malawi_hiv_program_reports 1.0.1 → 1.0.3

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

@@ -0,0 +1,317 @@
+# frozen_string_literal: true
+
+# Produces an Appointment Report
+
+# rubocop:disable Metrics/ClassLength
+module MalawiHivProgramReports
+  module Clinic
+    class AppointmentsReport
+      include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
+
+      ENCOUNTER_NAMES = [
+        'VITALS', 'HIV STAGING',
+        'APPOINTMENT', 'HIV CLINIC REGISTRATION',
+        'ART_FOLLOWUP', 'TREATMENT', 'UPDATE OUTCOME',
+        'HIV RECEPTION', 'LAB', 'HIV CLINIC CONSULTATION',
+        'DISPENSING', 'LAB ORDERS', 'ART ADHERENCE',
+        'GIVE LAB RESULTS', 'CERVICAL CANCER SCREENING',
+        'HYPERTENSION MANAGEMENT', 'FAST TRACK ASSESMENT'
+      ].freeze
+
+      HIV_ENCOUNTERS = ::EncounterType.where('name IN(?)', ENCOUNTER_NAMES).map(&:id)
+
+      def initialize(start_date:, end_date:, **kwargs)
+        @start_date = start_date
+        @end_date = end_date
+        @occupation = kwargs[:occupation]
+      end
+
+      # rubocop:disable Metrics/MethodLength
+      # rubocop:disable Metrics/AbcSize
+      def missed_appointments
+        appointments = ::Observation.joins(:encounter)
+                                    .joins("LEFT JOIN (#{current_occupation_query} )AS a ON a.person_id = obs.person_id")
+                                    .merge(appointment_encounters)
+                                    .where.not(person_id: referral_patients.select(:person_id))
+                                    .where(concept: ::ConceptName.where(name: 'Appointment date').select(:concept_id))
+                                    .where('value_datetime BETWEEN ? AND ? AND encounter.program_id = ?',
+                                           @start_date.strftime('%Y-%m-%d 00:00:00'),
+                                           @end_date.strftime('%Y-%m-%d 23:59:59'), 1)
+                                    .where(occupation_filter(occupation: @occupation, field_name: 'value',
+                                                             table_name: 'a', include_clause: false).to_s)
+                                    .group(:person_id)
+
+        appointments.each_with_object([]) do |appointment, patients|
+          patient = missed_appointment?(appointment)
+
+          patients << patient unless patient.blank?
+        end
+      end
+      # rubocop:enable Metrics/AbcSize
+      # rubocop:enable Metrics/MethodLength
+
+      # rubocop:disable Metrics/MethodLength
+      # rubocop:disable Metrics/AbcSize
+      # rubocop:disable Metrics/PerceivedComplexity
+      # rubocop:disable Metrics/CyclomaticComplexity
+      def patient_visit_types
+        yes_concept = ::ConceptName.find_by_name('YES').concept_id
+        hiv_reception_breakdown = {}
+
+        (patient_visits || []).each do |v|
+          visit_date = v['obs_datetime'].to_date
+          visit_type = v['name']
+          ans_given = v['value_coded'].to_i == yes_concept
+          patient_id = v['patient_id'].to_i
+          patient_present = (visit_type.match(/patient/i) && ans_given ? true : false)
+          guardian_present = (visit_type.match(/person/i) && ans_given ? true : false)
+
+          if hiv_reception_breakdown[visit_date].blank?
+            hiv_reception_breakdown[visit_date] = {}
+            hiv_reception_breakdown[visit_date][patient_id] = {
+              patient_present: 0, guardian_present: 0
+            }
+          elsif hiv_reception_breakdown[visit_date][patient_id].blank?
+            hiv_reception_breakdown[visit_date][patient_id] = {
+              patient_present: false, guardian_present: false
+            }
+          end
+
+          if /patient/i.match?(visit_type)
+            hiv_reception_breakdown[visit_date][patient_id][:patient_present] = patient_present
+          end
+          if /person/i.match?(visit_type)
+            hiv_reception_breakdown[visit_date][patient_id][:guardian_present] = guardian_present
+          end
+        end
+
+        hiv_reception_breakdown
+      end
+      # rubocop:enable Metrics/CyclomaticComplexity
+      # rubocop:enable Metrics/PerceivedComplexity
+      # rubocop:enable Metrics/AbcSize
+      # rubocop:enable Metrics/MethodLength
+
+      # rubocop:disable Metrics/MethodLength
+      # rubocop:disable Metrics/AbcSize
+      # rubocop:disable Metrics/PerceivedComplexity
+      # rubocop:disable Metrics/CyclomaticComplexity
+      def patient_visit_list
+        yes_concept = ::ConceptName.find_by_name('YES').concept_id
+        hiv_reception_breakdown = {}
+
+        (patient_visits || []).each do |v|
+          # visit_date = v['obs_datetime'].to_date
+          visit_type = v['name']
+          ans_given = v['value_coded'].to_i == yes_concept
+          patient_id = v['patient_id'].to_i
+          patient_present = (visit_type.match(/patient/i) && ans_given ? true : false)
+          guardian_present = (visit_type.match(/person/i) && ans_given ? true : false)
+
+          if hiv_reception_breakdown[patient_id].blank?
+            demographics = client_data(patient_id)
+            hiv_reception_breakdown[patient_id] = {
+              patient_present: false, guardian_present: false,
+              given_name: demographics['given_name'],
+              family_name: demographics['family_name'],
+              gender: demographics['gender'],
+              birthdate: demographics['birthdate'],
+              arv_number: demographics['arv_number']
+            }
+          end
+
+          hiv_reception_breakdown[patient_id][:patient_present] = patient_present if /patient/i.match?(visit_type)
+          hiv_reception_breakdown[patient_id][:guardian_present] = guardian_present if /person/i.match?(visit_type)
+        end
+
+        hiv_reception_breakdown
+      end
+      # rubocop:enable Metrics/CyclomaticComplexity
+      # rubocop:enable Metrics/PerceivedComplexity
+      # rubocop:enable Metrics/AbcSize
+      # rubocop:enable Metrics/MethodLength
+
+      private
+
+      def client_data(patient_id)
+        ActiveRecord::Base.connection.select_one <<~SQL
+          SELECT
+            n.given_name, n.family_name, p.birthdate, p.gender,
+            i.identifier arv_number, a.value cell_number,
+            s.state_province district, s.county_district ta,
+            s.city_village village
+          FROM person p
+          LEFT JOIN person_name n ON n.person_id = p.person_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_attribute a ON a.person_id = p.person_id
+          AND a.voided = 0 AND a.person_attribute_type_id = 12
+          LEFT JOIN person_address s ON s.person_id = p.person_id
+          AND s.voided = 0 WHERE p.person_id = #{patient_id}
+          GROUP BY p.person_id, DATE(p.date_created)
+          ORDER BY p.person_id, p.date_created;
+        SQL
+      end
+
+      def patient_visits
+        encounter_type = ::EncounterType.find_by_name('HIV RECEPTION')
+
+        ::Observation.joins("INNER JOIN encounter e ON e.encounter_id = obs.encounter_id
+          INNER JOIN concept_name c ON c.concept_id = obs.concept_id")
+                     .where('encounter_type = ? AND (obs_datetime BETWEEN ? AND ?)',
+                            encounter_type.id, @start_date.strftime('%Y-%m-%d 00:00:00'),
+                            @end_date.strftime('%Y-%m-%d 23:59:59'))
+                     .select("e.patient_id, obs.obs_datetime, c.name,
+                  c.concept_id, obs.value_coded").group("DATE(obs.obs_datetime),
+                     e.patient_id, c.concept_id").order('obs_datetime ASC')
+      end
+
+      def missed_appointment?(obs)
+        client_came?(obs.person_id, obs.value_datetime, obs.encounter.encounter_datetime.to_date + 1.day)
+      end
+
+      def client_came?(person_id, value_datetime, day_after_visit_date)
+        # we need to check if the client had a dispensing encounter
+        # check if the client was given arv drugs via the orders table and drug_order table
+        # on the drug_order table check if the quantity column is greater than 0
+        # if the quantity is greater than 0 then the client was given drugs
+        # arv drugs are easily found by ::Drug.arv_drugs
+        value_datetime = value_datetime.to_date + 14.day
+        encounters = ::Encounter.joins(:orders)
+                                .joins("INNER JOIN drug_order d ON d.order_id = orders.order_id AND d.quantity > 0
+                                      AND d.drug_inventory_id IN(#{arv_drugs})")
+                                .where(patient_id: person_id, encounter_type: treatment_encounter)
+                                .where('encounter_datetime BETWEEN ? AND ?',
+                                       day_after_visit_date.strftime('%Y-%m-%d 00:00:00'),
+                                       value_datetime.strftime('%Y-%m-%d 23:59:59'))
+                                .where(orders: { voided: 0 })
+                                .where(voided: 0)
+
+        client_info(person_id, value_datetime - 14.day) if encounters.blank? && client_alive?(person_id, value_datetime)
+      end
+
+      def client_alive?(person_id, value_datetime)
+        # check if the client is alive and doesn't have an adverse outcome
+        result = ActiveRecord::Base.connection.select_one <<~SQL
+          SELECT patient_outcome(#{person_id}, '#{value_datetime.to_date}') outcome;
+        SQL
+
+        result['outcome'].match(/Patient died|Patient transferred out|Treatment stopped/i).blank?
+      end
+
+      def arv_drugs
+        @arv_drugs ||= ::Drug.arv_drugs.pluck(:drug_id).join(',')
+      end
+
+      def treatment_encounter
+        @treatment_encounter ||= ::EncounterType.find_by_name('TREATMENT').id
+      end
+
+      # rubocop:disable Metrics/MethodLength
+      # rubocop:disable Metrics/AbcSize
+      def client_info(patient_id, appointment_date)
+        person = ActiveRecord::Base.connection.select_one <<~SQL
+          SELECT
+            n.given_name, n.family_name, p.birthdate, p.gender,
+            i.identifier arv_number, a.value cell_number,
+            s.state_province district, s.county_district ta,
+            s.city_village village
+          FROM person p
+          LEFT JOIN person_name n ON n.person_id = p.person_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_attribute a ON a.person_id = p.person_id
+          AND a.voided = 0 AND a.person_attribute_type_id = 12
+          LEFT JOIN person_address s ON s.person_id = p.person_id
+          AND s.voided = 0 WHERE p.person_id = #{patient_id}
+          GROUP BY p.person_id, DATE(p.date_created)
+          ORDER BY p.person_id, p.date_created;
+        SQL
+
+        current_outcome = get_current_outcome(patient_id)
+        if current_outcome.match(/died/i) || current_outcome.match(/transfer/i) || current_outcome.match(/stop/i)
+          return nil
+        end
+
+        {
+          given_name: person['given_name'],
+          family_name: person['family_name'],
+          birthdate: person['birthdate'],
+          gender: person['gender'],
+          cell_number: person['cell_number'],
+          district: person['district'],
+          ta: person['ta'],
+          village: person['village'],
+          arv_number: (person['arv_number'].blank? ? 'N/A' : person['arv_number']),
+          appointment_date: appointment_date.to_date,
+          days_missed: days_missed(appointment_date.to_date),
+          current_outcome:,
+          person_id: patient_id
+        }
+      end
+      # rubocop:enable Metrics/MethodLength
+      # rubocop:enable Metrics/AbcSize
+
+      def days_missed(set_date)
+        missed_days = ActiveRecord::Base.connection.select_one <<~SQL
+          SELECT TIMESTAMPDIFF(day, DATE('#{set_date}'), DATE('#{@end_date}')) days;
+        SQL
+
+        missed_days['days'].to_i
+      end
+
+      # rubocop:disable Metrics/MethodLength
+      def eventually_came_on(patient_id, date)
+        data = ActiveRecord::Base.connection.select_one <<~SQL
+          SELECT MIN(encounter_datetime) visit_date FROM encounter
+          WHERE patient_id = #{patient_id}
+          AND encounter_type IN(#{HIV_ENCOUNTERS.join(',')})
+          AND encounter_datetime > '#{date.to_date.strftime('%Y-%m-%d 23:59:59')}';
+        SQL
+
+        begin
+          data['visit_date'].to_date
+        rescue StandardError
+          nil
+        end
+      end
+      # rubocop:enable Metrics/MethodLength
+
+      def concept(name)
+        ::ConceptName.find_by_name name
+      end
+
+      def encounter_type(name)
+        ::EncounterType.find_by_name name
+      end
+
+      def get_current_outcome(patient_id)
+        current_outcome_info = ActiveRecord::Base.connection.select_one <<~SQL
+          SELECT patient_outcome(#{patient_id}, DATE('#{@end_date}')) as outcome;
+        SQL
+
+        current_outcome_info['outcome']
+      end
+
+      def referral_patients
+        ::Observation.where(concept: ::ConceptName.where(name: 'Type of patient').select(:concept_id),
+                            value_coded: ::ConceptName.where("name = 'External consultation' OR name = 'Drug refill'")
+                                                  .select(:concept_id),
+                            person_id: registration_encounters.select(:patient_id))
+                     .where('obs_datetime < DATE(?) + INTERVAL 1 DAY', @end_date)
+                     .distinct(:person_id)
+      end
+
+      def appointment_encounters
+        ::Encounter.where(program: ::Program.where(name: 'HIV PROGRAM'),
+                          type: ::EncounterType.where(name: 'Appointment'))
+      end
+
+      def registration_encounters
+        ::Encounter.where(program: ::Program.where(name: 'HIV PROGRAM'),
+                          type: ::EncounterType.where(name: 'Registration'))
+      end
+    end
+  end
+end
+# rubocop:enable Metrics/ClassLength

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

@@ -0,0 +1,42 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Clinic
+    # Generates a discrepancy report for a clinic
+    class DiscrepancyReport
+      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
+        discrepancy_report
+      end
+
+      private
+
+      def discrepancy_report
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT
+              pbi.drug_id,
+              d.name,
+              d.short_name,
+              psv.verification_date,
+              psv.reason as verification_reason,
+              po_expected.quantity expected_quantity,
+              po.quantity difference,
+              po_expected.quantity + po.quantity as current_quantity,
+              po.transaction_reason as variance_reason
+          FROM pharmacy_stock_verifications psv
+          INNER JOIN pharmacy_obs po ON po.stock_verification_id = psv.id AND po.voided = 0 AND po.obs_group_id IS NULL
+          INNER JOIN pharmacy_batch_items pbi ON pbi.id = po.batch_item_id AND pbi.voided = 0
+          INNER JOIN drug_cms d ON d.drug_inventory_id = pbi.drug_id AND d.voided = 0
+          LEFT JOIN pharmacy_obs po_expected ON po_expected.obs_group_id = po.pharmacy_module_id AND po_expected.voided = 0
+          WHERE psv.verification_date BETWEEN #{@start_date} AND #{@end_date}
+          GROUP BY psv.id
+        SQL
+      end
+    end
+  end
+end

data/app/services/malawi_hiv_program_reports/clinic/docs/hypertension_report.md

@@ -0,0 +1,31 @@
+# Code Documentation
+
+## Summary
+The code snippet is a part of the HypertensionReport class in the Clinic module. It initializes a report structure with nested hashes to store hypertension data based on age groups and gender. It also defines methods to process data and populate the report structure.
+
+## Example Usage
+```ruby
+report = Hypertension::Report.new(start_date: '2021-01-01', end_date: '2021-12-31')
+report.find_report
+```
+ The full namespace
+```ruby
+Clinic::Hypertension::Report.new(start_date: '2021-01-01', end_date: '2021-12-31')
+```
+
+## Code Analysis
+### Inputs
+```start_date``` (String): The start date of the report period.
+```end_date``` (String): The end date of the report period.
+
+## Flow
+The ```init_report``` method is called to initialize the report structure with nested hashes for each age group and gender combination.
+The ```initialize_gender_metrics``` method is called to initialize the metrics hash for each gender.
+The ```process_data``` method is called to process the data and populate the report structure.
+The ```data``` method is called to fetch the necessary data from the database using a SQL query.
+The fetched data is iterated over, and the relevant information is extracted and stored in the report structure.
+The report structure is returned as the result of the ```find_report``` method.
+
+## Outputs
+The output of the ```find_report``` method is the report structure, which is a nested hash containing hypertension data categorized by age groups and gender.
+

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

@@ -0,0 +1,48 @@
+# frozen_string_literal: true
+
+##
+# MER drug dispensation report
+#
+# Captures total number of packs of each drug dispensed in a given time period.
+module MalawiHivProgramReports
+  module Clinic
+    class DrugDispensations
+      attr_reader :start_date, :end_date
+
+      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
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT drug.name AS drug_name,
+                 dispensation.value_numeric AS pack_size,
+                 COUNT(*) AS packs_dispensed
+          FROM obs AS dispensation
+          INNER JOIN encounter
+            ON encounter.encounter_id = dispensation.encounter_id
+            AND 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 = 'Dispensing')
+            AND encounter.voided = 0
+          INNER JOIN orders
+            ON orders.order_id = dispensation.order_id
+            AND orders.start_date BETWEEN #{start_date} AND #{end_date}
+            AND orders.order_type_id IN (SELECT order_type_id FROM order_type WHERE name = 'Drug order')
+            AND orders.voided = 0
+          INNER JOIN drug_order
+            ON drug_order.order_id = orders.order_id
+            AND drug_order.drug_inventory_id IN (SELECT drug_id FROM arv_drug)
+            AND drug_order.quantity > 0
+          INNER JOIN drug
+            ON  drug.drug_id = drug_order.drug_inventory_id
+            AND drug.retired = 0
+          WHERE dispensation.voided = 0
+            AND dispensation.value_numeric > 0
+            AND dispensation.concept_id IN (SELECT concept_id FROM concept_name WHERE name = 'Amount dispensed' AND voided = 0)
+          GROUP BY dispensation.value_numeric
+        SQL
+      end
+    end
+  end
+end

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

@@ -0,0 +1,69 @@
+# frozen_string_literal:true
+
+# Fetches all clients that are not new patients at between the specified period
+
+# Exteranal Consultation Clients
+module MalawiHivProgramReports
+  module Clinic
+    class ExternalConsultationClients
+      include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
+
+      def initialize(start_date:, end_date:, **kwargs)
+        @start_date = start_date.to_date
+        @end_date = end_date.to_date
+        @occupation = kwargs[:occupation]
+      end
+
+      def list
+        other_clients
+      end
+
+      private
+
+      def other_clients
+        ext_consultation_concept_id = ::ConceptName.find_by_name('External consultation').concept_id
+        drug_refill_concept_id = ::ConceptName.find_by_name('Drug refill').concept_id
+        # internal_client_concept_id = ::ConceptName.find_by_name('New patient').concept_id
+        type_of_client_concept_id = ::ConceptName.find_by_name('Type of patient').concept_id
+        npid_identifier_type_id = ::PatientIdentifierType.find_by_name('National ID').id
+
+        possible_clients = ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT
+          	p.person_id patient_id, npid.identifier npid, main.value_coded,
+          	p.birthdate, p.gender, main.obs_datetime, n.family_name, n.given_name, main.value_coded
+          FROM obs main
+          INNER JOIN person p ON p.person_id = main.person_id
+          LEFT JOIN patient_identifier npid ON npid.patient_id = p.person_id
+          LEFT JOIN (#{current_occupation_query}) a ON a.person_id = p.person_id
+          AND npid.identifier_type = #{npid_identifier_type_id} AND npid.voided = 0
+          LEFT JOIN person_name n ON n.person_id = p.person_id AND n.voided = 0
+          INNER JOIN (
+          	SELECT person_id, MAX(obs_datetime) as obs_datetime, concept_id FROM obs
+          	WHERE concept_id = #{type_of_client_concept_id}
+          	AND voided = 0
+          	AND obs.obs_datetime BETWEEN "#{@start_date.strftime('%Y-%m-%d 00:00:00')}"
+          	AND "#{@end_date.strftime('%Y-%m-%d 23:59:59')}"
+          	GROUP BY person_id
+          ) sub_group ON main.person_id = sub_group.person_id
+          AND main.obs_datetime = sub_group.obs_datetime
+          AND main.concept_id = sub_group.concept_id
+          WHERE main.value_coded IN (#{ext_consultation_concept_id}, #{drug_refill_concept_id}) #{%w[Military Civilian].include?(@occupation) ? 'AND' : ''} #{occupation_filter(occupation: @occupation, field_name: 'value', table_name: 'a', include_clause: false)}
+          ORDER BY n.date_created DESC
+        SQL
+
+        (possible_clients || []).map do |client|
+          {
+            patient_id: client['patient_id'].to_i,
+            patient_type: client['value_coded'] == ext_consultation_concept_id ? 'External consultation' : 'Drug refill',
+            npid: client['npid'],
+            birthdate: client['birthdate'].to_date,
+            gender: client['gender'],
+            given_name: client['given_name'],
+            family_name: client['family_name'],
+            date_set: client['obs_datetime'].to_date
+          }
+        end
+      end
+    end
+  end
+end