feat(OpenSRP Exporter): Selective Exporting (#5684)

**Story card:**
[sc-16544](https://app.shortcut.com/simpledotorg/story/16544/opensrp-selective-exporting)

## Because

To reduce impact on data, we need to enable differential exports.

## This addresses

- Refactoring the `opensrp:export` task into a one-off service
- Testing that service
- Filtering selected patients for export [probably from config file]

## Test instructions

suite tests

Author: igbanam

app/services/one_off/opensrp/exporter.rb

@@ -4,9 +4,263 @@ module Opensrp
     #
     # Base class which acts as an entry point for the rake task.
     class Exporter
+      class Config
+        attr_reader :report_start, :report_end, :facilities, :time_window, :patients
+
+        def initialize config_file
+          data = YAML.load_file(config_file).deep_symbolize_keys.with_indifferent_access
+          time_boundaries = data[:time_boundaries]
+
+          @report_start = if has_report_start?(data)
+            time_boundaries[:report_start]
+          else
+            DateTime.parse("2020-01-01")
+          end
+          @report_end = if has_report_end?(data)
+            time_boundaries[:report_end]
+          else
+            DateTime.now
+          end
+          @facilities = data[:facilities]
+          @time_bound = using_time_boundaries? data
+          @time_window = @report_start..@report_end
+          @patients = get_patients data
+        end
+
+        def time_bound?
+          @time_bound || false
+        end
+
+        def using_time_boundaries?(config)
+          config.has_key? :time_boundaries
+        end
+
+        def has_report_start?(config)
+          using_time_boundaries?(config) && config[:time_boundaries].has_key?(:report_start)
+        end
+
+        def has_report_end?(config)
+          using_time_boundaries?(config) && config[:time_boundaries].has_key?(:report_end)
+        end
+
+        def get_patients config
+          config[:patients] || []
+        end
+      end
+
+      attr_reader :tally
+
       def self.export config, output
         new(config, output).call!
       end
+
+      def initialize config_file, output_file, logger: nil
+        raise "Config file should be YAML" unless %w[yaml yml].include?(config_file.split(".").last)
+        raise "Output file should be JSON" unless output_file.split(".").last == "json"
+
+        if logger.nil?
+          initialize_logger
+        else
+          @logger = logger
+        end
+
+        @config = Config.new config_file
+        @logger.info "Exporting data using config at #{config_file}"
+        @output = output_file
+        @resources = []
+        @encounters = []
+        @tally = Hash.new(0)
+      end
+
+      def initialize_logger
+        logfile = Rails.root.join("log", "#{Rails.env}.log")
+        @logger = ActiveSupport::Logger.new(logfile)
+        @logger.extend(ActiveSupport::Logger.broadcast(ActiveSupport::Logger.new($stdout)))
+      end
+
+      def call!
+        @logger.info "Time Boundaries: [#{@config.report_start}..#{@config.report_end}]"
+
+        patients = select_patients from_facilities: @config.facilities.keys
+        patients.each do |patient|
+          export_patient_details patient
+          export_blood_pressure_details patient
+          export_blood_sugar_details patient
+          export_prescription_drugs_details patient
+          export_appointments_details patient
+          export_medical_history_details patient
+        end
+
+        @tally[:encounters] += @encounters.size
+        @resources << OneOff::Opensrp::EncounterGenerator.new(@encounters).generate
+
+        write_audit_trail patients
+      end
+
+      def select_patients from_facilities: []
+        raise "No facility selected for export" if from_facilities.empty?
+
+        relation = Patient.where(assigned_facility_id: from_facilities)
+        if @config.patients.empty?
+          relation
+        else
+          relation.where(id: @config.patients)
+        end
+      end
+
+      def export_patient_details patient
+        return unless @config.time_window.cover?(patient.recorded_at)
+
+        patient_exporter = OneOff::Opensrp::PatientExporter.new(patient, @config.facilities)
+        @resources << patient_exporter.export
+        @tally[:patients] += 1
+
+        @resources << patient_exporter.export_registration_questionnaire_response
+        @tally[:questionnaire_response] += 1
+
+        @encounters << patient_exporter.export_registration_encounter
+      end
+
+      def export_blood_pressure_details patient
+        blood_pressures = if @config.time_bound?
+          patient
+            .blood_pressures
+            .where(recorded_at: @config.time_window)
+            .or(patient
+            .blood_pressures
+            .where(updated_at: @config.time_window))
+        else
+          patient.blood_pressures
+        end
+        @logger.debug "Patient[##{patient.id}] has #{blood_pressures.size} blood pressure readings."
+        @tally[:observation] += blood_pressures.size
+        blood_pressures.each do |bp|
+          # This is technically an FHIR::Observation, with code set to a blood pressure code
+          bp_exporter = OneOff::Opensrp::BloodPressureExporter.new(bp, @config.facilities)
+          @resources << bp_exporter.export
+          @encounters << bp_exporter.export_encounter
+        end
+      end
+
+      def export_blood_sugar_details patient
+        blood_sugars = if @config.time_bound?
+          patient
+            .blood_sugars
+            .where(recorded_at: @config.time_window)
+            .or(patient
+            .blood_sugars
+            .where(updated_at: @config.time_window))
+        else
+          patient.blood_sugars
+        end
+        @logger.debug "Patient[##{patient.id}] has #{blood_sugars.size} blood sugar readings."
+        @tally[:observation] += blood_sugars.size
+        blood_sugars.each do |bs|
+          # This is technically an FHIR::Observation, with code set to a blood sugar code
+          bs_exporter = OneOff::Opensrp::BloodSugarExporter.new(bs, @config.facilities)
+          if patient.medical_history.diabetes_no?
+            @resources << bs_exporter.export_no_diabetes_observation
+          end
+          @resources << bs_exporter.export
+          @encounters << bs_exporter.export_encounter
+        end
+      end
+
+      def export_prescription_drugs_details patient
+        prescription_drugs = if @config.time_bound?
+          patient
+            .prescription_drugs
+            .where(created_at: @config.time_window)
+            .or(patient
+            .prescription_drugs
+            .where(updated_at: @config.time_window))
+        else
+          patient.prescription_drugs
+        end
+        @logger.debug "Patient[##{patient.id}] has #{prescription_drugs.size} drugs prescribed."
+        @tally[:flags] += prescription_drugs.size
+        prescription_drugs.each do |drug|
+          drug_exporter = OneOff::Opensrp::PrescriptionDrugExporter.new(drug, @config.facilities)
+          @resources << drug_exporter.export_dosage_flag
+          @encounters << drug_exporter.export_encounter
+        end
+      end
+
+      def export_appointments_details patient
+        appointments = if @config.time_bound?
+          patient
+            .appointments
+            .where(created_at: @config.time_window)
+            .or(patient
+            .appointments
+            .where(updated_at: @config.time_window))
+        else
+          patient.appointments
+        end
+        @logger.debug "Patient[##{patient.id}] has #{appointments.size} appointments."
+        @tally[:appointments] += appointments.size
+        @tally[:tasks] += appointments.includes(:call_results).where.not(call_results: {id: nil}).size
+        @tally[:flags] += appointments.includes(:call_results).where.not(call_results: {id: nil}).size
+        appointments.each do |appointment|
+          appointment_exporter = OneOff::Opensrp::AppointmentExporter.new(appointment, @config.facilities)
+          @resources << appointment_exporter.export
+          if appointment.call_results.present?
+            @resources << appointment_exporter.export_call_outcome_task
+            @resources << appointment_exporter.export_call_outcome_flag
+          end
+          @encounters << appointment_exporter.export_encounter
+        end
+      end
+
+      def export_medical_history_details patient
+        OneOff::Opensrp::MedicalHistoryExporter.new(patient.medical_history, @config.facilities).then do |medical_history_exporter|
+          @resources << medical_history_exporter.export
+          @encounters << medical_history_exporter.export_encounter
+        end
+        @tally[:conditions] += 1
+      end
+
+      def write_audit_trail patients
+        CSV.open("audit_trail.csv", "w") do |csv|
+          csv << create_audit_record(@config.facilities, patients.first).keys
+          patients.each do |patient|
+            csv << create_audit_record(@config.facilities, patient).values
+          end
+        end
+      end
+
+      def create_audit_record(facilities, patient)
+        return {} if patient.nil?
+
+        {
+          patient_id: patient.id,
+          sri_lanka_personal_health_number: patient.business_identifiers.where(identifier_type: "sri_lanka_personal_health_number")&.first&.identifier,
+          patient_bp_passport_number: patient.business_identifiers.where(identifier_type: "simple_bp_passport")&.first&.identifier,
+          patient_name: patient.full_name,
+          patient_gender: patient.gender,
+          patient_date_of_birth: patient.date_of_birth || patient.age_updated_at - patient.age.years,
+          patient_address: patient.address ? patient.address.street_address : "",
+          patient_telephone: patient.phone_numbers.pluck(:number).join(";"),
+          patient_facility: facilities[patient.assigned_facility_id][:name],
+          patient_preferred_language: "Sinhala",
+          patient_active: patient.status_active?,
+          patient_deceased: patient.status_dead?,
+          condition: ("HTN" if patient.medical_history.hypertension_yes?) || ("DM" if patient.medical_history.diabetes_yes?),
+          blood_pressure: patient.latest_blood_pressure&.values_at(:systolic, :diastolic)&.join("/"),
+          bmi: nil,
+          appointment_date: patient.appointments.order(device_updated_at: :desc).where(status: "scheduled")&.first&.device_updated_at&.to_date&.iso8601,
+          medication: patient.prescription_drugs.order(device_updated_at: :desc).where(is_deleted: false)&.first&.values_at(:name, :dosage)&.join(" "),
+          glucose_measure: patient.latest_blood_sugar&.blood_sugar_value.then { |bs| "%.2f" % bs if bs },
+          glucose_measure_type: patient.latest_blood_sugar&.blood_sugar_type,
+          call_outcome: patient.appointments.order(device_updated_at: :desc)&.first&.call_results&.order(device_created_at: :desc)&.first&.result_type
+        }
+      end
+
+      private
+
+      def read config_file
+        YAML.load_file(config_file).deep_symbolize_keys.with_indifferent_access
+      end
     end
   end
 end