malawi_hiv_program_reports 1.0.1 → 1.0.2

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

@@ -0,0 +1,283 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Pepfar
+    # TxTb report
+    # rubocop:disable Metrics/ClassLength
+    class TxTb
+      attr_accessor :start_date, :end_date, :report, :rebuild_outcome
+
+      include Utils
+
+      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')
+        @rebuild_outcome = ActiveModel::Type::Boolean.new.cast(kwargs[:rebuild_outcome]) || false
+        @occupation = kwargs[:occupation]
+        @location = kwargs[:location]
+      end
+
+      def find_report
+        drop_temporary_tables
+        create_temp_earliest_start_date unless temp_eartliest_start_date_exists?
+        init_report
+        build_cohort_tables
+        process_tb_screening
+        process_tb_confirmed_and_on_treatment
+        process_patients_alive_and_on_art
+        process_tb_screened
+        process_tb_confirmed
+        report
+      end
+
+      private
+
+      def init_report
+        @report = initialize_report_structure
+      end
+
+      def initialize_report_structure
+        pepfar_age_groups.each_with_object({}) do |age_group, report|
+          genders = %i[M F]
+          genders.each do |gender|
+            report[age_group] ||= {}
+            report[age_group][gender] = initialize_gender_metrics
+          end
+        end
+      end
+
+      def initialize_gender_metrics
+        {
+          tx_curr: [],
+          symptom_screen_alone: [],
+          cxr_screen: [],
+          mwrd_screen: [],
+          sceen_pos_new: [],
+          sceen_neg_new: [],
+          started_tb_new: [],
+          sceen_pos_prev: [],
+          sceen_neg_prev: [],
+          started_tb_prev: []
+        }
+      end
+
+      def drop_temporary_tables
+        execute_action('DROP TABLE IF EXISTS temp_tb_screened;')
+        execute_action('DROP TABLE IF EXISTS temp_tb_confirmed_and_on_treatment;')
+      end
+
+      def build_cohort_tables
+        return unless rebuild_outcome || @occupation.present?
+
+        cohort_builder = MalawiHivProgramReports::Moh::CohortBuilder.new(outcomes_definition: 'pepfar', location: @location)
+        cohort_builder.init_temporary_tables(start_date, end_date, @occupation)
+      end
+
+      def process_tb_screening
+        execute_action(create_temp_tb_screened_query)
+      end
+
+      def create_temp_tb_screened_query
+        <<~SQL
+          CREATE TABLE temp_tb_screened AS
+          SELECT
+            o.person_id as patient_id,
+            LEFT(current_obs.gender, 1) AS gender, MAX(o.obs_datetime) AS screened_date,
+            current_obs.earliest_start_date as enrollment_date,
+            disaggregated_age_group(current_obs.birthdate, DATE('#{end_date.to_date}')) AS age_group,
+            cn.name AS tb_status,
+            GROUP_CONCAT(DISTINCT vcn.name) AS screening_methods
+          FROM obs o
+          INNER JOIN (
+            SELECT o.person_id, MAX(o.obs_datetime) AS obs_datetime, tesd.earliest_start_date, tesd.gender, tesd.birthdate
+            FROM obs o
+            INNER JOIN temp_earliest_start_date tesd ON tesd.patient_id = o.person_id
+            WHERE o.concept_id = #{::ConceptName.find_by_name('TB status').concept_id}
+            AND o.value_coded IN (SELECT concept_id FROM concept_name WHERE name IN ('TB Suspected', 'TB NOT suspected') AND voided = 0)
+            AND o.voided = 0 AND o.obs_datetime BETWEEN '#{start_date}' AND '#{end_date}'
+            GROUP BY o.person_id
+          ) current_obs ON current_obs.person_id = o.person_id AND current_obs.obs_datetime = o.obs_datetime
+          INNER JOIN concept_name cn ON cn.concept_id = o.value_coded AND cn.voided = 0
+          LEFT JOIN obs screen_method ON screen_method.concept_id = #{::ConceptName.find_by_name('TB screening method used').concept_id} AND screen_method.voided = 0 AND screen_method.person_id = o.person_id AND DATE(screen_method.obs_datetime) = DATE(current_obs.obs_datetime)
+          LEFT JOIN concept_name vcn ON vcn.concept_id = screen_method.value_coded AND vcn.voided = 0 AND vcn.name IN ('CXR', 'MWRD')
+          WHERE o.concept_id = #{::ConceptName.find_by_name('TB status').concept_id}
+          AND o.voided = 0
+          AND o.value_coded IN (SELECT concept_id FROM concept_name WHERE name IN ('TB Suspected', 'TB NOT suspected') AND voided = 0)
+          AND o.obs_datetime BETWEEN '#{start_date}' AND '#{end_date}'
+          GROUP BY o.person_id
+        SQL
+      end
+
+      def temp_eartliest_start_date_exists?
+        ActiveRecord::Base.connection.table_exists?('temp_earliest_start_date')
+      end
+
+      def create_temp_earliest_start_date
+        cohort_builder = MalawiHivProgramReports::Moh::CohortBuilder.new(outcomes_definition: 'pepfar', location: @location)
+        cohort_builder.init_temporary_tables(start_date, end_date, @occupation)
+      end
+
+      def process_tb_confirmed_and_on_treatment
+        execute_action(create_temp_tb_confirmed_query)
+      end
+
+      def create_temp_tb_confirmed_query
+        <<~SQL
+          CREATE TABLE temp_tb_confirmed_and_on_treatment AS
+          SELECT
+            o.person_id as patient_id,
+            LEFT(p.gender, 1) AS gender,
+            disaggregated_age_group(p.birthdate, DATE('#{end_date.to_date}')) AS age_group,
+            COALESCE(MIN(tcd.value_datetime),MIN(o.obs_datetime)) AS tb_confirmed_date,
+            CASE
+              WHEN COUNT(tcd.value_datetime) > 0 THEN TRUE
+              ELSE FALSE
+            END AS has_tb_confirmed_date,
+            tesd.earliest_start_date as enrollment_date,
+            prev.tb_confirmed_date prev_reading
+          FROM obs o
+          INNER JOIN temp_earliest_start_date tesd ON tesd.patient_id = o.person_id
+          INNER JOIN person p ON p.person_id = o.person_id AND p.voided = 0
+          LEFT JOIN obs tcd ON tcd.concept_id = #{::ConceptName.find_by_name('TB treatment start date').concept_id} AND tcd.voided = 0 AND tcd.person_id = o.person_id
+          LEFT JOIN (
+            SELECT
+              o.person_id,
+              COALESCE(MAX(tcd.value_datetime),MAX(o.obs_datetime)) AS tb_confirmed_date
+            FROM obs o
+            LEFT JOIN obs tcd ON tcd.concept_id = #{::ConceptName.find_by_name('TB treatment start date').concept_id} AND tcd.voided = 0 AND tcd.person_id = o.person_id
+            WHERE o.concept_id = #{::ConceptName.find_by_name('TB status').concept_id}
+            AND o.value_coded = #{::ConceptName.find_by_name('Confirmed TB on treatment').concept_id}
+            AND o.voided = 0
+            AND o.obs_datetime <= '#{start_date}'
+            GROUP BY o.person_id
+          ) prev ON prev.person_id = o.person_id
+          WHERE o.concept_id = #{::ConceptName.find_by_name('TB status').concept_id}
+          AND o.value_coded = #{::ConceptName.find_by_name('Confirmed TB on treatment').concept_id}
+          AND o.voided = 0
+          AND o.obs_datetime BETWEEN '#{start_date}' AND '#{end_date}'
+          GROUP BY o.person_id
+        SQL
+      end
+
+      def process_patients_alive_and_on_art
+        find_patients_alive_and_on_art.each do |patient|
+          next unless pepfar_age_groups.include?(patient['age_group'])
+
+          @report[patient['age_group']][patient['gender'].to_sym][:tx_curr] << patient['patient_id']
+        end
+      end
+
+      def find_patients_alive_and_on_art
+        execute_query(create_patients_alive_and_on_art_query)
+      end
+
+      def create_patients_alive_and_on_art_query
+        <<~SQL
+          SELECT tpo.patient_id, LEFT(tesd.gender, 1) AS gender, disaggregated_age_group(tesd.birthdate, DATE('#{end_date.to_date}')) age_group
+          FROM temp_patient_outcomes tpo
+          INNER JOIN temp_earliest_start_date tesd ON tesd.patient_id = tpo.patient_id
+          WHERE tpo.cum_outcome = 'On antiretrovirals'
+        SQL
+      end
+
+      # rubocop:disable Metrics/AbcSize
+      # rubocop:disable Metrics/MethodLength
+      def process_tb_screened
+        tb_screened_data = find_tb_screened_data
+        tb_screened_data.each do |patient|
+          age_group = patient['age_group']
+          next unless pepfar_age_groups.include?(age_group)
+
+          gender = patient['gender'].to_sym
+          metrics = @report[age_group][gender]
+          enrollment_date = patient['enrollment_date']
+          tb_status = patient['tb_status'].downcase
+          screening_methods = patient['screening_methods']&.split(',')&.map(&:downcase)
+          patient_id = patient['patient_id']
+          process_method(metrics, screening_methods, patient_id)
+          process_screening_results(metrics, enrollment_date, tb_status, patient_id)
+        end
+      end
+
+      def process_tb_confirmed
+        find_tb_confirmed_data.each do |patient|
+          age_group = patient['age_group']
+          next unless pepfar_age_groups.include?(age_group)
+
+          gender = patient['gender'].to_sym
+          metrics = @report[age_group][gender]
+          enrollment_date = patient['enrollment_date']
+
+          if new_on_art(enrollment_date)
+            metrics[:started_tb_new] << patient['patient_id']
+          else
+            metrics[:started_tb_prev] << patient['patient_id']
+          end
+        end
+      end
+
+      def process_screening_results(metrics, enrollment_date, tb_status, patient_id)
+        if new_on_art(enrollment_date)
+          metrics[:sceen_pos_new] << patient_id if ['tb suspected', 'sup', 'confirmed tb not on treatment', 'norx',
+                                                    'confirmed tb on treatment', 'rx'].include?(tb_status)
+          metrics[:sceen_neg_new] << patient_id if ['tb not suspected', 'nosup'].include?(tb_status)
+        else
+          metrics[:sceen_pos_prev] << patient_id if ['tb suspected', 'sup', 'confirmed tb not on treatment',
+                                                     'norx'].include?(tb_status)
+          metrics[:sceen_neg_prev] << patient_id if ['tb not suspected', 'nosup'].include?(tb_status)
+        end
+      end
+
+      def process_method(metrics, methods, patient_id)
+        metrics[:symptom_screen_alone] << patient_id if methods.blank?
+        metrics[:cxr_screen] << patient_id if methods&.include?('cxr') && !methods&.include?('mwrd')
+        metrics[:mwrd_screen] << patient_id if methods&.include?('mwrd')
+      end
+
+      # rubocop:enable Metrics/AbcSize
+      # rubocop:enable Metrics/MethodLength
+
+      def execute_query(query)
+        ActiveRecord::Base.connection.select_all(query)
+      end
+
+      def execute_action(query)
+        ActiveRecord::Base.connection.execute(query)
+      end
+
+      def find_tb_screened_data
+        execute_query(find_tb_screened_data_query)
+      end
+
+      def find_tb_confirmed_data
+        execute_query(find_tb_confirmed_data_query)
+      end
+
+      def find_tb_method_data
+        execute_query(find_tb_method_data_query)
+      end
+
+      def find_tb_screened_data_query
+        <<~SQL
+          SELECT tbs.patient_id, tbs.enrollment_date, LEFT(tbs.gender, 1) AS gender, tbs.age_group, tbs.tb_status, tbs.screened_date, tbs.screening_methods
+          FROM temp_tb_screened tbs
+        SQL
+      end
+
+      def find_tb_confirmed_data_query
+        <<~SQL
+          SELECT t.patient_id, t.gender, t.age_group, t.enrollment_date, t.tb_confirmed_date
+          FROM temp_tb_confirmed_and_on_treatment t
+          WHERE t.tb_confirmed_date > '#{start_date}'
+          AND (t.has_tb_confirmed_date = TRUE OR t.prev_reading IS NULL OR TIMESTAMPDIFF(MONTH,t.prev_reading, t.tb_confirmed_date) > 6)
+        SQL
+      end
+
+      def new_on_art(earliest_start_date)
+        six_months_later = earliest_start_date.to_date + 6.months
+        six_months_later > end_date.to_date
+      end
+    end
+    # rubocop:enable Metrics/ClassLength
+  end
+end

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

@@ -0,0 +1,141 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Pepfar
+    ##
+    # Common utilities for Pepfar reports
+    module Utils
+      ##
+      # An array of all groups as required by Pepfar.
+      def pepfar_age_groups
+        @pepfar_age_groups ||= [
+          'Unknown',
+          '<1 year',
+          '1-4 years', '5-9 years',
+          '10-14 years', '15-19 years',
+          '20-24 years',
+          '25-29 years', '30-34 years',
+          '35-39 years', '40-44 years',
+          '45-49 years', '50-54 years',
+          '55-59 years', '60-64 years',
+          '65-69 years', '70-74 years',
+          '75-79 years', '80-84 years',
+          '85-89 years',
+          '90 plus years'
+        ].freeze
+      end
+
+      ##
+      # Returns the drilldown information for all specified patients (ie patient_ids)
+      #
+      # Information returned for a patient is as follows:
+      #   * patient_id
+      #   * arv_number or filing_number
+      #   * age_group
+      #   * birthdate
+      #   * gender
+      def pepfar_patient_drilldown_information(patients, current_date)
+        raise ::ArgumentError, "current_date can't be nil" unless current_date
+
+        ::Person.joins("LEFT JOIN patient_identifier ON patient_identifier.patient_id = person.person_id
+                          AND patient_identifier.voided = 0
+                          AND patient_identifier.identifier_type IN (#{pepfar_patient_identifier_type.to_sql})")
+                .where(person_id: patients)
+                .select("person.person_id AS patient_id,
+                         person.gender,
+                         person.birthdate,
+                         disaggregated_age_group(person.birthdate, DATE(#{ActiveRecord::Base.connection.quote(current_date)})) AS age_group,
+                         patient_identifier.identifier AS arv_number")
+      end
+
+      ##
+      # Returns the preferred Pepfar identifier type.
+      #
+      # In some clinics like Lighthouse Filing numbers are used exclusively and in other
+      # sites, ARV Numbers are used.
+      def pepfar_patient_identifier_type
+        name = GlobalProperty.find_by(property: 'use.filing.numbers')&.property_value 
+        name = (name.present? && name == 'true') ? 'Filing number' : 'ARV Number'
+        ::PatientIdentifierType.where(name:).select(:patient_identifier_type_id)
+      end
+
+      FULL_6H_COURSE_PILLS = 146
+      FULL_3HP_COURSE_DAYS = 12.days
+      # NOTE: Arrived at 12 days above from how 3HP is prescribed. 1st time prescription
+      #       A patient takes 3HP once every week. Therefore it is 4 times a months
+      #       Multiply that with 3 months we arrive at 12
+      #       Hence the patient is taking this drug 12 times to be considered complete on
+      #       3HP
+
+      ##
+      # Returns whether a patient completed their course of TPT
+      def patient_completed_tpt?(patient, tpt)
+        if tpt == '3HP'
+          # return true if patient['total_days_on_medication'].to_i >= 83 # 3 months
+          return true if patient['months_on_tpt'].to_i >= 3
+
+          divider = patient['drug_concepts'].split(',').length > 1 ? 14.0 : 7.0
+          days_on_medication = (patient['total_days_on_medication'] / divider).round
+          days_on_medication.days >= FULL_3HP_COURSE_DAYS
+        else
+          patient['total_days_on_medication'].to_i >= FULL_6H_COURSE_PILLS
+        end
+      end
+
+      # this just gives all clients who are truly external or drug refill
+      # rubocop:disable Metrics/MethodLength
+      # rubocop:disable Metrics/AbcSize
+      def drug_refills_and_external_consultation_list
+        to_remove = [0]
+
+        type_of_patient_concept = ::ConceptName.find_by_name('Type of patient').concept_id
+        new_patient_concept = ::ConceptName.find_by_name('New patient').concept_id
+        drug_refill_concept = ::ConceptName.find_by_name('Drug refill').concept_id
+        external_concept = ::ConceptName.find_by_name('External consultation').concept_id
+        hiv_clinic_registration_id = ::EncounterType.find_by_name('HIV CLINIC REGISTRATION').encounter_type_id
+
+        ActiveRecord::Base.connection.select_all("
+            SELECT p.person_id patient_id
+            FROM person p
+            INNER JOIN patient_program pp ON pp.patient_id = p.person_id AND pp.program_id = #{::Program.find_by_name('HIV PROGRAM').id} AND pp.voided = 0
+            INNER JOIN patient_state ps ON ps.patient_program_id = pp.patient_program_id AND ps.state = 7 AND ps.start_date IS NOT NULL
+            #{site_manager(operator: 'AND', column: 'pp.site_id', location: @location)}
+            LEFT JOIN encounter as hiv_registration ON hiv_registration.patient_id = p.person_id AND hiv_registration.encounter_datetime < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) AND hiv_registration.encounter_type = #{hiv_clinic_registration_id} AND hiv_registration.voided = 0
+            #{site_manager(operator: 'AND', column: 'hiv_registration.site_id', location: @location)}
+            LEFT JOIN (SELECT * FROM obs WHERE concept_id = #{type_of_patient_concept} AND voided = 0 AND value_coded = #{new_patient_concept} AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
+            #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}) AS new_patient ON p.person_id = new_patient.person_id
+            LEFT JOIN (SELECT * FROM obs WHERE concept_id = #{type_of_patient_concept} AND voided = 0 AND value_coded = #{drug_refill_concept} AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')} #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}) AS refill ON p.person_id = refill.person_id
+            LEFT JOIN (SELECT * FROM obs WHERE concept_id = #{type_of_patient_concept} AND voided = 0 AND value_coded = #{external_concept} AND obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')} #{site_manager(operator: 'AND', column: 'obs.site_id', location: @location)}) AS external ON p.person_id = external.person_id
+            WHERE (refill.value_coded IS NOT NULL OR external.value_coded IS NOT NULL)
+            AND NOT (hiv_registration.encounter_id IS NOT NULL OR new_patient.value_coded IS NOT NULL)
+            #{site_manager(operator: 'AND', column: 'p.site_id', location: @location)}
+            GROUP BY p.person_id
+            ORDER BY hiv_registration.encounter_datetime DESC, refill.obs_datetime DESC, external.obs_datetime DESC;").each do |record|
+          to_remove << record['patient_id'].to_i
+        end
+        to_remove.join(',')
+      end
+      # rubocop:enable Metrics/MethodLength
+      # rubocop:enable Metrics/AbcSize
+
+      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
+
+      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 patient_on_tb_treatment?(patient_id)
+        ::Observation.where(person_id: patient_id, concept_id: ::ConceptName.find_by_name('TB status').concept_id,
+                            value_coded: ::ConceptName.find_by_name('Confirmed TB on treatment').concept_id)
+                     .where("obs_datetime < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}").exists?
+      end
+    end
+  end
+end