malawi_hiv_program_reports 1.0.1 → 1.0.2

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

@@ -0,0 +1,235 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Moh
+    ##
+    # Patients newly initiated on TPT disaggregated by regimen type and age group.
+    #
+    # Newly initiated is defined as patients who have received TPT for the first
+    # time in the reporting period or patients who have gone on a TPT course
+    # break for a period that is at least 9 months long before restarting TPT
+    # in the current reporting period.
+    # rubocop:disable Metrics/ClassLength
+    class TptNewlyInitiated
+      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)
+        @occupation = kwargs[:occupation]
+        @location = kwargs[:location]
+        @adapter = ActiveRecord::Base.connection.adapter_name.downcase
+      end
+
+      def find_report
+        report = init_report
+        newly_initiated_on_tpt.each do |tpt, patients|
+          patients.each do |patient|
+            patient_id = patient['patient_id']
+            person = ActiveRecord::Base.connection.select_one <<~SQL
+              SELECT disaggregated_age_group(birthdate, DATE('#{end_date.to_date}')) AS age_group,
+              patient_identifier.identifier AS arv_number, person.*
+              FROM person
+              LEFT JOIN patient_identifier ON patient_identifier.patient_id = person.person_id
+              AND patient_identifier.identifier_type IN (SELECT patient_identifier_type_id FROM patient_identifier_type
+              WHERE name = 'ARV Number') AND patient_identifier.voided = 0
+              WHERE person_id = #{patient_id} LIMIT 1;
+            SQL
+            age_group = person['age_group']
+            gender = person['gender']&.strip&.first&.upcase || 'Unknown'
+            # course = patient_on_3hp?(patient) ? '3HP' : '6H'
+
+            report[age_group][tpt][gender] << {
+              patient_id: person['person_id'],
+              birthdate: person['birthdate'],
+              arv_number: person['arv_number'],
+              gender:,
+              dispensation_date: dispensation_date(patient_id, patient['drug_concepts']),
+              art_start_date: patient['earliest_start_date'],
+              tpt_start_date: patient['tpt_start_date']
+            }
+          end
+        end
+        report['Location'] = Location.current.city_village
+        report
+      end
+
+      private
+
+      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
+
+      def dispensation_date(patient_id, concept_ids)
+        order = ActiveRecord::Base.connection.select_one <<~SQL
+          SELECT MIN(orders.start_date) start_date FROM orders
+          INNER JOIN drug_order
+            ON drug_order.order_id = orders.order_id
+            AND drug_order.quantity > 0  /* This implies that a dispensation was made */
+          INNER JOIN drug
+            ON drug.drug_id = drug_order.drug_inventory_id
+            AND drug.concept_id IN(#{concept_ids})
+          INNER JOIN encounter ON encounter.encounter_id = orders.encounter_id
+          AND encounter.program_id = 1
+          WHERE DATE(orders.start_date) BETWEEN '#{start_date.to_date}' AND '#{end_date.to_date}'
+          AND orders.voided = 0 AND orders.patient_id = #{patient_id};
+        SQL
+
+        order['start_date'].to_date
+      end
+
+      def init_report
+        AGE_GROUPS.each_with_object({}) do |age_group, report|
+          report[age_group] = {
+            '3HP_new' => { 'M' => [], 'F' => [], 'Unknown' => [] },
+            '6H_new' => { 'M' => [], 'F' => [], 'Unknown' => [] },
+            '3HP_prev' => { 'M' => [], 'F' => [], 'Unknown' => [] },
+            '6H_prev' => { 'M' => [], 'F' => [], 'Unknown' => [] }
+          }
+        end
+      end
+
+      def patient_on_3hp?(patient)
+        patient['drug_concepts'].split(',').collect(&:to_i).include?(rifapentine_concept.concept_id)
+      end
+
+      def rifapentine_concept
+        @rifapentine_concept ||= ::ConceptName.find_by!(name: 'Rifapentine')
+      end
+
+      def newly_initiated_on_tpt
+        tpt = Cohort::Tpt.new(start_date: start_date.to_date, end_date: end_date.to_date, occupation: @occupation,
+                              location: @location)
+        data = {}
+        three_hp = tpt.newly_initiated_on_3hp
+        ipt = tpt.newly_initiated_on_ipt
+        data['3HP_new'] = three_hp.select do |record|
+          record['earliest_start_date'].to_date > end_date.to_date - 3.month
+        end
+        data['6H_new'] = ipt.select { |record| record['earliest_start_date'].to_date > end_date.to_date - 3.month }
+        data['3HP_prev'] = three_hp.select do |record|
+          record['earliest_start_date'].to_date <= end_date.to_date - 3.month
+        end
+        data['6H_prev'] = ipt.select { |record| record['earliest_start_date'].to_date <= end_date.to_date - 3.month }
+        data
+      end
+
+      def newly_initiated_on_tpt_old
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT patient_program.patient_id,
+                 disaggregated_age_group(person.birthdate, DATE(#{end_date})) AS age_group,
+                 DATE(prescription_encounter.encounter_datetime) AS prescription_date,
+                 person_name.given_name,
+                 person_name.family_name,
+                 person.birthdate,
+                 person.gender,
+                 patient_identifier.identifier AS arv_number,
+                 GROUP_CONCAT(DISTINCT orders.concept_id SEPARATOR ',') AS drug_concepts
+          FROM person
+          LEFT JOIN person_name
+            ON person_name.person_id = person.person_id
+            AND person_name.voided = 0
+          LEFT JOIN patient_identifier
+            ON patient_identifier.patient_id = person.person_id
+            AND patient_identifier.identifier_type IN (SELECT patient_identifier_type_id FROM patient_identifier_type WHERE name = 'ARV Number')
+            AND patient_identifier.voided = 0
+          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')
+          INNER JOIN encounter AS prescription_encounter
+            ON prescription_encounter.patient_id = person.person_id
+            AND prescription_encounter.encounter_type IN (SELECT encounter_type_id FROM encounter_type WHERE name = 'Treatment')
+            AND prescription_encounter.program_id IN (SELECT program_id FROM program WHERE name = 'HIV PROGRAM')
+            AND prescription_encounter.encounter_datetime >= #{start_date}
+            AND prescription_encounter.encounter_datetime < DATE(#{end_date}) + INTERVAL 1 DAY
+            AND prescription_encounter.voided = 0
+          INNER JOIN orders AS orders
+            ON orders.encounter_id = prescription_encounter.encounter_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 < DATE(#{end_date}) + INTERVAL 1 DAY
+            AND orders.voided = 0
+          INNER JOIN drug_order
+            ON drug_order.order_id = orders.order_id
+            AND drug_order.quantity > 0  /* This implies that a dispensation was made */
+          INNER JOIN drug
+            ON drug.drug_id = drug_order.drug_inventory_id
+          INNER JOIN concept_name AS tpt_drug_concepts
+            ON tpt_drug_concepts.concept_id = drug.concept_id
+            AND tpt_drug_concepts.name IN ('Rifapentine', 'Isoniazid')
+            AND tpt_drug_concepts.voided = 0
+          WHERE patient_program.patient_id NOT IN (
+            /* Filter out patients who received TPT before current reporting period */
+            SELECT DISTINCT patient_program.patient_id
+            FROM patient_program
+            INNER JOIN encounter AS prescription_encounter
+              ON prescription_encounter.patient_id = patient_program.patient_id
+              AND prescription_encounter.encounter_type IN (SELECT encounter_type_id FROM encounter_type WHERE name = 'Treatment')
+              AND prescription_encounter.program_id = (SELECT program_id FROM program WHERE name = 'HIV PROGRAM' LIMIT 1)
+              AND prescription_encounter.voided = 0
+            INNER JOIN orders
+              ON orders.encounter_id = prescription_encounter.encounter_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}
+              /* Re-initiates defined as those who stopped TPT for a period of at least 9 months
+                 and have restarted TPT are also included in the report */
+              AND orders.start_date >= DATE(#{start_date}) - INTERVAL 9 MONTH
+              AND orders.voided = 0
+            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')
+              AND tpt_drug_concepts.voided = 0
+            INNER JOIN drug_order AS drug_order
+              ON drug_order.order_id = orders.order_id
+              AND drug_order.quantity > 0
+            WHERE patient_program.program_id IN (SELECT program_id FROM program WHERE name = 'HIV PROGRAM')
+          ) AND patient_program.patient_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 patient_program.patient_id
+        SQL
+      end
+    end
+    # rubocop:enable Metrics/ClassLength
+  end
+end

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

@@ -0,0 +1,25 @@
+module MalawiHivProgramReports
+  module Pepfar
+    class DefaulterList
+
+        attr_reader :start_date, :end_date, :location
+
+        def initialize(start_date:, end_date:, **kwargs)
+            @start_date = start_date
+            @end_date = end_date
+            @location = kwargs[:location]
+        end
+
+        def find_report
+            MalawiHivProgramReports::Moh::Cohort.new(
+                                        type: 'defaulter_list',
+                                        location: @location,
+                                        name: 'defaulter_list',
+                                        start_date: start_date,
+                                        end_date: end_date
+                                    ).defaulter_list('pepfar')
+        end
+
+    end
+  end
+end

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

@@ -0,0 +1,29 @@
+module MalawiHivProgramReports
+  module Pepfar
+    # rubocop:disable Metrics/ClassLength
+    class MaternalStatus
+        include Utils
+        include MalawiHivProgramReports::Utils::CommonSqlQueryUtils
+        include MalawiHivProgramReports::Adapters::Moh::Custom
+        include MalawiHivProgramReports::Utils::ModelUtils
+        attr_reader :start_date, :end_date, :location
+
+      def initialize(start_date:, end_date:, **kwargs)
+        @start_date = start_date&.to_date
+        raise InvalidParameterError, 'start_date is required' unless @start_date
+
+        @end_date = end_date&.to_date || @start_date + 12.months
+        raise InvalidParameterError, "start_date can't be greater than end_date" if @start_date > @end_date
+
+        @occupation = kwargs.delete(:occupation)
+        @type = kwargs.delete(:application)
+        @location = kwargs.delete(:location)
+        @patient_ids = kwargs.delete(:patient_ids)&.split(',') || []
+      end
+
+      def find_report
+        MalawiHivProgramReports::Pepfar::ViralLoadCoverage2.new(tx_curr_definition: 'pepfar', start_date: @start_date, end_date: @end_date, location: @location).vl_maternal_status(@patient_ids)
+      end
+    end
+  end
+end

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

@@ -0,0 +1,45 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Pepfar
+    # this module returns all the patient records on when
+    # when the patient started ART
+    # plus the last viral load result
+    class PatientStartVl
+
+      attr_reader :start_date, :end_date, :location, :patient_ids
+
+      include Utils
+      include MalawiHivProgramReports::Adapters::Moh::Custom
+
+      def initialize(start_date:, end_date:, **kwargs)
+        @start_date = start_date
+        @end_date = end_date
+        @location = kwargs[:location]
+        @patient_ids = kwargs[:patient_ids]
+        raise InvalidParameterError, 'Patient IDs are required' if patient_ids.blank?
+      end
+
+      def find_report
+        get_patients_last_vl_and_latest_result
+      end
+
+      def get_patients_last_vl_and_latest_result
+        ids = patient_ids.split(',')
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT p.person_id AS patient_id,
+          patient_start_date(p.person_id) AS art_start_date,
+          p.birthdate AS birthdate,
+          p.gender,
+          MIN(pi.identifier)
+          FROM person p
+          LEFT JOIN patient_identifier pi ON pi.patient_id = p.person_id AND pi.voided = 0 AND pi.identifier_type = 4
+          WHERE p.voided = 0
+          AND #{in_manager(column: 'p.person_id', values: ids)}
+          #{site_manager(operator: 'AND', column: 'p.site_id', location: location)}
+          GROUP BY p.person_id, p.birthdate, p.gender
+        SQL
+      end
+    end
+  end
+end