malawi_hiv_program_reports 1.0.1 → 1.0.3

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

@@ -0,0 +1,172 @@
+# frozen_string_literal: true
+
+##
+# TB Preventive Therapy indicators for ART cohort
+module MalawiHivProgramReports
+  module Cohort
+    class Tpt
+      include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
+      include MalawiHivProgramReports::Adapters::Moh::Custom
+
+      def initialize(start_date:, end_date:, **kwargs)
+        @start_date = start_date
+        @end_date = end_date
+        @occupation = kwargs[:occupation]
+        @location = kwargs[:location]
+        @adapter = ActiveRecord::Base.connection.adapter_name.downcase
+        return unless @occupation.present?
+
+        process_occupation(start_date: @start_date, end_date: @end_date,
+                           occupation: @occupation, location: @location)
+      end
+
+      ##
+      # Patients (re-)initiated on 3HP in current reporting period.
+      #
+      # Candidates for this indicator are patients who either have
+      # had their first dispensation in the current reporting period
+      # or patients who have restarted 3HP in the current reporting
+      # period after breaking from the course for a period of at least
+      # 9 months (3 quarters).
+      def newly_initiated_on_3hp
+        # newly_initiated_on_tpt(start_date, end_date).each_with_object([]) do |patient, patients|
+        #   patients << patient['patient_id'] unless patient_on_3hp?(patient)
+        # end
+        processed_tpt_clients.select { |patient| patient_on_3hp?(patient) }
+      end
+
+      ##
+      # Patients (re-)initiated on IPT in current reporting period
+      #
+      # Has a similar definition to 3HP, please refer to 3HP docs
+      # above.
+      def newly_initiated_on_ipt
+        # newly_initiated_on_tpt(start_date, end_date).each_with_object([]) do |patient, patients|
+        #   patients << patient['patient_id'] if patient_on_3hp?(patient)
+        # end
+        processed_tpt_clients.reject { |patient| patient_on_3hp?(patient) }
+      end
+
+      private
+
+      def patient_on_3hp?(patient)
+        drug_concepts = patient['drug_concepts'].split(',').collect(&:to_i)
+        drug_concepts.intersect?([rifapentine_concept.concept_id, three_hp_concept&.concept_id])
+      end
+
+      def rifapentine_concept
+        @rifapentine_concept ||= ::ConceptName.find_by!(name: 'Rifapentine')
+      end
+
+      def three_hp_concept
+        @three_hp_concept ||= ::ConceptName.find_by!(name: 'Isoniazid/Rifapentine')
+      end
+
+      def processed_tpt_clients
+        @processed_tpt_clients ||= process_tpt_clients
+      end
+
+      def process_tpt_clients
+        patients = []
+        newly_initiated_on_tpt.each do |patient|
+          course = patient['course'].include?('3HP') ? '3HP' : 'IPT'
+          next if patient['last_course'].present?
+          if patient['tpt_initial_start_date'].present? && patient['tpt_initial_start_date'].to_date < @start_date.to_date
+            next
+          end
+
+          if patient['transfer_course'].blank? && patient['last_course'].blank?
+            patients << patient
+          elsif patient['transfer_course'].present? && patient['last_course'].blank?
+            patients << patient if patient['months_since_tpt_transfer'].to_i >= (course == '3HP' ? 1 : 2)
+          elsif patient['transfer_course'].blank? && patient['last_course'].present?
+            patients << patient if patient['months_since_last_tpt'].to_i >= (course == '3HP' ? 1 : 2)
+          elsif patient['last_tpt_end_date'].to_date >= patient['transfer_end_date'].to_date
+            patients << patient if patient['months_since_last_tpt'].to_i >= (course == '3HP' ? 1 : 2)
+          elsif patient['last_tpt_end_date'].to_date < patient['transfer_end_date'].to_date
+            patients << patient if patient['months_since_tpt_transfer'].to_i >= (course == '3HP' ? 1 : 2)
+          end
+        end
+        patients
+      end
+
+      def newly_initiated_on_tpt
+        start_date = ActiveRecord::Base.connection.quote(@start_date)
+        end_date = ActiveRecord::Base.connection.quote(@end_date)
+
+        @newly_initiated_on_tpt ||= ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT
+            cohort_patients.patient_id,
+            cohort_patients.earliest_start_date,
+            MIN(orders.start_date )as tpt_start_date,
+            #{@adapter == 'mysql2' ? "GROUP_CONCAT(DISTINCT orders.concept_id SEPARATOR ',') AS drug_concepts," : "(SELECT STRING_AGG(concept_id::VARCHAR, ',') FROM (SELECT DISTINCT orders.concept_id FROM orders) AS subquery) AS drug_concepts,"}
+            CASE
+              WHEN count(distinct(orders.concept_id)) > 1 THEN '3HP old'
+              WHEN orders.concept_id = #{three_hp_concept.concept_id} THEN '3HP new'
+              ELSE '6H'
+            END AS course,
+            tpt_transfer_in_obs.value_datetime AS tpt_initial_start_date,
+            CASE
+              WHEN tpt_transfer_in_obs.concept_id IS NULL THEN NULL
+              WHEN count(distinct(tpt_transfer_in_obs.concept_id)) > 1 THEN '3HP old'
+              WHEN tpt_transfer_in_obs.concept_id = #{three_hp_concept.concept_id} THEN '3HP new'
+              ELSE '6H'
+            END AS transfer_course,
+            tpt_transfer_in_obs.obs_datetime AS transfer_end_date,
+            tpt_transfer_in_obs.value_numeric AS transfer_amount,
+            #{@adapter == 'mysql2' ? 'TIMESTAMPDIFF(MONTH, tpt_transfer_in_obs.obs_datetime, MIN(orders.start_date)) AS months_since_tpt_transfer,' : '(EXTRACT(YEAR FROM AGE(MIN(orders.start_date), tpt_transfer_in_obs.obs_datetime)) * 12 + EXTRACT(MONTH FROM AGE(MIN(orders.start_date), tpt_transfer_in_obs.obs_datetime))) AS months_since_tpt_transfer,'}
+            #{@adapter == 'mysql2' ? 'TIMESTAMPDIFF(MONTH, last_tpt_prescription.auto_expire_date, MIN(orders.start_date)) AS months_since_last_tpt,' : '(EXTRACT(YEAR FROM AGE(MIN(orders.start_date), last_tpt_prescription.auto_expire_date)) * 12 + EXTRACT(MONTH FROM AGE(MIN(orders.start_date), last_tpt_prescription.auto_expire_date))) AS months_since_last_tpt,'}
+            last_tpt_prescription.course AS last_course,
+            last_tpt_prescription.start_date AS last_tpt_start_date,
+            last_tpt_prescription.auto_expire_date AS last_tpt_end_date
+          FROM temp_earliest_start_date AS cohort_patients
+          INNER JOIN orders
+            ON orders.patient_id = cohort_patients.patient_id
+            AND orders.order_type_id = (SELECT order_type_id FROM order_type WHERE name = 'Drug order' LIMIT 1)
+            AND orders.start_date >= #{start_date}
+            AND orders.start_date < #{interval_manager(date: end_date, value: 1, interval: 'DAY', operator: '+')}
+            AND orders.voided = 0 #{site_manager(operator: 'AND', column: 'orders.site_id', location: @location)}
+          INNER JOIN concept_name AS tpt_drug_concepts
+            ON tpt_drug_concepts.concept_id = orders.concept_id
+            AND tpt_drug_concepts.name IN ('Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine')
+            AND tpt_drug_concepts.voided = 0
+          INNER JOIN drug_order AS drug_orders
+            ON drug_orders.order_id = orders.order_id
+            AND drug_orders.quantity > 0 #{site_manager(operator: 'AND', column: 'drug_orders.site_id', location: @location)}
+          INNER JOIN encounter
+            /* Ensure we are dealing with ART prescriptions (Treatment encounter) */
+            ON encounter.encounter_id = orders.encounter_id
+            AND encounter.encounter_type = (SELECT encounter_type_id FROM encounter_type WHERE name = 'Treatment' LIMIT 1)
+            AND encounter.program_id = (SELECT program_id FROM program WHERE name = 'HIV PROGRAM' LIMIT 1)
+            AND encounter.voided = 0
+          LEFT JOIN obs tpt_transfer_in_obs
+            ON tpt_transfer_in_obs.person_id = orders.patient_id
+            AND tpt_transfer_in_obs.concept_id = #{::ConceptName.find_by_name('TPT Drugs Received').concept_id}
+            AND tpt_transfer_in_obs.voided = 0  #{site_manager(operator: 'AND', column: 'tpt_transfer_in_obs.site_id', location: @location)}
+            AND tpt_transfer_in_obs.value_drug IN (SELECT drug_id FROM drug WHERE concept_id IN (SELECT concept_id FROM concept_name WHERE name IN ('Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine')))
+          -- Get the last TPT prescription
+          LEFT JOIN (
+            SELECT
+              o.patient_id,
+              MAX(o.start_date) AS start_date,
+              MAX(o.auto_expire_date) AS auto_expire_date,
+              CASE
+                WHEN count(distinct(o.concept_id)) > 1 THEN '3HP old'
+                WHEN o.concept_id = #{three_hp_concept.concept_id} THEN '3HP new'
+                ELSE '6H'
+              END AS course
+            FROM temp_earliest_start_date
+            INNER JOIN orders o ON o.patient_id = temp_earliest_start_date.patient_id #{site_manager(operator: 'AND', column: 'o.site_id', location: @location)}
+            INNER JOIN concept_name AS tpt_drug_concepts ON tpt_drug_concepts.concept_id = o.concept_id AND tpt_drug_concepts.name IN ('Rifapentine', 'Isoniazid', 'Isoniazid/Rifapentine') AND tpt_drug_concepts.voided = 0
+            INNER JOIN drug_order AS drug_orders ON drug_orders.order_id = o.order_id AND drug_orders.quantity > 0 #{site_manager(operator: 'AND', column: 'drug_orders.site_id', location: @location)}
+            INNER JOIN encounter ON encounter.encounter_id = o.encounter_id AND encounter.encounter_type = (SELECT encounter_type_id FROM encounter_type WHERE LOWER(name) = Lower('Treatment') LIMIT 1) AND encounter.program_id = (SELECT program_id FROM program WHERE LOWER(name) = LOWER('HIV Program') LIMIT 1) AND encounter.voided = 0
+            WHERE o.voided = 0 #{site_manager(operator: 'AND', column: 'temp_earliest_start_date.site_id', location: @location)}
+            AND o.start_date < #{start_date}
+            GROUP BY o.patient_id, o.concept_id
+          ) AS last_tpt_prescription ON last_tpt_prescription.patient_id = orders.patient_id
+          GROUP BY cohort_patients.patient_id #{@adapter == 'mysql2' ? '' : ', tpt_transfer_in_obs.concept_id, tpt_transfer_in_obs.obs_datetime, tpt_transfer_in_obs.value_numeric, last_tpt_prescription.course, last_tpt_prescription.start_date, last_tpt_prescription.auto_expire_date, orders.concept_id, tpt_transfer_in_obs.value_datetime, tpt_transfer_in_obs.concept_id'}
+        SQL
+      end
+    end
+  end
+end

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

@@ -0,0 +1,278 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Moh
+    # Cohort report builder class.
+    #
+    # This class only provides one public method (start_build_report) besides
+    # the constructor. This method must be called to build report and save
+    # it to database.
+    # rubocop:disable Metrics/ClassLength
+    class Cohort
+      include MalawiHivProgramReports::Utils::ConcurrencyUtils
+      include MalawiHivProgramReports::Utils::ModelUtils
+      include MalawiHivProgramReports::Adapters::Moh::Custom
+
+      LOCK_FILE = 'art_service/reports/cohort.lock'
+
+      def initialize(name:, type:, start_date:, end_date:, **kwargs)
+        @name = name
+        @start_date = start_date
+        @end_date = end_date
+        @type = type
+        @occupation = kwargs[:occupation]
+        @location = kwargs[:location]
+        @cohort_builder = CohortBuilder.new(outcomes_definition: 'moh', **kwargs)
+        @cohort_struct = CohortStruct.new
+        @location_name = @location && Location.find(@location).name
+      end
+
+      def build_report
+        with_lock(LOCK_FILE, blocking: false) do
+          init_drill_down_table
+          clear_drill_down
+          @cohort_builder.build(@cohort_struct, @start_date, @end_date, @occupation)
+          save_report
+        end
+      rescue ::FailedToAcquireLock => e
+        Rails.logger.warn("ART#Cohort report is locked by another process: #{e}")
+      end
+
+      def find_report
+        ::Report.where(type: @type, name: "#{@name}#{"-#{@occupation}"}#{"-#{@location_name}"}",
+                       start_date: @start_date, end_date: @end_date)
+                .order(date_created: :desc)
+                .first
+      end
+
+      def defaulter_list(pepfar)
+        report_type = (pepfar ? 'pepfar' : 'moh')
+        defaulter_date_sql = pepfar ? 'current_pepfar_defaulter_date' : 'current_defaulter_date'
+        CohortBuilder.new(outcomes_definition: report_type, location: @location)
+                     .init_temporary_tables(@start_date, @end_date, @occupation)
+
+        data = ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT
+            e.patient_id, i.identifier arv_number, e.birthdate,
+            e.gender, n.given_name, n.family_name,
+            art_reason.name art_reason, a.value cell_number, landmark.value landmark,
+            s.state_province district, s.county_district ta,
+            s.city_village village, TIMESTAMPDIFF(year, DATE(e.birthdate), DATE('#{@end_date}')) age,
+            #{defaulter_date_sql}(e.patient_id, TIMESTAMP('#{@end_date.to_date.strftime('%Y-%m-%d 23:59:59')}')) AS defaulter_date,
+            appointment.appointment_date AS appointment_date
+          FROM temp_earliest_start_date e
+          INNER JOIN temp_patient_outcomes o ON e.patient_id = o.patient_id
+          INNER JOIN (
+            SELECT e.patient_id, MAX(o.value_datetime) appointment_date
+            FROM encounter e
+            INNER JOIN obs o ON o.encounter_id = e.encounter_id AND o.voided = 0 AND o.concept_id = 5096 -- appointment date
+            WHERE e.encounter_type = 7 -- appointment encounter type
+            AND e.program_id = 1 -- HIV PROGRAM
+            AND e.patient_id IN (SELECT patient_id FROM temp_patient_outcomes WHERE cum_outcome = 'Defaulted')
+            AND e.encounter_datetime < DATE('#{@end_date}') + INTERVAL 1 DAY
+            GROUP BY e.patient_id
+          ) appointment ON appointment.patient_id = e.patient_id
+          LEFT JOIN patient_identifier i ON i.patient_id = e.patient_id
+          AND i.voided = 0 AND i.identifier_type = 4
+          INNER JOIN person_name n ON n.person_id = e.patient_id AND n.voided = 0
+          LEFT JOIN person_attribute a ON a.person_id = e.patient_id
+          AND a.voided = 0 AND a.person_attribute_type_id = 12
+          LEFT JOIN person_attribute landmark ON landmark.person_id = e.patient_id AND landmark.voided = 0 AND landmark.person_attribute_type_id = 19
+          LEFT JOIN person_address s ON s.person_id = e.patient_id AND s.voided = 0
+          LEFT JOIN concept_name art_reason ON art_reason.concept_id = e.reason_for_starting_art AND art_reason.voided = 0
+          WHERE o.cum_outcome = 'Defaulted' GROUP BY e.patient_id
+          ORDER BY e.patient_id, n.date_created DESC;
+        SQL
+
+        patients = []
+
+        (data || []).each do |person|
+          defaulter_date = person['defaulter_date']&.to_date || 'N/A'
+
+          unless defaulter_date == 'N/A'
+            next if defaulter_date < @start_date.to_date
+            next if defaulter_date > @end_date.to_date
+          end
+
+          patients << {
+            person_id: person['patient_id'],
+            given_name: person['given_name'],
+            family_name: person['family_name'],
+            birthdate: person['birthdate'],
+            gender: person['gender'],
+            arv_number: person['arv_number'],
+            outcome: 'Defaulted',
+            defaulter_date:,
+            appointment_date: person['appointment_date'].to_date.strftime('%Y-%m-%d'),
+            art_reason: person['art_reason'],
+            cell_number: person['cell_number'],
+            district: person['district'],
+            ta: person['ta'],
+            village: person['village'],
+            current_age: person['age'],
+            landmark: person['landmark']
+          }
+        end
+
+        patients
+      end
+
+      def cohort_report_drill_down(id)
+        id = ActiveRecord::Base.connection.quote(id)
+
+        patients = ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT i.identifier arv_number, p.birthdate,
+                 p.gender, n.given_name, n.family_name, p.person_id patient_id,
+                 outcomes.cum_outcome AS outcome
+          FROM person p
+          INNER JOIN cohort_drill_down c ON c.patient_id = p.person_id
+          INNER JOIN temp_patient_outcomes AS outcomes
+            ON outcomes.patient_id = c.patient_id
+          LEFT JOIN patient_identifier i ON i.patient_id = p.person_id
+          AND i.voided = 0 AND i.identifier_type = 4
+          LEFT JOIN person_name n ON n.person_id = p.person_id AND n.voided = 0
+          WHERE c.reporting_report_design_resource_id = #{id}
+          GROUP BY p.person_id ORDER BY p.person_id, p.date_created;
+        SQL
+
+        patients.map do |person|
+          {
+            person_id: person['patient_id'],
+            given_name: person['given_name'],
+            family_name: person['family_name'],
+            birthdate: person['birthdate'],
+            gender: person['gender'],
+            arv_number: person['arv_number'],
+            outcome: person['outcome']
+          }
+        end
+      end
+
+      private
+
+      LOGGER = Rails.logger
+
+      # Writes the report to database
+      def save_report
+        ::Report.transaction do
+          report = ::Report.create(name: "#{@name}#{"-#{@occupation}"}#{"-#{@location_name}"}",
+                                   start_date: @start_date,
+                                   end_date: @end_date,
+                                   type: @type,
+                                   creator: ::User.current.id,
+                                   renderer_type: 'PDF')
+          values = save_report_values(report)
+
+          { report:, values: }
+        end
+      rescue StandardError => e
+        LOGGER.error("Failed to save report: #{e}")
+      end
+
+      # Writes the report values to database
+      def save_report_values(report)
+        @cohort_struct.values.collect do |value|
+          puts "Saving #{value.name} = #{value_contents_to_json(value.contents)}"
+          report_value = ::ReportValue.create(report:,
+                                              name: value.name,
+                                              indicator_name: value.indicator_name,
+                                              indicator_short_name: value.indicator_short_name,
+                                              creator: ::User.current.id,
+                                              description: value.description,
+                                              contents: value_contents_to_json(value.contents))
+
+          raise "Failed to save report value: #{report_value.errors.as_json}" unless report_value.errors.empty?
+
+          save_patients(report_value, value_contents_to_json(value).contents)
+
+          report_value
+        end
+      end
+
+      def init_drill_down_table
+        exe_create_drill_down_table(adapter: ActiveRecord::Base.connection.adapter_name.downcase)
+      end
+
+      def clear_drill_down
+        ActiveRecord::Base.connection.execute <<~SQL
+          DELETE FROM cohort_drill_down #{site_manager(operator: 'WHERE', column: 'site_id', location: @location)}
+        SQL
+      rescue StandardError => e
+        ActiveRecord::Base.connection.execute 'DROP TABLE IF EXISTS cohort_drill_down;'
+        LOGGER.error("Failed to clear drill down table: #{e}")
+        raise e
+      end
+
+      def value_contents_to_json(value_contents)
+        if value_contents.respond_to?(:each) && !value_contents.is_a?(String)
+          if value_contents.respond_to?(:length)
+            value_contents.length
+          elsif value_contents.respond_to?(:size)
+            value_contents.size
+          else
+            value_contents
+          end
+        else
+          value_contents
+        end
+      end
+
+      PATIENT_ID_KEYS = ['patient_id', :patient_id, 'person_id', :person_id].freeze
+
+      def save_patients(r, values)
+        return if values.blank? || !values.respond_to?(:each)
+
+        get_patient_id = lambda do |patient, keys = PATIENT_ID_KEYS|
+          break nil if keys.empty?
+
+          patient[keys.first] || get_patient_id[patient, keys[1..keys.size]]
+        end
+
+        patient_ids = values.map do |patient|
+          if patient.respond_to?(:key?) && PATIENT_ID_KEYS.any? { |key| patient.key?(key) }
+            get_patient_id[patient]
+          elsif patient.respond_to?(:each) && patient.respond_to?(:first)
+            patient.first
+          else
+            patient
+          end
+        end
+
+        sql_insert_statement = nil
+        patient_ids.select do |patient_id|
+          if sql_insert_statement.blank?
+            sql_insert_statement = "(#{r.id}, #{patient_id}, #{@location})"
+          else
+            sql_insert_statement += ",(#{r.id}, #{patient_id}, #{@location})"
+          end
+        end
+
+        return if sql_insert_statement.blank?
+
+        ActiveRecord::Base.connection.execute <<~SQL
+          INSERT INTO cohort_drill_down (reporting_report_design_resource_id, patient_id, site_id)
+          VALUES #{sql_insert_statement};
+        SQL
+      rescue StandardError => e
+        LOGGER.error("Failed to save patients: #{e}")
+        raise e
+      end
+
+      def calculate_age(birthdate)
+        birthdate = begin
+          birthdate.to_date
+        rescue StandardError
+          nil
+        end
+        return 'N/A' if birthdate.blank?
+
+        birthdate = ActiveRecord::Base.connection.select_one <<~SQL
+          SELECT #{timestampdiff_manager(date1: DATE(birthdate), date2: DATE(@end_date), interval: 'YEAR')} age;
+        SQL
+
+        birthdate['age']
+      end
+    end
+    # rubocop:enable Metrics/ClassLength
+  end
+end