Module: EmrOhspInterface::EmrLimsInterfaceService
- Defined in:
- app/services/emr_ohsp_interface/emr_lims_interface_service.rb
Class Method Summary collapse
- .check_patient_number(patient_id) ⇒ Object
- .create_lab_order(lab_details, clinician_id) ⇒ Object
-
.create_local_tracking_number ⇒ Object
lims tracking number ###############.
- .create_patient(firstname, surname, user_id, address, gender, dob, dob_estimated, external_patient_number, patient_number, date) ⇒ Object
- .create_specimens(user_id, specimen_type, tracking_number) ⇒ Object
- .create_test(specimen_id, requested_by, test_type) ⇒ Object
- .create_unsync_orders(date, specimen_id) ⇒ Object
- .create_visit(patient_number, date) ⇒ Object
- .filterpatient_number(data) ⇒ Object
- .get_day(day) ⇒ Object
- .get_last_accession_number ⇒ Object
-
.get_lims_test_results(tracking_number, patient_id) ⇒ Object
get results from lims ###############.
- .get_month(month) ⇒ Object
- .get_patient_dentifier(patient_id) ⇒ Object
- .get_patient_number ⇒ Object
- .get_specimen_id ⇒ Object
- .get_user_details(user_id) ⇒ Object
- .get_visit_id ⇒ Object
- .initialize ⇒ Object
- .mysql ⇒ Object
- .mysql_connection ⇒ Object
- .mysql_connection=(connection) ⇒ Object
- .new_accession_number ⇒ Object
- .prepare_next_tracking_number ⇒ Object
-
.query(sql) ⇒ Object
start connection to lims database ######################################################.
-
.settings ⇒ Object
start creation of lab test in lims #####################################################.
Class Method Details
.check_patient_number(patient_id) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 30 def check_patient_number(patient_id) get_patient_id = query "SELECT patient_number FROM patients WHERE `external_patient_number` ='#{patient_id}'; " get_patient_id.each do |x| return patient_number = x['patient_number'] end end |
.create_lab_order(lab_details, clinician_id) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 51 def create_lab_order(lab_details, clinician_id) external_patient_number = get_patient_dentifier(lab_details[0][:patient_id]) patient_number = check_patient_number(external_patient_number) time = Time.new date = time.strftime('%Y-%m-%d %H:%M:%S') lab_details.map do |order_params| if patient_number.blank? patient_number = get_patient_number() + 1 person_data = Person.where('person_id= ?', order_params[:patient_id])[0] address_data = PersonAddress.where('person_id= ?', order_params[:patient_id])[0] name_data = PersonName.where('person_id= ?', order_params[:patient_id])[0] gender = person_data[:gender].match(/f/i) ? 1 : (person_data[:gender].match(/m/i) ? 0 : 2) create_patient( name_data[:given_name], name_data[:family_name], clinician_id[0][:requesting_clinician_id], address_data[:address1], gender, person_data[:birthdate], person_data[:birthdate_estimated], external_patient_number, patient_number, date ) end create_visit(patient_number, date) create_specimens( clinician_id[0][:requesting_clinician_id], order_params[:specimen][:name], order_params[:accession_number] ) specimen_id = get_specimen_id create_unsync_orders(date, specimen_id) create_test(specimen_id, order_params[:requesting_clinician], order_params[:tests][0][:name]) end end |
.create_local_tracking_number ⇒ Object
lims tracking number ###############
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 196 def create_local_tracking_number configs = YAML.load_file "#{Rails.root}/config/application.yml" site_code = configs['facility_code'] file = JSON.parse(File.read("#{Rails.root}/public/tracker.json")) todate = Time.now.strftime('%Y%m%d') year = Time.now.strftime('%Y%m%d').to_s.slice(2..3) month = Time.now.strftime('%m') day = Time.now.strftime('%d') key = file.keys if todate > key[0] fi = {} fi[todate] = 1 File.open("#{Rails.root}/public/tracker.json", 'w') do |f| f.write(fi.to_json) end value = '001' tracking_number = "X#{site_code}#{year}#{get_month(month)}#{get_day(day)}#{value}" else counter = file[todate] value = if counter.to_s.length == 1 '00' + counter.to_s elsif counter.to_s.length == 2 '0' + counter.to_s else begin counter.to_s rescue StandardError '001' end end tracking_number = "X#{site_code}#{year}#{get_month(month)}#{get_day(day)}#{value}" end tracking_number end |
.create_patient(firstname, surname, user_id, address, gender, dob, dob_estimated, external_patient_number, patient_number, date) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 91 def create_patient( firstname, surname, user_id, address, gender, dob, dob_estimated, external_patient_number, patient_number, date ) query( "INSERT INTO `patients` (`name`, `first_name_code`, `last_name_code`, `created_by`, `address`, `gender`, `patient_number`, `dob`, `dob_estimated`, `external_patient_number`, `created_at`, `updated_at`) VALUES ('#{firstname} #{surname}', SOUNDEX('#{firstname}'), SOUNDEX('#{surname}'), #{user_id}, '#{address}',#{gender},'#{patient_number}', '#{dob}', '#{dob_estimated}', '#{external_patient_number}', '#{date}', '#{date}')" ) end |
.create_specimens(user_id, specimen_type, tracking_number) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 109 def create_specimens(user_id, specimen_type, tracking_number) specimen_type_id = settings['lims_specimen_map'][specimen_type.to_s] accession_number = new_accession_number # prepare_next_tracking_number() # tracking_number = create_local_tracking_number() query(" INSERT INTO `specimens` (`specimen_type_id`, `accepted_by`, `priority`, `accession_number`, `tracking_number`) VALUES ('#{specimen_type_id}', '#{user_id}', 'Stat', '#{accession_number}', '#{tracking_number}')") end |
.create_test(specimen_id, requested_by, test_type) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 123 def create_test(specimen_id, requested_by, test_type) visit_id = get_visit_id test_type_id = settings['lims_test_type_map'][test_type.to_s] query("INSERT INTO `tests` (`visit_id`, `test_type_id`, `specimen_id`, `test_status_id`, `not_done_reasons`, `person_talked_to_for_not_done`, `created_by`, `requested_by`) VALUES ('#{visit_id}', '#{test_type_id}', '#{specimen_id}', '2', '0', '0', 1, '#{requested_by}')") end |
.create_unsync_orders(date, specimen_id) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 118 def create_unsync_orders(date, specimen_id) query(" INSERT INTO `unsync_orders` (`specimen_id`, `data_not_synced`, `data_level`, `sync_status`, `updated_by_name`, `updated_by_id`, `created_at`, `updated_at`) VALUES ('#{specimen_id}', 'new order', 'specimen', 'not-synced', 'kBLIS Administrator', '1', '#{date}', '#{date}')") end |
.create_visit(patient_number, date) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 104 def create_visit(patient_number, date) query "INSERT INTO `visits` (`patient_id`, `visit_type`, `ward_or_location`, `created_at`, `updated_at`) VALUES ('#{patient_number}', 'Out Patient', 'EM OPD', '#{date}', '#{date}')" end |
.filterpatient_number(data) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 39 def filterpatient_number(data) patient_number = 0 data.each do |x| patient_number = x['patient_identify'] end patient_number end |
.get_day(day) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 269 def get_day(day) case day when '01' '1' when '02' '2' when '03' '3' when '04' '4' when '05' '5' when '06' '6' when '07' '7' when '08' '8' when '09' '9' when '10' 'A' when '11' 'B' when '12' 'C' when '13' 'E' when '14' 'F' when '15' 'G' when '16' 'H' when '17' 'Y' when '18' 'J' when '19' 'K' when '20' 'Z' when '21' 'M' when '22' 'N' when '23' 'O' when '24' 'P' when '25' 'Q' when '26' 'R' when '27' 'S' when '28' 'T' when '29' 'V' when '30' 'W' when '31' 'X' end end |
.get_last_accession_number ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 161 def get_last_accession_number data = query('SELECT * FROM specimens WHERE accession_number IS NOT NULL ORDER BY id DESC LIMIT 1') data.each do |x| return last_accession_number = x['accession_number'] end end |
.get_lims_test_results(tracking_number, patient_id) ⇒ Object
get results from lims ###############
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 340 def get_lims_test_results(tracking_number,patient_id) external_patient_number = get_patient_dentifier(patient_id) data = query(" SELECT visits.ward_or_location, specimens.accession_number, tests.created_by, tests.verified_by, tests.time_completed,tests.requested_by,tests.interpretation, tests.time_created as tests_time_created, test_types.name as test_types_name, test_categories.name as test_categories_name, tests.time_verified as tests_time_verified, users.name as users_name, specimen_types.name as specimen_types_name, specimen_statuses.name as specimen_statuses_name, test_results.result as test_results_result, test_results.device_name as test_results_device_name, measures.name as measures_name, measures.unit as measures_unit, measure_ranges.range_lower as measure_ranges_range_lower, measure_ranges.range_upper as measure_ranges_range_upper FROM iblis.patients inner join iblis.visits on `visits`.`patient_id` = `patients`.`patient_number` inner join iblis.tests on `tests`.`visit_id` = `visits`.`id` inner join iblis.test_types on `test_types`.`id` = `tests`.`test_type_id` inner join iblis.test_categories on `test_categories`.`id` = `test_types`.`test_category_id` inner join iblis.users on `users`.`id` = `tests`.`tested_by` inner join iblis.specimens on `specimens`.`id` = `tests`.`specimen_id` inner join iblis.specimen_types on `specimen_types`.`id` = `specimens`.`specimen_type_id` inner join iblis.specimen_statuses on `specimen_statuses`.`id` = `specimens`.`specimen_status_id` right join iblis.test_results on `test_results`.`test_id` = `tests`.`id` right join iblis.measures on `measures`.`id` = `test_results`.`measure_id` right join iblis.measure_ranges on `measure_ranges`.`measure_id` = `measures`.`id` where `patients`.`deleted_at` is null and `specimens`.`tracking_number` = '#{tracking_number}' and `patients`.`external_patient_number` = '#{external_patient_number}' and `measure_ranges`.`deleted_at` is null group by(`measure_ranges`.`measure_id`) order by time_completed asc ; ") data end |
.get_month(month) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 239 def get_month(month) case month when '01' '1' when '02' '2' when '03' '3' when '04' '4' when '05' '5' when '06' '6' when '07' '7' when '08' '8' when '09' '9' when '10' 'A' when '11' 'B' when '12' 'C' end end |
.get_patient_dentifier(patient_id) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 47 def get_patient_dentifier(patient_id) patient_dentifier =PatientIdentifier.where('patient_id= ? AND identifier_type = ?', patient_id,3)[0] patient_dentifier[:identifier] end |
.get_patient_number ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 19 def get_patient_number get_patient_id = query "SELECT id FROM iblis.patients order by id desc limit 1;" get_patient_id.each do |x| return patient_number = x['id'] end end |
.get_specimen_id ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 168 def get_specimen_id data = query('SELECT * FROM specimens WHERE accession_number IS NOT NULL ORDER BY id DESC LIMIT 1') data.each do |x| return specimen_id = x['id'] end end |
.get_user_details(user_id) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 377 def get_user_details(user_id) data = query("SELECT * FROM iblis.users where id = #{user_id};") data end |
.get_visit_id ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 175 def get_visit_id data = query('SELECT * FROM visits WHERE id IS NOT NULL ORDER BY id DESC LIMIT 1') data.each do |x| return specimen_id = x['id'] end end |
.initialize ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 10 def initialize @mysql_connection_pool = {} end |
.mysql ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 387 def mysql # self.initialize return mysql_connection if mysql_connection connection = Mysql2::Client.new(host: settings['headers']['host'], username: settings['headers']['username'], password: settings['headers']['password'], port: settings['headers']['port'], database: settings['headers']['database'], reconnect: true) self.mysql_connection = connection end |
.mysql_connection ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 404 def mysql_connection @mysql_connection_pool end |
.mysql_connection=(connection) ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 400 def mysql_connection=(connection) @mysql_connection_pool = connection end |
.new_accession_number ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 130 def new_accession_number # Generate the next accession number for specimen registration @mutex = Mutex.new if @mutex.blank? @mutex.lock max_acc_num = 0 return_value = nil sentinel = 99_999_999 settings = YAML.load_file("#{Rails.root}/config/application.yml")[Rails.env] code = settings['facility_code'] year = Date.today.year.to_s[2..3] record = get_last_accession_number unless record.blank? max_acc_num = record[5..20].match(/\d+/)[0].to_i # first 5 chars are for facility code and 2 digit year end if max_acc_num < sentinel max_acc_num += 1 else max_acc_num = 1 end max_acc_num = max_acc_num.to_s.rjust(8, '0') return_value = "#{code}#{year}#{max_acc_num}" @mutex.unlock return_value end |
.prepare_next_tracking_number ⇒ Object
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 182 def prepare_next_tracking_number file = JSON.parse(File.read("#{Rails.root}/public/tracker.json")) todate = Time.now.strftime('%Y%m%d') counter = file[todate] counter = counter.to_i + 1 fi = {} fi[todate] = counter File.open("#{Rails.root}/public/tracker.json", 'w') do |f| f.write(fi.to_json) end end |
.query(sql) ⇒ Object
start connection to lims database ######################################################
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 382 def query(sql) Rails.logger.debug(sql.to_s) result = mysql.query(sql) end |
.settings ⇒ Object
start creation of lab test in lims #####################################################
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# File 'app/services/emr_ohsp_interface/emr_lims_interface_service.rb', line 14 def settings file = File.read(Rails.root.join('db', 'lims_metadata', 'lims_map.json')) JSON.parse(file) end |