person_id))
+        end
+
+        max_weights = patients_with_known_weight.select('MAX(obs_datetime) AS obs_datetime, person_id').to_sql
+
+        patients_with_known_weight
+          .joins("INNER JOIN (#{max_weights}) AS max_weights
+                  ON max_weights.person_id = obs.person_id AND max_weights.obs_datetime = obs.obs_datetime")
+          .where(value_numeric: (start_weight..end_weight))
+          .select(:person_id)
+      end
+
+      def patients_with_known_weight
+        ::Observation.joins('INNER JOIN temp_patient_outcomes AS outcomes ON outcomes.patient_id = obs.person_id')
+                     .where(concept_id: ::ConceptName.where(name: 'Weight (kg)').select(:concept_id),
+                            outcomes: { cum_outcome: 'On antiretrovirals' })
+                     .where('DATE(obs.obs_datetime) <= ?', end_date)
+                     .group(:person_id)
+      end
+    end
+  end
+end

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

@@ -0,0 +1,246 @@
+# frozen_string_literal: true
+
+# Retrieve patients who are completing their first 1st, 3rd, and 6th month on ART
+# in the reporting period.
+module MalawiHivProgramReports
+  module Clinic
+    class Retention
+      attr_reader :start_date, :end_date
+
+      include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
+
+      DAYS_IN_MONTH = 28
+      MONTHS = [1, 3, 6].freeze
+
+      def initialize(start_date:, end_date:, **kwargs)
+        @start_date = start_date.to_s
+        @end_date = end_date.to_s
+        @use_filing_number = ::GlobalProperty.find_by(property: 'use.filing.numbers')
+                                             &.property_value
+                                             &.casecmp?('true')
+        @occupation = kwargs[:occupation]
+      end
+
+      def find_report
+        matched_patients = MONTHS.each_with_object({}) do |month, hash|
+          hash[month] = { retained: [], all: [] }
+        end
+
+        find_patients_retention_period(retained_patients(as_of: Date.parse(start_date) - MONTHS.max.months)) do |period, patient|
+          matched_patients[period][:retained] << {
+            patient_id: patient.patient_id,
+            arv_number: patient.arv_number,
+            start_date: patient.start_date,
+            gender: begin
+              patient.gender.upcase.first
+            rescue StandardError
+              nil
+            end,
+            age_group: patient.age_group,
+            end_date: patient.start_date + period.months
+          }
+        end
+
+        find_patients_retention_period(all_patients(as_of: Date.parse(start_date) - MONTHS.max.months)) do |period, patient|
+          matched_patients[period][:all] << {
+            patient_id: patient.patient_id,
+            arv_number: patient.arv_number,
+            gender: begin
+              patient.gender.upcase.first
+            rescue StandardError
+              nil
+            end,
+            age_group: patient.age_group,
+            start_date: patient.start_date
+          }
+        end
+
+        matched_patients
+      end
+
+      def find_patients_retention_period(patients)
+        patients.each do |patient|
+          retention_period = MONTHS.find do |period|
+            (start_date..end_date).cover?((patient.start_date + period.months).to_s)
+          end
+
+          next unless retention_period
+
+          yield retention_period, patient
+        end
+      end
+
+      # Pull all patients who started medication before the current reporting period but after
+      # the given `as_of` date and have any dispensation that ends in the current reporting
+      # period... That's a mouthful woah!!!
+      def retained_patients(as_of:)
+        start_date = ActiveRecord::Base.connection.quote(self.start_date)
+        end_date = ActiveRecord::Base.connection.quote(self.end_date)
+        as_of = ActiveRecord::Base.connection.quote(as_of)
+        ::Order.find_by_sql(
+          <<~SQL
+            SELECT
+              initial_orders.patient_id AS patient_id,
+              DATE(initial_orders.start_date) AS start_date,
+              last_orders.auto_expire_date AS auto_expire_date,
+              patient_identifier.identifier AS arv_number,
+              disaggregated_age_group(p.birthdate, DATE('#{@end_date}')) age_group,
+              p.gender gender
+            FROM orders initial_orders
+            INNER JOIN encounter initial_encounter ON initial_encounter.encounter_id = initial_orders.encounter_id AND initial_encounter.voided = 0 AND initial_encounter.program_id = 1
+            INNER JOIN person p ON p.person_id = initial_orders.patient_id AND p.voided = 0
+            LEFT JOIN patient_identifier ON patient_identifier.patient_id = initial_orders.patient_id AND patient_identifier.identifier_type = #{patient_identifier_type_id}
+            INNER JOIN (
+              SELECT last_order.patient_id, MAX(last_order.auto_expire_date) AS auto_expire_date
+                FROM orders last_order
+                INNER JOIN encounter last_encounter ON last_encounter.encounter_id = last_order.encounter_id AND last_encounter.voided = 0 AND last_encounter.program_id = 1
+                WHERE last_order.auto_expire_date BETWEEN #{start_date} AND #{end_date}
+                AND last_order.order_type_id = #{drug_order_type_id}
+              AND last_order.voided = 0
+                GROUP BY last_order.patient_id
+            ) last_orders ON initial_orders.patient_id = last_orders.patient_id
+            LEFT JOIN (#{current_occupation_query}) a ON a.person_id = initial_orders.patient_id
+            WHERE initial_orders.start_date BETWEEN #{as_of} AND #{start_date}
+            AND initial_orders.order_type_id = #{drug_order_type_id} #{%w[Military Civilian].include?(@occupation) ? 'AND' : ''} #{occupation_filter(occupation: @occupation, field_name: 'value', table_name: 'a', include_clause: false)}
+            AND initial_orders.auto_expire_date IS NOT NULL
+            AND initial_orders.patient_id NOT IN (
+              SELECT o.patient_id
+              FROM orders o
+              INNER JOIN encounter e ON e.encounter_id = o.encounter_id AND e.voided = 0 AND e.program_id = 1
+              WHERE o.order_type_id =  #{drug_order_type_id} AND o.start_date < #{as_of} AND o.auto_expire_date IS NOT NULL AND o.voided = 0
+            )
+            GROUP BY initial_orders.patient_id
+          SQL
+        )
+      end
+
+      def all_patients(as_of:)
+        start_date = ActiveRecord::Base.connection.quote(self.start_date)
+        as_of = ActiveRecord::Base.connection.quote(as_of)
+
+        ::Order.find_by_sql(
+          <<~SQL
+            SELECT initial_order.patient_id AS patient_id,
+                   DATE(initial_order.start_date) AS start_date,
+                   patient_identifier.identifier AS arv_number,
+                   disaggregated_age_group(p.birthdate, DATE('#{@end_date}')) age_group,
+                   p.gender gender
+            FROM orders initial_order
+            INNER JOIN encounter initial_encounter ON initial_encounter.encounter_id = initial_order.encounter_id AND initial_encounter.program_id = 1
+            INNER JOIN person p ON p.person_id = initial_encounter.patient_id
+            LEFT JOIN patient_identifier ON patient_identifier.patient_id = initial_order.patient_id AND patient_identifier.identifier_type = #{patient_identifier_type_id}
+            LEFT JOIN (#{current_occupation_query}) a ON a.person_id = initial_order.patient_id
+            WHERE initial_order.start_date BETWEEN #{as_of} AND #{start_date}
+              AND initial_order.voided = 0
+              AND initial_order.auto_expire_date IS NOT NULL
+              AND initial_order.order_type_id = #{drug_order_type_id}
+              AND p.voided = 0 #{%w[Military Civilian].include?(@occupation) ? 'AND' : ''} #{occupation_filter(occupation: @occupation, field_name: 'value', table_name: 'a', include_clause: false)}
+              AND initial_order.patient_id NOT IN (
+                SELECT orders.patient_id
+                FROM orders
+                  INNER JOIN encounter ON encounter.encounter_id = orders.encounter_id AND encounter.program_id = 1 AND encounter.voided = 0
+                WHERE start_date < #{as_of} AND order_type_id = #{drug_order_type_id} AND orders.voided = 0
+              )
+            GROUP BY initial_order.patient_id
+          SQL
+        )
+      end
+
+      # def retained_patients(as_of:)
+      #   start_date = ActiveRecord::Base.connection.quote(self.start_date)
+      #   end_date = ActiveRecord::Base.connection.quote(self.end_date)
+      #   as_of = ActiveRecord::Base.connection.quote(as_of)
+
+      #   ::Order.find_by_sql(
+      #     <<~SQL
+      #       SELECT initial_order.patient_id AS patient_id,
+      #              initial_order.start_date AS start_date,
+      #              last_order.auto_expire_date AS auto_expire_date,
+      #              patient_identifier.identifier AS arv_number,
+      #              disaggregated_age_group(p.birthdate, DATE('#{@end_date}')) age_group,
+      #              p.gender gender
+      #       FROM orders initial_order
+      #         INNER JOIN encounter initial_encounter ON initial_encounter.encounter_id = initial_order.encounter_id AND initial_encounter.program_id = 1
+      #         INNER JOIN orders last_order ON last_order.patient_id = initial_order.patient_id
+      #         INNER JOIN encounter last_encounter ON last_encounter.encounter_id = last_order.encounter_id
+      #         INNER JOIN person p ON p.person_id = initial_encounter.patient_id
+      #         LEFT JOIN patient_identifier ON patient_identifier.patient_id = initial_order.patient_id
+      #       WHERE initial_order.start_date BETWEEN #{as_of} AND #{start_date}
+      #         AND initial_order.voided = 0
+      #         AND initial_order.auto_expire_date IS NOT NULL
+      #         AND initial_order.order_type_id = #{drug_order_type_id}
+      #         AND last_order.auto_expire_date BETWEEN #{start_date} AND #{end_date}
+      #         AND last_order.order_type_id = #{drug_order_type_id}
+      #         AND last_order.voided = 0
+      #         AND p.voided = 0
+      #         AND initial_order.start_date = (
+      #           SELECT MIN(start_date) FROM orders
+      #           WHERE patient_id = initial_order.patient_id
+      #             AND start_date BETWEEN #{as_of} AND #{start_date}
+      #             AND order_type_id = #{drug_order_type_id}
+      #             AND voided = 0
+      #         )
+      #         AND initial_order.patient_id NOT IN (
+      #           SELECT orders.patient_id
+      #           FROM orders
+      #             INNER JOIN encounter ON encounter.encounter_id = orders.encounter_id AND encounter.program_id = 1
+      #           WHERE start_date < #{as_of} AND order_type_id = #{drug_order_type_id} AND orders.voided = 0
+      #         )
+      #       GROUP BY initial_order.patient_id
+      #     SQL
+      #   )
+      # end
+
+      # def all_patients(as_of:)
+      #   start_date = ActiveRecord::Base.connection.quote(self.start_date)
+      #   as_of = ActiveRecord::Base.connection.quote(as_of)
+
+      #   ::Order.find_by_sql(
+      #     <<~SQL
+      #       SELECT initial_order.patient_id AS patient_id,
+      #              initial_order.start_date AS start_date,
+      #              patient_identifier.identifier AS arv_number,
+      #              disaggregated_age_group(p.birthdate, DATE('#{@end_date}')) age_group,
+      #              p.gender gender
+      #       FROM orders initial_order
+      #         INNER JOIN encounter initial_encounter ON initial_encounter.encounter_id = initial_order.encounter_id AND initial_encounter.program_id = 1
+      #         INNER JOIN person p ON p.person_id = initial_encounter.patient_id
+      #         LEFT JOIN patient_identifier ON patient_identifier.patient_id = initial_order.patient_id AND patient_identifier.identifier_type = #{patient_identifier_type_id}
+      #       WHERE initial_order.start_date BETWEEN #{as_of} AND #{start_date}
+      #         AND initial_order.voided = 0
+      #         AND initial_order.auto_expire_date IS NOT NULL
+      #         AND initial_order.order_type_id = #{drug_order_type_id}
+      #         AND p.voided = 0
+      #         AND initial_order.start_date = (
+      #           SELECT MIN(start_date) FROM orders
+      #           WHERE patient_id = initial_order.patient_id
+      #             AND start_date BETWEEN #{as_of} AND #{start_date}
+      #             AND order_type_id = #{drug_order_type_id}
+      #             AND voided = 0
+      #         )
+      #         AND initial_order.patient_id NOT IN (
+      #           SELECT orders.patient_id
+      #           FROM orders
+      #             INNER JOIN encounter ON encounter.encounter_id = orders.encounter_id AND encounter.program_id = 1
+      #           WHERE start_date < #{as_of} AND order_type_id = #{drug_order_type_id} AND orders.voided = 0
+      #         )
+      #       GROUP BY initial_order.patient_id
+      #     SQL
+      #   )
+      # end
+
+      def drug_order_type_id
+        @drug_order_type_id ||= ::OrderType.find_by_name('Drug order').order_type_id
+      end
+
+      def patient_identifier_type_id
+        return @patient_identifier_type_id if @patient_identifier_type_id
+
+        identifier_type_name = @use_filing_number ? 'Filing Number' : 'ARV Number'
+        identifier_type = ::PatientIdentifierType.find_by_name!(identifier_type_name)
+
+        @patient_identifier_type_id ||= ActiveRecord::Base.connection.quote(identifier_type.id)
+      end
+    end
+  end
+end

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

@@ -0,0 +1,65 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Clinic
+    # Generates a stock card report for a clinic
+    class StockCardReport
+      def initialize(start_date:, end_date:, **_kwargs)
+        @start_date = ActiveRecord::Base.connection.quote(start_date)
+        @end_date = ActiveRecord::Base.connection.quote(end_date)
+      end
+
+      def find_report
+        # TODO: Implement this
+        stock_card_report
+      end
+
+      private
+
+      def stock_card_report
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT
+            pbi.drug_id AS drug_id,
+            COALESCE(d.name, 'Unkown') AS drug_name,
+            COALESCE(psb_opening.close_balance, 0)/pbi.pack_size AS opening_balance,
+            COALESCE(psb_closing.close_balance, 0)/pbi.pack_size  AS closing_balance,
+            SUM(ABS(po.quantity))/pbi.pack_size AS dispensed_quantity,
+            pbi.pack_size
+          FROM pharmacy_batch_items AS pbi
+          INNER JOIN drug AS d ON d.drug_id = pbi.drug_id
+          LEFT JOIN pharmacy_obs AS po ON po.batch_item_id = pbi.id
+            AND po.voided = 0
+            AND po.pharmacy_encounter_type = 3 -- Pharmacy dispensing
+            AND po.transaction_date BETWEEN #{@start_date} AND #{@end_date}
+            AND po.dispensation_obs_id IS NOT NULL
+          LEFT JOIN (
+              SELECT
+                  drug_id,
+                  MAX(transaction_date) AS transaction_date,
+                  pack_size
+              FROM pharmacy_stock_balances
+              WHERE transaction_date <= #{@end_date}
+              GROUP BY drug_id, pack_size
+          ) AS psb_max ON pbi.drug_id = psb_max.drug_id AND pbi.pack_size = psb_max.pack_size
+          LEFT JOIN (
+            SELECT
+                drug_id,
+                MAX(transaction_date) AS transaction_date,
+                pack_size
+            FROM pharmacy_stock_balances
+            WHERE transaction_date < #{@start_date} -- Opening balance can be anything less than end_date
+            GROUP BY drug_id, pack_size
+          ) AS psb_min ON pbi.drug_id = psb_min.drug_id AND pbi.pack_size = psb_min.pack_size
+          LEFT JOIN pharmacy_stock_balances AS psb_opening ON
+              pbi.drug_id = psb_opening.drug_id AND pbi.pack_size = psb_opening.pack_size
+              AND psb_opening.transaction_date = psb_min.transaction_date
+          LEFT JOIN pharmacy_stock_balances AS psb_closing ON
+              pbi.drug_id = psb_closing.drug_id AND pbi.pack_size = psb_closing.pack_size
+              AND psb_closing.transaction_date = psb_max.transaction_date
+          WHERE pbi.voided = 0
+          GROUP BY pbi.drug_id, pbi.pack_size
+        SQL
+      end
+    end
+  end
+end