malawi_hiv_program_reports 1.0.1 → 1.0.3

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

@@ -0,0 +1,98 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Pepfar
+    # This class is used to generate the SC_CURR report
+    # The current number of ARV drug units (bottles) at the end of the reporting period by ARV drug category
+    class ScCurr
+      DRUG_CATEGORY = {
+        'TLD 30-count bottles' => { drugs: [983], quantity: 30 },
+        'TLD 90-count bottles' => { drugs: [983], quantity: 90 },
+        'TLD 180-count bottles' => { drugs: [983], quantity: 180 },
+        'TLE/400 30-count bottles' => { drugs: [735], quantity: 30 },
+        'TLE/400 90-count bottles' => { drugs: [735], quantity: 90 },
+        'TLE 600/TEE bottles' => { drugs: [11], quantity: 'N/A' },
+        'DTG 10 90-count bottles' => { drugs: [980], quantity: 90 },
+        'DTG 50 30-count bottles' => { drugs: [982], quantity: 30 },
+        'LPV/r 100/25 tabs 60 tabs/bottle' => { drugs: [23, 73, 74, 739, 977, 1045], quantity: 60 },
+        'LPV/r 40/10 (pediatrics) bottles' => { drugs: [94, 979], quantity: 'N/A' },
+        'NVP (adult) bottles' => { drugs: [22, 613], quantity: 'N/A' },
+        'NVP (pediatric) bottles' => { drugs: [21, 817, 968, 971], quantity: 'N/A' },
+        'Other (adult) bottles' => { drugs: [
+          3, 5, 6, 10, 38, 39, 40, 42, 89, 614, 730, 731, 734, 738,
+          814, 815, 932, 933, 934, 952, 954, 955, 957, 969, 976, 978, 984, 1217, 1213, 14
+        ], quantity: 'N/A' },
+        'Other (pediatric) bottles' => { drugs: [
+          2, 9, 28, 29, 30, 31, 32, 36, 37, 41, 70, 71, 72, 90, 91,
+          95, 104, 177, 732, 733, 736, 737, 813, 816, 981, 1043, 1044, 1214, 1215
+        ], quantity: 'N/A' }
+      }.freeze
+
+      def initialize(start_date:, end_date:, **_kwargs)
+        @start_date = start_date
+        @end_date = end_date
+        @location = _kwargs[:location]
+      end
+
+      def find_report
+        initialize_report
+        process_report
+        # remove the drug_id from the report
+        @report.each { |category| category.delete(:drug_id) }
+        @report
+      end
+
+      private
+
+      def initialize_report
+        @report = []
+        DRUG_CATEGORY.each do |category, drug|
+          @report << {
+            category:,
+            drug_id: drug[:drugs],
+            units: 0,
+            quantity: drug[:quantity],
+            granular_spec: []
+          }
+        end
+      end
+
+      # rubocop:disable Metrics/AbcSize
+      # rubocop:disable Metrics/CyclomaticComplexity
+      def process_report
+        current_stock.each do |item|
+          # Find the drug category
+          drug_category = @report.find do |category|
+            category[:drug_id].include?(item.drug_id) && category[:quantity] == item.pack_size
+          end
+          drug_category ||= @report.find do |category|
+            category[:drug_id].include?(item.drug_id) && category[:quantity] == 'N/A'
+          end
+          next unless drug_category
+
+          bottles = (item.current_quantity / item.pack_size).to_i
+          drug_category[:units] += bottles
+          # check if the drug is already in the granular_spec
+          granular_spec = drug_category[:granular_spec].find { |spec| spec[:drug_name] == item.drug.name }
+          if granular_spec
+            granular_spec[:units] += bottles
+          else
+            drug_category[:granular_spec] << {
+              drug_name: item.drug.name,
+              units: bottles
+            }
+          end
+        end
+      end
+      # rubocop:enable Metrics/AbcSize
+      # rubocop:enable Metrics/CyclomaticComplexity
+
+      def current_stock
+        drugs = DRUG_CATEGORY.map { |_, drug| drug[:drugs] }.flatten.uniq
+        ::PharmacyBatchItem.where(
+          "expiry_date >= ? AND delivery_date <= ? AND drug_id IN (?) AND current_quantity > 0 #{!@location.blank? ? "AND site_id = #{@location}" : ''}", @end_date, @end_date, drugs
+        )
+      end
+    end
+  end
+end

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

@@ -0,0 +1,163 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Pepfar
+    class TbPrev
+
+      include MalawiHivProgramReports::Adapters::Moh::Custom
+      attr_accessor :start_date, :end_date, :location
+      
+      def initialize(start_date:, end_date:, **kwargs)
+        @completion_start_date = start_date&.to_date.strftime('%Y-%m-%d 00:00:00')
+        @completion_end_date = end_date&.to_date.strftime('%Y-%m-%d 23:59:59')
+        @location = kwargs[:location]
+      end
+
+      def find_report
+        data
+      end
+
+      private
+
+      def data
+        meds = tb_med_dispensations
+        return {} if meds.blank?
+
+        patient_ids = meds.map { |m| m['patient_id'].to_i }.uniq
+        hiv_program_clients = on_art_in_reporting_period(patient_ids)
+        return if hiv_program_clients.blank?
+
+        clients_in_hiv_program = {}
+
+        hiv_program_clients.each do |e|
+          clients_in_hiv_program[e['patient_id'].to_i] = e
+        end
+
+        clients = {}
+        initiation_start_date = (@completion_start_date&.to_date - 6.month)&.to_date
+
+        meds.each do |m|
+          patient_id = m['patient_id'].to_i
+          inh_start_date = min_inh_start_date(patient_id)
+          next unless inh_start_date&.to_date >= initiation_start_date&.to_date &&
+                      inh_start_date&.to_date < @completion_start_date&.to_date
+
+          p = clients_in_hiv_program[patient_id]
+          next if p.blank?
+
+          earliest_start_date = begin
+            p['earliest_start_date']&.to_date
+          rescue StandardError
+            p['date_enrolled']&.to_date
+          end
+
+          quantity = m['quantity'].to_f
+          if clients[patient_id].blank?
+            clients[patient_id] = {
+              date_enrolled: p['date_enrolled']&.to_date,
+              earliest_start_date:,
+              gender: begin
+                p['gender'].upcase.first
+              rescue StandardError
+                'Unknown'
+              end,
+              birthdate: begin
+                p['birthdate']&.to_date
+              rescue StandardError
+                'Unknow'
+              end,
+              age_group: p['age_group'],
+              course_completed: false,
+              client: new_client(earliest_start_date, inh_start_date),
+              quantity: 0
+            }
+          end
+
+          clients[patient_id][:quantity] += quantity
+
+          clients[patient_id][:course_completed] = true if clients[patient_id][:quantity] >= 168
+        end
+
+        clients
+      end
+
+      def min_inh_start_date(patient_id)
+        start_date = ActiveRecord::Base.connection.select_one <<-SQL
+            SELECT
+                DATE(MIN(o.start_date)) date
+            FROM person p
+            INNER JOIN orders o ON o.patient_id = p.person_id
+            INNER JOIN drug_order t ON o.order_id = t.order_id
+            INNER JOIN drug d ON d.drug_id = t.drug_inventory_id
+            INNER JOIN encounter e ON e.patient_id = o.patient_id AND e.program_id = 1
+            WHERE o.voided = 0 AND o.patient_id = #{patient_id}
+            AND d.concept_id = 656 AND t.quantity > 0;
+        SQL
+
+        start_date['date']&.to_date
+      end
+
+      def new_client(earliest_start_date, min_date)
+        return 'Previously on ART' if earliest_start_date.blank?
+        
+        med_start_date = min_date&.to_date
+        med_end_date = (earliest_start_date&.to_date + 90.day)&.to_date
+
+        return 'New on ART' if med_start_date >= earliest_start_date&.to_date && med_start_date < med_end_date
+
+        'Previously on ART'
+      end
+
+      def client_outcome(patient_id)
+        outcome_string = ActiveRecord::Base.connection.select_one <<-SQL
+            SELECT pepfar_patient_outcome(#{patient_id}, DATE('#{@end_date}')) outcome;
+        SQL
+
+        outcome_string['outcome']
+      end
+
+      def on_art_in_reporting_period(patient_ids)
+        ActiveRecord::Base.connection.select_all <<-SQL
+            select
+               p.patient_id AS patient_id, pe.birthdate, pe.gender,
+               patient_date_enrolled(CAST(p.patient_id AS INT), CAST(#{@location} AS INT)) AS date_enrolled,
+               date_antiretrovirals_started(CAST(p.patient_id AS INT), CAST(MIN(s.start_date) AS DATE), CAST(#{@location} AS INT)) AS earliest_start_date,
+               disaggregated_age_group(CAST(pe.birthdate AS DATE), DATE('#{@completion_end_date}')) age_group
+            from
+              patient_program p
+              left join person pe ON pe.person_id = p.patient_id
+              left join patient_state s ON p.patient_program_id = s.patient_program_id
+              left join person ON person.person_id = p.patient_id
+            where
+                  p.voided = 0
+                  and s.voided = 0
+                  and p.program_id = 1
+                  and s.state = 7
+                  and #{in_manager(column: 'p.patient_id', values: patient_ids)}
+            group by p.patient_id, pe.birthdate, pe.gender, p.date_enrolled
+            HAVING date_enrolled IS NOT NULL;
+        SQL
+      end
+
+      def tb_med_dispensations
+        initiation_start_date = (@completion_start_date&.to_date - 6.month).strftime('%Y-%m-%d 00:00:00')
+
+        ActiveRecord::Base.connection.select_all <<-SQL
+            SELECT
+                o.patient_id, t.drug_inventory_id, t.quantity,
+                o.start_date, o.auto_expire_date
+            FROM person p
+            INNER JOIN orders o ON o.patient_id = p.person_id
+            INNER JOIN drug_order t ON o.order_id = t.order_id
+            INNER JOIN drug d ON d.drug_id = t.drug_inventory_id
+            INNER JOIN encounter e ON e.patient_id = o.patient_id AND e.program_id = 1
+            WHERE o.voided = 0 AND (o.start_date
+            BETWEEN '#{initiation_start_date}' AND '#{@completion_end_date}')
+            AND d.concept_id = 656 AND t.quantity > 0
+            GROUP BY o.patient_id, t.drug_inventory_id, DATE(o.start_date), t.quantity, o.start_date, o.auto_expire_date
+            ORDER BY o.patient_id;
+        SQL
+      end
+    end
+  end
+end

data/app/services/malawi_hiv_program_reports/pepfar/tb_prev2.rb

@@ -0,0 +1,222 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Pepfar
+    ##
+    # Patients who started TPT just before the start of the current
+    # and have finished within the current reporting period.
+    class TbPrev2
+      attr_reader :start_date, :end_date
+
+      include Utils
+
+      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
+        report = init_report
+        patients = group_patients_by_tpt_course(patients_on_tpt)
+
+        load_patients_into_report(report, patients.six_h, '6H') do |patient|
+          # 6H has a constant dosage of 1 pill per day
+          patient['total_pills_taken'].to_i >= FULL_6H_COURSE_PILLS
+        end
+
+        load_patients_into_report(report, patients.three_hp, '3HP') do |patient|
+          # 3HP daily dosages vary by patient weight can't use easily use pills
+          # to determine course completion
+          patient['total_days_on_medication'].days >= FULL_3HP_COURSE_DAYS
+        end
+
+        report
+      end
+
+      private
+
+      FULL_6H_COURSE_PILLS = 168
+      FULL_3HP_COURSE_DAYS = (28.days - 1.day) + (56.days - 1.day) # 82 Days
+      # NOTE: Arrived at 82 days above from how 3HP is prescribed. 1st time prescription
+      #       is 1 month (28 days) then 2 months (56 days). And we assume that patients
+      #       start taking medication the very same they are given thus we subtract 1.
+
+      def init_report
+        pepfar_age_groups.each_with_object({}) do |age_group, report|
+          report[age_group] = %w[M F Unknown].each_with_object({}) do |gender, gender_sub_report|
+            gender_sub_report[gender] = %w[6H 3HP].each_with_object({}) do |tpt, tpt_sub_report|
+              tpt_sub_report[tpt] = {
+                started_new_on_art: [],
+                started_previously_on_art: [],
+                completed_new_on_art: [],
+                completed_previously_on_art: []
+              }
+            end
+          end
+        end
+      end
+
+      def load_patients_into_report(report, patients, tpt, &patient_has_completed_tpt)
+        patients.each do |patient|
+          age_group = patient['age_group']
+          gender = patient['gender']&.first&.upcase || 'Unknown'
+          tpt_states = find_patient_tpt_state(patient, &patient_has_completed_tpt)
+
+          tpt_states.each do |tpt_state|
+            report[age_group][gender][tpt][tpt_state] << patient
+          end
+        end
+      end
+
+      def find_patient_tpt_state(patient, &patient_has_completed_tpt)
+        if patient_has_completed_tpt[patient]
+          return %i[started_new_on_art completed_new_on_art] if patient_new_on_art?(patient)
+
+          return %i[started_previously_on_art completed_previously_on_art]
+        end
+
+        return %i[started_new_on_art] if patient_new_on_art?(patient)
+
+        %i[started_previously_on_art]
+      end
+
+      def patient_new_on_art?(patient)
+        tpt_initiation_date = patient['tpt_initiation_date'].to_date
+        art_start_date = patient['art_start_date'].to_date
+
+        (tpt_initiation_date >= art_start_date) && (tpt_initiation_date < art_start_date + 90.days)
+      end
+
+      def patients_on_tpt
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT person.person_id AS patient_id,
+                 patient_identifier.identifier AS arv_number,
+                 DATE(MIN(orders.start_date)) AS tpt_initiation_date,
+                 date_antiretrovirals_started(person.person_id, MIN(patient_state.start_date)) AS art_start_date,
+                 SUM(drug_order.quantity) AS total_pills_taken,
+                 SUM(DATEDIFF(orders.auto_expire_date, orders.start_date)) AS total_days_on_medication,
+                 person.gender,
+                 person.birthdate,
+                 disaggregated_age_group(person.birthdate, DATE(#{end_date})) AS age_group,
+                 GROUP_CONCAT(DISTINCT orders.concept_id SEPARATOR ',') AS drug_concepts
+          FROM person
+          LEFT JOIN patient_identifier
+            ON patient_identifier.patient_id = person.person_id
+            AND patient_identifier.voided = 0
+            AND patient_identifier.identifier_type IN (SELECT patient_identifier_type_id FROM patient_identifier_type WHERE name = 'ARV Number')
+          INNER JOIN patient_program
+            ON patient_program.patient_id = person.person_id
+            AND patient_program.program_id IN (SELECT program_id FROM program WHERE name = 'HIV PROGRAM')
+            AND patient_program.voided = 0
+          INNER JOIN patient_state
+            ON patient_state.patient_program_id = patient_program.patient_program_id
+            AND patient_state.state = 7 /* State: 7 == On antiretrovirals */
+            AND patient_state.start_date < DATE(#{start_date})
+            AND patient_state.voided = 0
+          INNER JOIN encounter AS prescription_encounter
+            ON prescription_encounter.patient_id = patient_program.patient_id
+            AND prescription_encounter.program_id IN (SELECT program_id FROM program WHERE name = 'HIV PROGRAM')
+            AND prescription_encounter.encounter_type IN (SELECT encounter_type_id FROM encounter_type WHERE name = 'Treatment')
+            AND prescription_encounter.encounter_datetime >= DATE(#{start_date}) - INTERVAL 6 MONTH
+            AND prescription_encounter.encounter_datetime < DATE(#{start_date})
+            AND prescription_encounter.voided = 0
+          INNER JOIN orders
+            ON orders.encounter_id = prescription_encounter.encounter_id
+            AND orders.order_type_id IN (SELECT order_type_id FROM order_type WHERE name = 'Drug order')
+            AND orders.start_date >= DATE(#{start_date}) - INTERVAL 6 MONTH
+            AND orders.start_date < DATE(#{start_date})
+            AND orders.voided = 0
+          INNER JOIN concept_name
+            ON concept_name.concept_id = orders.concept_id
+            AND concept_name.name IN ('Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine')
+          INNER JOIN drug_order
+            ON drug_order.order_id = orders.order_id
+            AND drug_order.quantity > 0
+          WHERE person.voided = 0
+            AND person.person_id NOT IN (
+               /* People who had a dispensation prior to the 3 to 9 months before start of reporting period.
+                 Continuing medication after a 9 months break is considered a restart hence such patients
+                 are classified as new on TPT.
+               */
+              SELECT DISTINCT encounter.patient_id
+              FROM encounter
+              INNER JOIN orders
+                ON orders.encounter_id = encounter.encounter_id
+                AND orders.concept_id IN (SELECT concept_id FROM concept_name WHERE name IN ('Rifapentine', 'Isoniazid') AND voided = 0)
+                AND orders.order_type_id IN (SELECT order_type_id FROM order_type WHERE name = 'Drug order')
+                AND orders.start_date < DATE(#{start_date}) - INTERVAL 6 MONTH
+                AND orders.start_date >= DATE(#{start_date}) - INTERVAL 15 MONTH
+                AND orders.voided = 0
+              INNER JOIN drug_order
+                ON drug_order.order_id = orders.order_id
+                AND drug_order.quantity > 0
+              WHERE encounter.program_id IN (SELECT program_id FROM program WHERE name = 'HIV PROGRAM')
+                AND encounter.encounter_type IN (SELECT encounter_type_id FROM encounter_type WHERE name = 'Treatment')
+                AND encounter.encounter_datetime < DATE(#{start_date}) - INTERVAL 6 MONTH
+                AND encounter.encounter_datetime >= DATE(#{start_date}) - INTERVAL 15 MONTH
+                AND encounter.voided = 0
+            ) AND person.person_id NOT IN (
+            /* External consultations */
+            SELECT DISTINCT registration_encounter.patient_id
+            FROM patient_program
+            INNER JOIN program ON program.name = 'HIV PROGRAM'
+            INNER JOIN encounter AS registration_encounter
+              ON registration_encounter.patient_id = patient_program.patient_id
+              AND registration_encounter.program_id = patient_program.program_id
+              AND registration_encounter.encounter_datetime < DATE(#{end_date}) + INTERVAL 1 DAY
+              AND registration_encounter.voided = 0
+            INNER JOIN (
+              SELECT MAX(encounter.encounter_datetime) AS encounter_datetime, encounter.patient_id
+              FROM encounter
+              INNER JOIN encounter_type
+                ON encounter_type.encounter_type_id = encounter.encounter_type
+                AND encounter_type.name = 'Registration'
+              INNER JOIN program
+                ON program.program_id = encounter.program_id
+                AND program.name = 'HIV PROGRAM'
+              WHERE encounter.encounter_datetime < DATE(#{end_date}) AND encounter.voided = 0
+              GROUP BY encounter.patient_id
+            ) AS max_registration_encounter
+              ON max_registration_encounter.patient_id = registration_encounter.patient_id
+              AND max_registration_encounter.encounter_datetime = registration_encounter.encounter_datetime
+            INNER JOIN obs AS patient_type_obs
+              ON patient_type_obs.encounter_id = registration_encounter.encounter_id
+              AND patient_type_obs.concept_id IN (SELECT concept_id FROM concept_name WHERE name = 'Type of patient' AND voided = 0)
+              AND patient_type_obs.value_coded IN (SELECT concept_id FROM concept_name WHERE name IN ('Drug refill', 'External consultation') AND voided = 0)
+              AND patient_type_obs.voided = 0
+            WHERE patient_program.voided = 0
+          )
+          GROUP BY person.person_id
+        SQL
+      end
+
+      ##
+      # Groups patients into their TPT categories (ie 6H and 3HP) based on their drugs
+      #
+      # Returns an object with a three_hp and six_h methods, each of which
+      # is an array of patients for that category.
+      def group_patients_by_tpt_course(patients)
+        patients.each_with_object(OpenStruct.new(six_h: [], three_hp: [])) do |patient, categories|
+          if patient_on_3hp?(patient)
+            categories.three_hp << patient
+          else
+            categories.six_h << patient
+          end
+        end
+      end
+
+      def patient_on_3hp?(patient)
+        drug_concepts = patient['drug_concepts'].split(',').collect(&:to_i)
+        drug_concepts.intersect?([rifapentine_concept.concept_id, isoniazid_rifapentine_concept&.concept_id])
+      end
+
+      def rifapentine_concept
+        @rifapentine_concept ||= ::ConceptName.find_by!(name: 'Rifapentine')
+      end
+
+      def isoniazid_rifapentine_concept
+        @isoniazid_rifapentine_concept ||= ::ConceptName.find_by!(name: 'Isoniazid/Rifapentine')
+      end
+    end
+  end
+end