malawi_hiv_program_reports 1.0.1 → 1.0.2

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

@@ -0,0 +1,414 @@
+# frozen_string_literal: true
+
+module MalawiHivProgramReports
+  module Pepfar
+    class ViralLoadCoverage
+      attr_reader :start_date, :end_date
+
+      include Utils
+
+      def initialize(**params)
+        @start_date = params[:start_date]&.to_date
+        raise ::InvalidParameterError, 'start_date is required' unless @start_date
+
+        @end_date = params[:end_date]&.to_date || (@start_date + 12.months)
+        raise ::InvalidParameterError, "start_date can't be greater than end_date" if @start_date > @end_date
+
+        @tx_curr_definition = params.fetch(:tx_curr_definition, 'pepfar')&.downcase
+        unless %w[moh pepfar].include?(@tx_curr_definition)
+          raise ::InvalidParameterError, "tx_curr_definition can only moh or pepfar not #{@tx_curr_definition}"
+        end
+
+        @rebuild_outcomes = params.fetch(:rebuild_outcomes, 'true')&.casecmp?('true')
+        @type = params.fetch(:application, 'poc')
+      end
+
+      def find_report
+        report = init_report
+
+        case @type
+        when /poc/i then build_poc_report(report)
+        when /emastercard/i then build_emastercard_report(report)
+        else raise ::InvalidParameterError, "Report type must be one of [poc, emastercard] not #{@type}"
+        end
+
+        report
+      end
+
+      def vl_maternal_status(patient_list)
+        pregnant = pregnant_women(patient_list).map { |woman| woman['person_id'].to_i }
+        feeding = breast_feeding(patient_list - pregnant).map { |woman| woman['person_id'].to_i }
+
+        {
+          FP: pregnant,
+          FBf: feeding
+        }
+      end
+
+      private
+
+      def pregnant_women(patient_list)
+        encounter_types = ::EncounterType.where(name: ['HIV CLINIC CONSULTATION', 'HIV STAGING'])
+                                         .select(:encounter_type_id)
+
+        pregnant_concepts = ::ConceptName.where(name: ['Is patient pregnant?', 'patient pregnant'])
+                                         .select(:concept_id)
+
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT obs.person_id,obs.value_coded
+          FROM obs obs
+          INNER JOIN encounter enc
+            ON enc.encounter_id = obs.encounter_id
+            AND enc.voided = 0
+            AND enc.encounter_type IN (#{encounter_types.to_sql})
+          INNER JOIN temp_earliest_start_date e
+            ON e.patient_id = enc.patient_id
+            AND LEFT(e.gender, 1) = 'F'
+          INNER JOIN temp_patient_outcomes
+            ON temp_patient_outcomes.patient_id = e.patient_id
+            AND temp_patient_outcomes.cum_outcome = 'On antiretrovirals'
+          INNER JOIN (
+            SELECT person_id, MAX(obs_datetime) AS obs_datetime
+            FROM obs
+            INNER JOIN encounter
+              ON encounter.encounter_id = obs.encounter_id
+              AND encounter.encounter_type IN (#{encounter_types.to_sql})
+              AND encounter.voided = 0
+            WHERE concept_id IN (#{pregnant_concepts.to_sql})
+              AND obs_datetime BETWEEN DATE('#{@start_date}') AND DATE('#{@end_date}') + INTERVAL 1 DAY
+              AND obs.voided = 0
+            GROUP BY person_id
+          ) AS max_obs
+            ON max_obs.person_id = obs.person_id
+            AND max_obs.obs_datetime = obs.obs_datetime
+          WHERE obs.concept_id IN (#{pregnant_concepts.to_sql})
+            AND obs.voided = 0
+            AND obs.person_id IN (#{patient_list.join(',')})
+          GROUP BY obs.person_id
+          HAVING obs.value_coded = 1065
+          ORDER BY obs.obs_datetime DESC;
+        SQL
+      end
+
+      def breast_feeding(patient_list)
+        encounter_types = ::EncounterType.where(name: ['HIV CLINIC CONSULTATION', 'HIV STAGING'])
+                                         .select(:encounter_type_id)
+
+        breastfeeding_concepts = ::ConceptName.where(name: ['Breast feeding?', 'Breast feeding', 'Breastfeeding'])
+                                              .select(:concept_id)
+
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT obs.person_id,obs.value_coded
+          FROM obs
+          INNER JOIN encounter enc
+            ON enc.encounter_id = obs.encounter_id
+            AND enc.voided = 0
+            AND enc.encounter_type IN (#{encounter_types.to_sql})
+          INNER JOIN temp_earliest_start_date e
+            ON e.patient_id = enc.patient_id
+            AND LEFT(e.gender, 1) = 'F'
+          INNER JOIN temp_patient_outcomes
+            ON temp_patient_outcomes.patient_id = e.patient_id
+            AND temp_patient_outcomes.cum_outcome = 'On antiretrovirals'
+          INNER JOIN (
+            SELECT person_id, MAX(obs_datetime) AS obs_datetime
+            FROM obs
+            INNER JOIN encounter
+            ON encounter.encounter_id = obs.encounter_id
+            AND encounter.encounter_type IN (#{encounter_types.to_sql})
+            AND encounter.voided = 0
+            WHERE person_id IN (SELECT patient_id FROM temp_patient_outcomes WHERE cum_outcome = 'On antiretrovirals')
+            AND concept_id IN (#{breastfeeding_concepts.to_sql})
+            AND obs.voided = 0
+            AND obs_datetime < DATE('#{end_date}') + INTERVAL 1 DAY
+            GROUP BY person_id
+          ) AS max_obs
+            ON max_obs.person_id = obs.person_id
+            AND max_obs.obs_datetime = obs.obs_datetime
+          WHERE obs.person_id = e.patient_id
+          AND obs.person_id IN (#{patient_list.join(',')})
+          AND obs.obs_datetime BETWEEN DATE("#{@start_date}") AND DATE("#{@end_date}") + INTERVAL 1 DAY
+          AND obs.concept_id IN (#{breastfeeding_concepts.to_sql})
+          AND obs.voided = 0
+          GROUP BY obs.person_id
+          HAVING obs.value_coded = 1065
+          ORDER BY obs.obs_datetime DESC;
+        SQL
+      end
+
+      def build_poc_report(report)
+        find_patients_alive_and_on_art.each { |patient| report[patient['age_group']][:tx_curr] << patient }
+        find_patients_due_for_initial_viral_load.each do |patient|
+          report[patient['age_group']][:due_for_vl] << patient
+        end
+        find_patients_with_overdue_viral_load.each { |patient| report[patient['age_group']][:due_for_vl] << patient }
+        load_patient_tests_into_report(report)
+      end
+
+      def build_emastercard_report(report)
+        find_patients_alive_and_on_art.each { |patient| report[patient['age_group']][:tx_curr] << patient }
+        load_emastercard_results_into_report(report)
+      end
+
+      def init_report
+        pepfar_age_groups.each_with_object({}) do |age_group, report|
+          report[age_group] = {
+            tx_curr: [],
+            due_for_vl: [],
+            drawn: { routine: [], targeted: [] },
+            high_vl: { routine: [], targeted: [] },
+            low_vl: { routine: [], targeted: [] }
+          }
+        end
+      end
+
+      def load_patient_tests_into_report(report)
+        find_patients_with_viral_load.each do |patient|
+          age_group = patient['age_group']
+          reason_for_test = (patient['reason_for_test'] || 'Routine').match?(/Routine/i) ? :routine : :targeted
+
+          report[age_group][:drawn][reason_for_test] << patient
+          next unless patient['result_value']
+
+          if patient['result_value'].casecmp?('LDL')
+            report[age_group][:low_vl][reason_for_test] << patient
+          elsif patient['result_value'].to_i < 1000
+            report[age_group][:low_vl][reason_for_test] << patient
+          else
+            report[age_group][:high_vl][reason_for_test] << patient
+          end
+        end
+      end
+
+      def load_emastercard_results_into_report(report)
+        find_emastercard_patient_results.each do |patient|
+          if patient['result_value'] < 1000
+            report[patient['age_group']][:low_vl][:routine] << patient
+          else
+            report[patient['age_group']][:high_vl][:routine] << patient
+          end
+        end
+      end
+
+      def find_patients_alive_and_on_art
+        patients = MalawiHivProgramReports::Clinic::PatientsAliveAndOnTreatment
+                   .new(start_date:, end_date:, outcomes_definition: @tx_curr_definition, rebuild_outcomes: @rebuild_outcomes)
+                   .query
+        pepfar_patient_drilldown_information(patients, end_date).map do |patient|
+          {
+            'patient_id' => patient.patient_id,
+            'arv_number' => patient.arv_number,
+            'age_group' => patient.age_group,
+            'birthdate' => patient.birthdate,
+            'gender' => patient.gender
+          }
+        end
+      end
+
+      ##
+      # Selects patients whose last viral load should have expired before the end of the reporting period.
+      #
+      # Patients returned by this aren't necessarily due for viral load, they may have
+      # their current milestone delayed. So extra processing on the patients is required
+      # to filter out the patients with delayed milestones.
+      def find_patients_with_overdue_viral_load
+        # Find all patients whose last order's expires in or before the reporting period (making them due)
+        # or patients whose first order comes at 6 months or greater after starting ART.
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT orders.patient_id,
+                 disaggregated_age_group(patient.birthdate,
+                                                DATE(#{ActiveRecord::Base.connection.quote(end_date)})) AS age_group,
+                 patient.birthdate,
+                 patient.gender,
+                 patient_identifier.identifier AS arv_number
+          FROM orders
+          INNER JOIN order_type
+            ON order_type.order_type_id = orders.order_type_id
+            AND order_type.name = 'Lab'
+            AND order_type.retired = 0
+          INNER JOIN concept_name
+            ON concept_name.concept_id = orders.concept_id
+            AND concept_name.name IN ('Blood', 'DBS (Free drop to DBS card)', 'DBS (Using capillary tube)')
+            AND concept_name.voided = 0
+          INNER JOIN (
+            /* Get the latest order dates for each patient */
+            SELECT orders.patient_id, MAX(orders.start_date) AS start_date
+            FROM orders
+            INNER JOIN order_type
+              ON order_type.order_type_id = orders.order_type_id
+              AND order_type.name = 'Lab'
+              AND order_type.retired = 0
+            INNER JOIN concept_name
+              ON concept_name.concept_id = orders.concept_id
+              AND concept_name.name IN ('Blood', 'DBS (Free drop to DBS card)', 'DBS (Using capillary tube)')
+              AND concept_name.voided = 0
+            WHERE orders.start_date <= DATE(#{ActiveRecord::Base.connection.quote(end_date)}) - INTERVAL 12 MONTH
+              AND orders.voided = 0
+            GROUP BY orders.patient_id
+          ) AS latest_patient_order_date
+            ON latest_patient_order_date.patient_id = orders.patient_id
+            AND latest_patient_order_date.start_date = orders.start_date
+          INNER JOIN temp_earliest_start_date AS patient ON patient.patient_id = orders.patient_id
+          INNER JOIN temp_patient_outcomes AS outcomes
+            ON outcomes.patient_id = patient.patient_id
+            AND outcomes.cum_outcome = 'On antiretrovirals'
+          LEFT JOIN patient_identifier
+            ON patient_identifier.patient_id = orders.patient_id
+            AND patient_identifier.identifier_type IN (#{pepfar_patient_identifier_type.to_sql})
+            AND patient_identifier.voided = 0
+          WHERE orders.start_date < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) - INTERVAL 12 MONTH
+          GROUP BY orders.patient_id
+        SQL
+      end
+
+      ##
+      # Returns all patients that have been on ART for at least 6 months and have never had a Viral Load.
+      def find_patients_due_for_initial_viral_load
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT patient.patient_id,
+                 disaggregated_age_group(patient.birthdate,
+                                                DATE(#{ActiveRecord::Base.connection.quote(end_date)})) AS age_group,
+                 patient.birthdate,
+                 patient.gender,
+                 patient_identifier.identifier AS arv_number
+          FROM temp_earliest_start_date AS patient
+          INNER JOIN temp_patient_outcomes AS outcomes
+            ON outcomes.patient_id = patient.patient_id
+            AND outcomes.cum_outcome = 'On antiretrovirals'
+          INNER JOIN patient_identifier
+            ON patient_identifier.patient_id = patient.patient_id
+            AND patient_identifier.identifier_type IN (#{pepfar_patient_identifier_type.to_sql})
+            AND patient_identifier.voided = 0
+          WHERE patient.patient_id NOT IN (
+            SELECT DISTINCT orders.patient_id FROM orders
+            INNER JOIN order_type ON order_type.order_type_id = orders.order_type_id AND order_type.name = 'Lab'
+            INNER JOIN obs ON orders.order_id = obs.order_id AND obs.voided = 0
+            INNER JOIN concept_name ON concept_name.concept_id = obs.concept_id AND concept_name.name = 'Test type' AND concept_name.voided = 0
+            INNER JOIN concept_name AS test_name ON test_name.concept_id = obs.value_coded AND test_name.name = 'HIV Viral Load' AND test_name.voided = 0
+            WHERE orders.start_date <= DATE(#{ActiveRecord::Base.connection.quote(end_date)}) - INTERVAL 12 MONTH
+              AND orders.concept_id IN (SELECT concept_id FROM concept_name WHERE name IN ('Blood', 'DBS (Free drop to DBS card)', 'DBS (Using capillary tube)'))
+              AND orders.voided = 0
+          ) AND patient.earliest_start_date <= DATE(#{ActiveRecord::Base.connection.quote(end_date)}) - INTERVAL 6 MONTH
+          GROUP BY patient.patient_id
+        SQL
+      end
+
+      ##
+      # Find all patients that are on treatment with at least one VL before end of reporting period.
+      def find_patients_with_viral_load
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT orders.patient_id,
+                 disaggregated_age_group(patient.birthdate,
+                                                DATE(#{ActiveRecord::Base.connection.quote(end_date)})) AS age_group,
+                 patient.birthdate,
+                 patient.gender,
+                 patient_identifier.identifier AS arv_number,
+                 orders.start_date AS order_date,
+                 COALESCE(orders.discontinued_date, orders.start_date) AS sample_draw_date,
+                 COALESCE(reason_for_test_value.name, reason_for_test.value_text) AS reason_for_test,
+                 result.value_modifier AS result_modifier,
+                 COALESCE(result.value_numeric, result.value_text) AS result_value
+          FROM orders
+          INNER JOIN order_type
+            ON order_type.order_type_id = orders.order_type_id
+            AND order_type.name = 'Lab'
+            AND order_type.retired = 0
+          INNER JOIN concept_name
+            ON concept_name.concept_id = orders.concept_id
+            AND concept_name.name IN ('Blood', 'DBS (Free drop to DBS card)', 'DBS (Using capillary tube)')
+            AND concept_name.voided = 0
+          LEFT JOIN obs AS reason_for_test
+            ON reason_for_test.order_id = orders.order_id
+            AND reason_for_test.concept_id IN (SELECT concept_id FROM concept_name WHERE name LIKE 'Reason for test' AND voided = 0)
+            AND reason_for_test.voided = 0
+          LEFT JOIN concept_name AS reason_for_test_value
+            ON reason_for_test_value.concept_id = reason_for_test.value_coded
+            AND reason_for_test_value.voided = 0
+          LEFT JOIN obs AS result
+            ON result.order_id = orders.order_id
+            AND result.concept_id IN (SELECT concept_id FROM concept_name WHERE name LIKE 'HIV Viral load' AND voided = 0)
+            AND result.voided = 0
+            AND (result.value_text IS NOT NULL OR result.value_numeric IS NOT NULL)
+          INNER JOIN (
+            /* Get the latest order dates for each patient */
+            SELECT orders.patient_id, MAX(orders.start_date) AS start_date
+            FROM orders
+            INNER JOIN order_type
+              ON order_type.order_type_id = orders.order_type_id
+              AND order_type.name = 'Lab'
+              AND order_type.retired = 0
+            INNER JOIN concept_name
+              ON concept_name.concept_id = orders.concept_id
+              AND concept_name.name IN ('Blood', 'DBS (Free drop to DBS card)', 'DBS (Using capillary tube)')
+              AND concept_name.voided = 0
+            WHERE orders.start_date < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) + INTERVAL 1 DAY
+              AND orders.voided = 0
+            GROUP BY orders.patient_id
+          ) AS latest_patient_order_date
+            ON latest_patient_order_date.patient_id = orders.patient_id
+            AND latest_patient_order_date.start_date = orders.start_date
+          INNER JOIN temp_earliest_start_date AS patient ON patient.patient_id = orders.patient_id
+          INNER JOIN temp_patient_outcomes AS outcomes
+            ON outcomes.patient_id = patient.patient_id
+            AND outcomes.cum_outcome = 'On antiretrovirals'
+          LEFT JOIN patient_identifier
+            ON patient_identifier.patient_id = orders.patient_id
+            AND patient_identifier.identifier_type IN (#{pepfar_patient_identifier_type.to_sql})
+            AND patient_identifier.voided = 0
+          WHERE orders.start_date < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) + INTERVAL 1 DAY
+            AND orders.start_date >= DATE(#{ActiveRecord::Base.connection.quote(start_date)})
+          GROUP BY orders.patient_id
+        SQL
+      end
+
+      ##
+      # Returns a Relation of all viral load tests.
+      def find_viral_load_tests
+        ::Lab::LabTest.where(value_coded: concept('Viral load'))
+      end
+
+      def find_emastercard_patient_results
+        ActiveRecord::Base.connection.select_all <<~SQL
+          SELECT obs.person_id AS patient_id,
+                 patient_identifier.identifier AS arv_number,
+                 patient.birthdate,
+                 patient.gender,
+                 disaggregated_age_group(patient.birthdate, #{ActiveRecord::Base.connection.quote(end_date)}) AS age_group,
+                 obs.value_numeric AS result_value
+          FROM obs
+          INNER JOIN encounter ON encounter.encounter_id = obs.encounter_id AND encounter.voided = 0
+          INNER JOIN encounter_type ON encounter_type.encounter_type_id = encounter.encounter_type AND encounter_type.name = 'Lab'
+          INNER JOIN temp_earliest_start_date AS patient ON patient.patient_id = obs.person_id
+          INNER JOIN temp_patient_outcomes
+            ON temp_patient_outcomes.patient_id = obs.person_id
+            AND temp_patient_outcomes.cum_outcome = 'On antiretrovirals'
+          LEFT JOIN patient_identifier
+            ON patient_identifier.patient_id = obs.person_id
+            AND patient_identifier.voided = 0
+            AND patient_identifier.identifier_type IN (#{pepfar_patient_identifier_type.to_sql})
+          INNER JOIN (
+            SELECT obs.person_id, MAX(obs.obs_datetime) AS obs_datetime
+            FROM obs
+            INNER JOIN encounter ON encounter.encounter_id = obs.encounter_id AND encounter.voided = 0
+            INNER JOIN encounter_type ON encounter_type.encounter_type_id = encounter.encounter_type AND encounter_type.name = 'Lab'
+            WHERE obs.concept_id IN (#{concept('Viral load').to_sql})
+              AND obs.obs_datetime > DATE(#{ActiveRecord::Base.connection.quote(start_date)}) - INTERVAL 1 DAY
+              AND obs.obs_datetime < DATE(#{ActiveRecord::Base.connection.quote(end_date)}) + INTERVAL 1 DAY
+              AND obs.voided = 0
+            GROUP BY obs.person_id
+          ) AS latest_results
+            ON latest_results.person_id = obs.person_id
+            AND latest_results.obs_datetime = obs.obs_datetime
+          WHERE obs.concept_id IN (#{concept('Viral load').to_sql})
+            AND obs.value_numeric IS NOT NULL
+            AND obs.voided = 0
+          GROUP BY obs.person_id
+        SQL
+      end
+
+      def concept(name)
+        ::ConceptName.where(name:).select(:concept_id)
+      end
+    end
+  end
+end