mahis_emr_api_lab 1.2.0

data/app/services/lab/lims/api/mysql_api.rb

@@ -0,0 +1,316 @@
+# frozen_string_literal: true
+
+module Lab
+  module Lims
+    module Api
+      class MysqlApi
+        def self.start
+          instance = MysqlApi.new
+          orders_processed = 0
+          instance.consume_orders(from: 0, limit: 1000) do |order|
+            puts "Order ##{orders_processed}"
+            pp order
+            orders_processed += 1
+            puts
+          end
+        end
+
+        def initialize(processes: 1, on_merge_processes: nil)
+          @processes = processes
+          @on_merge_processes = on_merge_processes
+          @mysql_connection_pool = {}
+        end
+
+        def multiprocessed?
+          @processes > 1
+        end
+
+        def consume_orders(from: nil, limit: 1000)
+          loop do
+            specimens_to_process = specimens(from, limit)
+            break if specimens_to_process.size.zero?
+
+            processes = multiprocessed? ? @processes : 0
+            on_merge_processes = ->(_item, index, _result) { @on_merge_processes&.call(from + index) }
+
+            Parallel.map(specimens_to_process, in_processes: processes, finish: on_merge_processes) do |specimen|
+              User.current ||= Utils.lab_user
+
+              tests = specimen_tests(specimen['specimen_id'])
+              results = tests.each_with_object({}) do |test, object|
+                object[test['test_name']] = test_results(test['test_id'])
+              end
+
+              dto = make_order_dto(
+                specimen: specimen,
+                patient: specimen_patient(specimen['specimen_id']),
+                test_results: results,
+                specimen_status_trail: specimen_status_trail(specimen['specimen_id']),
+                test_status_trail: tests.each_with_object({}) do |test, trails|
+                  trails[test['test_name']] = test_status_trail(test['test_id'])
+                end
+              )
+
+              yield dto, OpenStruct.new(last_seq: from)
+            end
+
+            from += limit
+          end
+        end
+
+        def parallel_map(items, on_merge: nil, &block); end
+
+        private
+
+        def specimens(start_id, limit)
+          query = <<~SQL
+            SELECT specimen.id AS specimen_id,
+                   specimen.couch_id AS doc_id,
+                   specimen_types.name AS specimen_name,
+                   specimen.tracking_number,
+                   specimen.priority,
+                   specimen.target_lab,
+                   specimen.sending_facility,
+                   specimen.drawn_by_id,
+                   specimen.drawn_by_name,
+                   specimen.drawn_by_phone_number,
+                   specimen.ward_id,
+                   specimen_statuses.name AS specimen_status,
+                   specimen.district,
+                   specimen.date_created AS order_date
+            FROM specimen
+            INNER JOIN specimen_types ON specimen_types.id = specimen.specimen_type_id
+            INNER JOIN specimen_statuses ON specimen_statuses.id = specimen.specimen_status_id
+          SQL
+
+          query = "#{query} WHERE specimen.id > #{sql_escape(start_id)}" if start_id
+          query = "#{query} LIMIT #{limit.to_i}"
+
+          Rails.logger.debug(query)
+          query(query)
+        end
+
+        ##
+        # Pull patient associated with given specimen
+        def specimen_patient(specimen_id)
+          results = query <<~SQL
+            SELECT patients.patient_number AS nhid,
+                   patients.name,
+                   patients.gender,
+                   DATE(patients.dob) AS birthdate
+            FROM patients
+            INNER JOIN tests
+              ON tests.patient_id = patients.id
+              AND tests.specimen_id = #{sql_escape(specimen_id)}
+            LIMIT 1
+          SQL
+
+          results.first
+        end
+
+        def specimen_tests(specimen_id)
+          query <<~SQL
+            SELECT tests.id AS test_id,
+                   test_types.name AS test_name,
+                   tests.created_by AS drawn_by_name
+            FROM tests
+            INNER JOIN test_types ON test_types.id = tests.test_type_id
+            WHERE tests.specimen_id = #{sql_escape(specimen_id)}
+          SQL
+        end
+
+        def specimen_status_trail(specimen_id)
+          query <<~SQL
+            SELECT specimen_statuses.name AS status_name,
+                   specimen_status_trails.who_updated_id AS updated_by_id,
+                   specimen_status_trails.who_updated_name AS updated_by_name,
+                   specimen_status_trails.who_updated_phone_number AS updated_by_phone_number,
+                   specimen_status_trails.time_updated AS date
+            FROM specimen_status_trails
+            INNER JOIN specimen_statuses
+              ON specimen_statuses.id = specimen_status_trails.specimen_status_id
+            WHERE specimen_status_trails.specimen_id = #{sql_escape(specimen_id)}
+          SQL
+        end
+
+        def test_status_trail(test_id)
+          query <<~SQL
+            SELECT test_statuses.name AS status_name,
+                   test_status_trails.who_updated_id AS updated_by_id,
+                   test_status_trails.who_updated_name AS updated_by_name,
+                   test_status_trails.who_updated_phone_number AS updated_by_phone_number,
+                   COALESCE(test_status_trails.time_updated, test_status_trails.created_at) AS date
+            FROM test_status_trails
+            INNER JOIN test_statuses
+              ON test_statuses.id = test_status_trails.test_status_id
+            WHERE test_status_trails.test_id = #{sql_escape(test_id)}
+          SQL
+        end
+
+        def test_results(test_id)
+          query <<~SQL
+            SELECT measures.name AS measure_name,
+                   test_results.result,
+                   test_results.time_entered AS date
+            FROM test_results
+            INNER JOIN measures ON measures.id = test_results.measure_id
+            WHERE test_results.test_id = #{sql_escape(test_id)}
+          SQL
+        end
+
+        def make_order_dto(specimen:, patient:, test_status_trail:, specimen_status_trail:, test_results:)
+          drawn_by_first_name, drawn_by_last_name = specimen['drawn_by_name']&.split
+          patient_first_name, patient_last_name = patient['name'].split
+
+          OrderDTO.new(
+            _id: specimen['doc_id'].blank? ? SecureRandom.uuid : specimen['doc_id'],
+            _rev: '0',
+            tracking_number: specimen['tracking_number'],
+            date_created: specimen['order_date'],
+            sample_type: specimen['specimen_name'],
+            tests: test_status_trail.keys,
+            districy: specimen['district'], # districy [sic] - That's how it's named
+            order_location: specimen['ward_id'],
+            sending_facility: specimen['sending_facility'],
+            receiving_facility: specimen['target_lab'],
+            priority: specimen['priority'],
+            patient: {
+              id: patient['nhid'],
+              first_name: patient_first_name,
+              last_name: patient_last_name,
+              gender: patient['gender'],
+              birthdate: patient['birthdate'],
+              email: nil,
+              phone_number: nil
+            },
+            type: 'Order',
+            who_order_test: {
+              first_name: drawn_by_first_name,
+              last_name: drawn_by_last_name,
+              id: specimen['drawn_by_id'],
+              phone_number: specimen['drawn_by_phone_number']
+            },
+            sample_status: specimen['specimen_status'],
+            sample_statuses: specimen_status_trail.each_with_object({}) do |trail_entry, object|
+              first_name, last_name = trail_entry['updated_by_name'].split
+
+              object[format_date(trail_entry['date'])] = {
+                status: trail_entry['status_name'],
+                updated_by: {
+                  first_name: first_name,
+                  last_name: last_name,
+                  phone_number: trail_entry['updated_by_phone_number'],
+                  id: trail_entry['updated_by_id']
+                }
+              }
+            end,
+            test_statuses: test_status_trail.each_with_object({}) do |trail_entry, formatted_trail|
+              test_name, test_statuses = trail_entry
+
+              formatted_trail[test_name] = test_statuses.each_with_object({}) do |test_status, formatted_statuses|
+                updated_by_first_name, updated_by_last_name = test_status['updated_by_name'].split
+
+                formatted_statuses[format_date(test_status['date'])] = {
+                  status: test_status['status_name'],
+                  updated_by: {
+                    first_name: updated_by_first_name,
+                    last_name: updated_by_last_name,
+                    phone_number: test_status['updated_by_phone_number'],
+                    id: test_status['updated_by_id']
+                  }
+                }
+              end
+            end,
+            test_results: test_results.each_with_object({}) do |results_entry, formatted_results|
+              test_name, results = results_entry
+
+              formatted_results[test_name] = format_test_result_for_dto(test_name, specimen, results, test_status_trail)
+            end
+          )
+        end
+
+        def format_test_result_for_dto(test_name, specimen, results, test_status_trail)
+          return {} if results.size.zero?
+
+          result_create_event = test_status_trail[test_name]&.find do |trail_entry|
+            trail_entry['status_name'].casecmp?('drawn')
+          end
+
+          result_creator_first_name, result_creator_last_name = result_create_event&.fetch('updated_by_name')&.split
+          unless result_creator_first_name
+            result_creator_first_name, result_creator_last_name = specimen['drawn_by_name']&.split
+          end
+
+          {
+            results: results.each_with_object({}) do |result, formatted_measures|
+              formatted_measures[result['measure_name']] = {
+                result_value: result['result']
+              }
+            end,
+            date_result_entered: format_date(result_create_event&.fetch('date') || specimen['order_date'], :iso),
+            result_entered_by: {
+              first_name: result_creator_first_name,
+              last_name: result_creator_last_name,
+              phone_number: result_create_event&.fetch('updated_by_phone_number') || specimen['drawn_by_phone_number'],
+              id: result_create_event&.fetch('updated_by_id') || specimen['updated_by_id']
+            }
+          }
+        end
+
+        def mysql
+          return mysql_connection if mysql_connection
+
+          config = lambda do |key|
+            @config ||= Lab::Lims::Config.database
+            @config['default'][key] || @config['development'][key]
+          end
+
+          connection = Mysql2::Client.new(host: config['host'] || 'localhost',
+                                          username: config['username'] || 'root',
+                                          password: config['password'],
+                                          port: config['port'] || '3306',
+                                          database: config['database'],
+                                          reconnect: true)
+
+          self.mysql_connection = connection
+        end
+
+        def pid
+          return -1 if Parallel.worker_number.nil?
+
+          Parallel.worker_number
+        end
+
+        def mysql_connection=(connection)
+          @mysql_connection_pool[pid] = connection
+        end
+
+        def mysql_connection
+          @mysql_connection_pool[pid]
+        end
+
+        def query(sql)
+          Rails.logger.debug("#{MysqlApi}: #{sql}")
+          mysql.query(sql)
+        end
+
+        def sql_escape(value)
+          mysql.escape(value.to_s)
+        end
+
+        ##
+        # Lims has some weird date formatting standards...
+        def format_date(date, format = nil)
+          date = date&.to_time
+
+          case format
+          when :iso
+            date&.strftime('%Y-%m-%d %H:%M:%S')
+          else
+            date&.strftime('%Y%m%d%H%M%S')
+          end
+        end
+      end
+    end
+  end
+end