his_emr_api_lab 1.1.19 → 1.1.22
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- checksums.yaml +4 -4
- metadata +8 -86
- data/MIT-LICENSE +0 -20
- data/README.md +0 -71
- data/Rakefile +0 -32
- data/app/controllers/lab/application_controller.rb +0 -6
- data/app/controllers/lab/labels_controller.rb +0 -17
- data/app/controllers/lab/orders_controller.rb +0 -38
- data/app/controllers/lab/reasons_for_test_controller.rb +0 -9
- data/app/controllers/lab/results_controller.rb +0 -19
- data/app/controllers/lab/specimen_types_controller.rb +0 -15
- data/app/controllers/lab/test_result_indicators_controller.rb +0 -9
- data/app/controllers/lab/test_types_controller.rb +0 -15
- data/app/controllers/lab/tests_controller.rb +0 -26
- data/app/jobs/lab/application_job.rb +0 -4
- data/app/jobs/lab/push_order_job.rb +0 -12
- data/app/jobs/lab/update_patient_orders_job.rb +0 -32
- data/app/jobs/lab/void_order_job.rb +0 -17
- data/app/mailers/lab/application_mailer.rb +0 -6
- data/app/models/lab/application_record.rb +0 -5
- data/app/models/lab/lab_accession_number_counter.rb +0 -13
- data/app/models/lab/lab_encounter.rb +0 -7
- data/app/models/lab/lab_order.rb +0 -54
- data/app/models/lab/lab_result.rb +0 -31
- data/app/models/lab/lab_test.rb +0 -19
- data/app/models/lab/lims_failed_import.rb +0 -4
- data/app/models/lab/lims_order_mapping.rb +0 -10
- data/app/serializers/lab/lab_order_serializer.rb +0 -55
- data/app/serializers/lab/result_serializer.rb +0 -36
- data/app/serializers/lab/test_serializer.rb +0 -29
- data/app/services/lab/accession_number_service.rb +0 -77
- data/app/services/lab/concepts_service.rb +0 -82
- data/app/services/lab/labelling_service/order_label.rb +0 -106
- data/app/services/lab/lims/api/blackhole_api.rb +0 -21
- data/app/services/lab/lims/api/couchdb_api.rb +0 -53
- data/app/services/lab/lims/api/mysql_api.rb +0 -316
- data/app/services/lab/lims/api/rest_api.rb +0 -413
- data/app/services/lab/lims/api/ws_api.rb +0 -121
- data/app/services/lab/lims/api_factory.rb +0 -19
- data/app/services/lab/lims/config.rb +0 -100
- data/app/services/lab/lims/exceptions.rb +0 -11
- data/app/services/lab/lims/migrator.rb +0 -216
- data/app/services/lab/lims/order_dto.rb +0 -105
- data/app/services/lab/lims/order_serializer.rb +0 -216
- data/app/services/lab/lims/pull_worker.rb +0 -289
- data/app/services/lab/lims/push_worker.rb +0 -144
- data/app/services/lab/lims/utils.rb +0 -91
- data/app/services/lab/lims/worker.rb +0 -86
- data/app/services/lab/metadata.rb +0 -24
- data/app/services/lab/orders_search_service.rb +0 -66
- data/app/services/lab/orders_service.rb +0 -212
- data/app/services/lab/results_service.rb +0 -122
- data/app/services/lab/tests_service.rb +0 -93
- data/config/routes.rb +0 -17
- data/db/migrate/20210126092910_create_lab_lab_accession_number_counters.rb +0 -12
- data/db/migrate/20210310115457_create_lab_lims_order_mappings.rb +0 -15
- data/db/migrate/20210323080140_change_lims_id_to_string_in_lims_order_mapping.rb +0 -15
- data/db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb +0 -5
- data/db/migrate/20210407071728_create_lab_lims_failed_imports.rb +0 -19
- data/db/migrate/20210610095024_fix_numeric_results_value_type.rb +0 -20
- data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb +0 -7
- data/lib/auto12epl.rb +0 -201
- data/lib/couch_bum/couch_bum.rb +0 -92
- data/lib/generators/lab/install/USAGE +0 -9
- data/lib/generators/lab/install/install_generator.rb +0 -19
- data/lib/generators/lab/install/templates/rswag-ui-lab.rb +0 -5
- data/lib/generators/lab/install/templates/start_worker.rb +0 -32
- data/lib/generators/lab/install/templates/swagger.yaml +0 -714
- data/lib/his_emr_api_lab.rb +0 -5
- data/lib/lab/engine.rb +0 -15
- data/lib/lab/version.rb +0 -5
- data/lib/logger_multiplexor.rb +0 -38
- data/lib/tasks/lab_tasks.rake +0 -25
- data/lib/tasks/loaders/data/reasons-for-test.csv +0 -7
- data/lib/tasks/loaders/data/test-measures.csv +0 -225
- data/lib/tasks/loaders/data/tests.csv +0 -161
- data/lib/tasks/loaders/loader_mixin.rb +0 -53
- data/lib/tasks/loaders/metadata_loader.rb +0 -26
- data/lib/tasks/loaders/reasons_for_test_loader.rb +0 -23
- data/lib/tasks/loaders/specimens_loader.rb +0 -65
- data/lib/tasks/loaders/test_result_indicators_loader.rb +0 -54
@@ -1,289 +0,0 @@
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# frozen_string_literal: true
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module Lab
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module Lims
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##
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# Pulls orders from a Lims API object and saves them to the local database.
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class PullWorker
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attr_reader :lims_api
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include Utils # for logger
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LIMS_LOG_PATH = Rails.root.join('log', 'lims')
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def initialize(lims_api)
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@lims_api = lims_api
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end
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##
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# Pulls orders from the LIMS queue and writes them to the local database
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def pull_orders(batch_size: 10_000, **kwargs)
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logger.info("Retrieving LIMS orders starting from #{last_seq}")
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lims_api.consume_orders(from: last_seq, limit: batch_size, **kwargs) do |order_dto, context|
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logger.debug("Retrieved order ##{order_dto[:tracking_number]}: #{order_dto}")
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patient = find_patient_by_nhid(order_dto[:patient][:id])
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unless patient
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logger.debug("Discarding order: Non local patient ##{order_dto[:patient][:id]} on order ##{order_dto[:tracking_number]}")
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order_rejected(order_dto, "Patient NPID, '#{order_dto[:patient][:id]}', didn't match any local NPIDs")
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next
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end
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if order_dto[:tests].empty?
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logger.debug("Discarding order: Missing tests on order ##{order_dto[:tracking_number]}")
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order_rejected(order_dto, 'Order is missing tests')
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next
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end
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diff = match_patient_demographics(patient, order_dto['patient'])
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if diff.empty?
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save_order(patient, order_dto)
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order_saved(order_dto)
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else
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save_failed_import(order_dto, 'Demographics not matching', diff)
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end
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update_last_seq(context.current_seq)
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rescue Lab::Lims::DuplicateNHID
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logger.warn("Failed to import order due to duplicate patient NHID: #{order_dto[:patient][:id]}")
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save_failed_import(order_dto, "Duplicate local patient NHID: #{order_dto[:patient][:id]}")
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rescue MissingAccessionNumber
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logger.warn("Failed to import order due to missing accession number: #{order_dto[:_id]}")
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save_failed_import(order_dto, 'Order missing tracking number')
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rescue LimsException => e
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logger.warn("Failed to import order due to #{e.class} - #{e.message}")
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save_failed_import(order_dto, e.message)
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end
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end
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protected
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def order_saved(order_dto); end
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def order_rejected(order_dto, message); end
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def last_seq
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File.open(last_seq_path, File::RDONLY | File::CREAT, 0o644) do |fin|
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data = fin.read&.strip
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return nil if data.blank?
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return data
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end
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end
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def update_last_seq(last_seq)
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File.open(last_seq_path, File::WRONLY | File::CREAT, 0o644) do |fout|
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fout.flock(File::LOCK_EX)
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fout.write(last_seq.to_s)
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end
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end
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private
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def find_patient_by_nhid(nhid)
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national_id_type = PatientIdentifierType.where(name: ['National id', 'Old Identification Number'])
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identifiers = PatientIdentifier.where(type: national_id_type, identifier: nhid)
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.joins('INNER JOIN person ON person.person_id = patient_identifier.patient_id AND person.voided = 0')
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if identifiers.count.zero?
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identifiers = PatientIdentifier.unscoped
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.where(voided: 1, type: national_id_type, identifier: nhid)
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.joins('INNER JOIN person ON person.person_id = patient_identifier.patient_id AND person.voided = 0')
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end
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# Joining to person above to ensure that the person is not voided,
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# it was noted at one site that there were some people that were voided
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# upon merging but the patient and patient_identifier was not voided
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return nil if identifiers.count.zero?
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patients = Patient.where(patient_id: identifiers.select(:patient_id))
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.distinct(:patient_id)
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.all
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raise Lab::Lims::DuplicateNHID, "Duplicate National Health ID: #{nhid}" if patients.size > 1
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patients.first
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end
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##
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# Matches a local patient's demographics to a LIMS patient's demographics
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def match_patient_demographics(local_patient, lims_patient)
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diff = {}
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person = Person.find(local_patient.id)
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person_name = PersonName.find_by_person_id(local_patient.id)
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unless (person.gender.blank? && lims_patient['gender'].blank?)\
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|| person.gender&.first&.casecmp?(lims_patient['gender']&.first)
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diff[:gender] = { local: person.gender, lims: lims_patient['gender'] }
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end
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unless names_match?(person_name&.given_name, lims_patient['first_name'])
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diff[:given_name] = { local: person_name&.given_name, lims: lims_patient['first_name'] }
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end
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unless names_match?(person_name&.family_name, lims_patient['last_name'])
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diff[:family_name] = { local: person_name&.family_name, lims: lims_patient['last_name'] }
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end
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diff
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end
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def names_match?(name1, name2)
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name1 = name1&.gsub(/'/, '')&.strip
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name2 = name2&.gsub(/'/, '')&.strip
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return true if name1.blank? && name2.blank?
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return false if name1.blank? || name2.blank?
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name1.casecmp?(name2)
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end
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def save_order(patient, order_dto)
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raise MissingAccessionNumber if order_dto[:tracking_number].blank?
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logger.info("Importing LIMS order ##{order_dto[:tracking_number]}")
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mapping = find_order_mapping_by_lims_id(order_dto[:_id])
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ActiveRecord::Base.transaction do
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if mapping
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order = update_order(patient, mapping.order_id, order_dto)
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mapping.update(pulled_at: Time.now)
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else
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order = create_order(patient, order_dto)
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mapping = LimsOrderMapping.create(lims_id: order_dto[:_id],
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order_id: order['id'],
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pulled_at: Time.now,
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revision: order_dto['_rev'])
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end
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order
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end
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end
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def create_order(patient, order_dto)
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logger.debug("Creating order ##{order_dto['_id']}")
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order = OrdersService.order_test(order_dto.to_order_service_params(patient_id: patient.patient_id))
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update_results(order, order_dto['test_results']) unless order_dto['test_results'].empty?
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order
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end
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def update_order(patient, order_id, order_dto)
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logger.debug("Updating order ##{order_dto['_id']}")
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order = OrdersService.update_order(order_id, order_dto.to_order_service_params(patient_id: patient.patient_id)
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.merge(force_update: 'true'))
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update_results(order, order_dto['test_results']) unless order_dto['test_results'].empty?
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order
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end
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def update_results(order, lims_results)
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logger.debug("Updating results for order ##{order[:accession_number]}: #{lims_results}")
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lims_results.each do |test_name, test_results|
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test = find_test(order['id'], test_name)
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unless test
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logger.warn("Couldn't find test, #{test_name}, in order ##{order[:id]}")
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next
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end
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next if test.result || test_results['results'].blank?
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measures = test_results['results'].map do |indicator, value|
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measure = find_measure(order, indicator, value)
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next nil unless measure
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measure
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end
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measures = measures.compact
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next if measures.empty?
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creator = format_result_entered_by(test_results['result_entered_by'])
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ResultsService.create_results(test.id, provider_id: User.current.person_id,
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date: Utils.parse_date(test_results['date_result_entered'], order[:order_date].to_s),
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comments: "LIMS import: Entered by: #{creator}",
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measures: measures)
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end
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end
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def find_test(order_id, test_name)
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test_name = Utils.translate_test_name(test_name)
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test_concept = Utils.find_concept_by_name(test_name)
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raise "Unknown test name, #{test_name}!" unless test_concept
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LabTest.find_by(order_id: order_id, value_coded: test_concept.concept_id)
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end
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def find_measure(_order, indicator_name, value)
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indicator = Utils.find_concept_by_name(indicator_name)
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unless indicator
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logger.warn("Result indicator #{indicator_name} not found in concepts list")
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return nil
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end
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value_modifier, value, value_type = parse_lims_result_value(value)
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return nil if value.blank?
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ActiveSupport::HashWithIndifferentAccess.new(
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indicator: { concept_id: indicator.concept_id },
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value_type: value_type,
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value: value_type == 'numeric' ? value.to_f : value,
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value_modifier: value_modifier.blank? ? '=' : value_modifier
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)
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end
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def parse_lims_result_value(value)
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value = value['result_value']&.strip
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return nil, nil, nil if value.blank?
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match = value&.match(/^(>|=|<|<=|>=)(.*)$/)
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return nil, value, guess_result_datatype(value) unless match
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[match[1], match[2].strip, guess_result_datatype(match[2])]
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end
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def guess_result_datatype(result)
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return 'numeric' if result.strip.match?(/^[+-]?((\d+(\.\d+)?)|\.\d+)$/)
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'text'
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end
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def format_result_entered_by(result_entered_by)
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first_name = result_entered_by['first_name']
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last_name = result_entered_by['last_name']
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phone_number = result_entered_by['phone_number']
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id = result_entered_by['id'] # Looks like a user_id of some sort
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"#{id}:#{first_name} #{last_name}:#{phone_number}"
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end
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def save_failed_import(order_dto, reason, diff = nil)
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logger.info("Failed to import LIMS order ##{order_dto[:tracking_number]} due to '#{reason}'")
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LimsFailedImport.create!(lims_id: order_dto[:_id],
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tracking_number: order_dto[:tracking_number],
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patient_nhid: order_dto[:patient][:id],
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reason: reason,
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diff: diff&.to_json)
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end
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def last_seq_path
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LIMS_LOG_PATH.join('last_seq.dat')
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end
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def find_order_mapping_by_lims_id(lims_id)
|
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mapping = Lab::LimsOrderMapping.find_by(lims_id: lims_id)
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return nil unless mapping
|
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return mapping if Lab::LabOrder.where(order_id: mapping.order_id).exists?
|
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mapping.destroy
|
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nil
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end
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end
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end
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end
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@@ -1,144 +0,0 @@
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# frozen_string_literal: true
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|
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|
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module Lab
|
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module Lims
|
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-
##
|
6
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# Pushes all local orders to a LIMS Api object.
|
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class PushWorker
|
8
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attr_reader :lims_api
|
9
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-
|
10
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include Utils # for logger
|
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|
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SECONDS_TO_WAIT_FOR_ORDERS = 30
|
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-
|
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def initialize(lims_api)
|
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@lims_api = lims_api
|
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end
|
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-
|
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def push_orders(batch_size: 1000, wait: false)
|
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loop do
|
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logger.info('Looking for new orders to push to LIMS...')
|
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orders = orders_pending_sync(batch_size).all
|
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|
23
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logger.debug("Found #{orders.size} orders...")
|
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orders.each do |order|
|
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push_order(order)
|
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rescue GatewayError => e
|
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logger.error("Failed to push order ##{order.accession_number}: #{e.class} - #{e.message}")
|
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-
end
|
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|
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break unless wait
|
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|
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logger.info('Waiting for orders...')
|
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sleep(Lab::Lims::Config.updates_poll_frequency)
|
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end
|
35
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-
end
|
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|
37
|
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def push_order_by_id(order_id)
|
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order = Lab::LabOrder.joins(order_type: { name: 'Lab' })
|
39
|
-
.unscoped
|
40
|
-
.find(order_id)
|
41
|
-
push_order(order)
|
42
|
-
end
|
43
|
-
|
44
|
-
##
|
45
|
-
# Pushes given order to LIMS queue
|
46
|
-
def push_order(order)
|
47
|
-
logger.info("Pushing order ##{order.order_id}")
|
48
|
-
|
49
|
-
order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
|
50
|
-
mapping = Lab::LimsOrderMapping.find_by(order_id: order.order_id)
|
51
|
-
|
52
|
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ActiveRecord::Base.transaction do
|
53
|
-
if mapping && !order.voided.zero?
|
54
|
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Rails.logger.info("Deleting order ##{order_dto[:accession_number]} from LIMS")
|
55
|
-
lims_api.delete_order(mapping.lims_id, order_dto)
|
56
|
-
mapping.destroy
|
57
|
-
elsif mapping
|
58
|
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Rails.logger.info("Updating order ##{order_dto[:accession_number]} in LIMS")
|
59
|
-
lims_api.update_order(mapping.lims_id, order_dto)
|
60
|
-
mapping.update(pushed_at: Time.now)
|
61
|
-
elsif order_dto[:_id] && Lab::LimsOrderMapping.where(lims_id: order_dto[:_id]).exists?
|
62
|
-
# HACK: v1.1.7 had a bug where duplicates of recently created orders where being created by
|
63
|
-
# the pull worker. This here detects those duplicates and voids them.
|
64
|
-
Rails.logger.warn("Duplicate accession number found: #{order_dto[:_id]}, skipping order...")
|
65
|
-
fix_duplicates!(order)
|
66
|
-
else
|
67
|
-
Rails.logger.info("Creating order ##{order_dto[:accession_number]} in LIMS")
|
68
|
-
update = lims_api.create_order(order_dto)
|
69
|
-
Lab::LimsOrderMapping.create!(order: order, lims_id: update['id'], revision: update['rev'],
|
70
|
-
pushed_at: Time.now)
|
71
|
-
end
|
72
|
-
end
|
73
|
-
|
74
|
-
order_dto
|
75
|
-
end
|
76
|
-
|
77
|
-
private
|
78
|
-
|
79
|
-
def orders_pending_sync(batch_size)
|
80
|
-
return new_orders.limit(batch_size) if new_orders.exists?
|
81
|
-
|
82
|
-
return voided_orders.limit(batch_size) if voided_orders.exists?
|
83
|
-
|
84
|
-
updated_orders.limit(batch_size)
|
85
|
-
end
|
86
|
-
|
87
|
-
def new_orders
|
88
|
-
Rails.logger.debug('Looking for new orders that need to be created in LIMS...')
|
89
|
-
Lab::LabOrder.where.not(order_id: Lab::LimsOrderMapping.all.select(:order_id))
|
90
|
-
.order(date_created: :desc)
|
91
|
-
end
|
92
|
-
|
93
|
-
def updated_orders
|
94
|
-
Rails.logger.debug('Looking for recently updated orders that need to be pushed to LIMS...')
|
95
|
-
last_updated = Lab::LimsOrderMapping.select('MAX(updated_at) AS last_updated')
|
96
|
-
.first
|
97
|
-
.last_updated
|
98
|
-
|
99
|
-
Lab::LabOrder.left_joins(:results)
|
100
|
-
.where('orders.discontinued_date > :last_updated
|
101
|
-
OR obs.date_created > orders.date_created',
|
102
|
-
last_updated: last_updated)
|
103
|
-
.group('orders.order_id')
|
104
|
-
.order(discontinued_date: :desc, date_created: :desc)
|
105
|
-
end
|
106
|
-
|
107
|
-
def voided_orders
|
108
|
-
Rails.logger.debug('Looking for voided orders that are being tracked by LIMS...')
|
109
|
-
Lab::LabOrder.unscoped
|
110
|
-
.where(order_type: OrderType.where(name: Lab::Metadata::ORDER_TYPE_NAME),
|
111
|
-
order_id: Lab::LimsOrderMapping.all.select(:order_id),
|
112
|
-
voided: 1)
|
113
|
-
.order(date_voided: :desc)
|
114
|
-
end
|
115
|
-
|
116
|
-
##
|
117
|
-
# HACK: Checks for duplicates previously created by version 1.1.7 pull worker bug due to this proving orders
|
118
|
-
# that have not been pushed to LIMS as orders awaiting updates.
|
119
|
-
def fix_duplicates!(order)
|
120
|
-
return order.void('Duplicate created by bug in HIS-EMR-API-Lab v1.1.7') unless order_has_specimen?(order)
|
121
|
-
|
122
|
-
duplicate_order = Lab::LabOrder.where(accession_number: order.accession_number)
|
123
|
-
.where.not(order_id: order.order_id)
|
124
|
-
.first
|
125
|
-
return unless duplicate_order
|
126
|
-
|
127
|
-
if !order_has_results?(order) && (order_has_results?(duplicate_order) || order_has_specimen?(duplicate_order))
|
128
|
-
order.void('DUplicate created by bug in HIS-EMR-API-Lab v1.1.7')
|
129
|
-
else
|
130
|
-
duplicate_order.void('Duplicate created by bug in HIS-EMR-API-Lab v1.1.7')
|
131
|
-
Lab::LimsOrderMapping.find_by_lims_id(order.accession_number)&.destroy
|
132
|
-
end
|
133
|
-
end
|
134
|
-
|
135
|
-
def order_has_results?(order)
|
136
|
-
order.results.exists?
|
137
|
-
end
|
138
|
-
|
139
|
-
def order_has_specimen?(order)
|
140
|
-
order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
|
141
|
-
end
|
142
|
-
end
|
143
|
-
end
|
144
|
-
end
|
@@ -1,91 +0,0 @@
|
|
1
|
-
# frozen_string_literal: true
|
2
|
-
|
3
|
-
require 'cgi/util'
|
4
|
-
|
5
|
-
module Lab
|
6
|
-
module Lims
|
7
|
-
##
|
8
|
-
# Various helper methods for modules in the Lims namespaces...
|
9
|
-
module Utils
|
10
|
-
LIMS_LOG_PATH = Rails.root.join('log', 'lims')
|
11
|
-
FileUtils.mkdir_p(LIMS_LOG_PATH) unless File.exist?(LIMS_LOG_PATH)
|
12
|
-
|
13
|
-
def logger
|
14
|
-
Rails.logger
|
15
|
-
end
|
16
|
-
|
17
|
-
TEST_NAME_MAPPINGS = {
|
18
|
-
# For some weird reason(s) some tests have multiple names in LIMS,
|
19
|
-
# this is used to sanitize those names.
|
20
|
-
'hiv_viral_load' => 'HIV Viral Load',
|
21
|
-
'viral laod' => 'HIV Viral Load',
|
22
|
-
'viral load' => 'HIV Viral Load',
|
23
|
-
'i/ink' => 'India ink',
|
24
|
-
'indian ink' => 'India ink'
|
25
|
-
}.freeze
|
26
|
-
|
27
|
-
def self.translate_test_name(test_name)
|
28
|
-
TEST_NAME_MAPPINGS.fetch(test_name.downcase, test_name)
|
29
|
-
end
|
30
|
-
|
31
|
-
def self.structify(object)
|
32
|
-
if object.is_a?(Hash)
|
33
|
-
object.each_with_object(OpenStruct.new) do |kv_pair, struct|
|
34
|
-
key, value = kv_pair
|
35
|
-
|
36
|
-
struct[key] = structify(value)
|
37
|
-
end
|
38
|
-
elsif object.respond_to?(:map)
|
39
|
-
object.map { |item| structify(item) }
|
40
|
-
else
|
41
|
-
object
|
42
|
-
end
|
43
|
-
end
|
44
|
-
|
45
|
-
def self.lab_user
|
46
|
-
user = User.find_by_username('lab_daemon')
|
47
|
-
return user if user
|
48
|
-
|
49
|
-
god_user = User.first
|
50
|
-
|
51
|
-
person = Person.create!(creator: god_user.user_id)
|
52
|
-
PersonName.create!(person: person, given_name: 'Lab', family_name: 'Daemon', creator: god_user.user_id)
|
53
|
-
|
54
|
-
User.create!(username: 'lab_daemon', person: person, creator: god_user.user_id)
|
55
|
-
end
|
56
|
-
|
57
|
-
def self.parse_date(str_date, fallback_date = nil)
|
58
|
-
str_date = str_date&.to_s
|
59
|
-
|
60
|
-
if str_date.blank? && fallback_date.blank?
|
61
|
-
raise "Can't parse blank date"
|
62
|
-
end
|
63
|
-
|
64
|
-
return parse_date(fallback_date) if str_date.blank?
|
65
|
-
|
66
|
-
str_date = str_date.gsub(/^00/, '20').gsub(/^180/, '20')
|
67
|
-
|
68
|
-
case str_date
|
69
|
-
when /\d{4}-\d{2}-\d{2}/
|
70
|
-
str_date
|
71
|
-
when /\d{2}-\d{2}-\d{2}/
|
72
|
-
Date.strptime(str_date, '%d-%m-%Y').strftime('%Y-%m-%d')
|
73
|
-
when /(\d{4}\d{2}\d{2})\d+/
|
74
|
-
Date.strptime(str_date, '%Y%m%d').strftime('%Y-%m-%d')
|
75
|
-
when %r{\d{2}/\d{2}/\d{4}}
|
76
|
-
str_date.to_date.to_s
|
77
|
-
else
|
78
|
-
Rails.logger.warn("Invalid date: #{str_date}")
|
79
|
-
parse_date(fallback_date)
|
80
|
-
end
|
81
|
-
end
|
82
|
-
|
83
|
-
def self.find_concept_by_name(name)
|
84
|
-
ConceptName.joins(:concept)
|
85
|
-
.merge(Concept.all) # Filter out voided
|
86
|
-
.where(name: CGI.unescapeHTML(name))
|
87
|
-
.first
|
88
|
-
end
|
89
|
-
end
|
90
|
-
end
|
91
|
-
end
|
@@ -1,86 +0,0 @@
|
|
1
|
-
# frozen_string_literal: true
|
2
|
-
|
3
|
-
require 'logger_multiplexor'
|
4
|
-
|
5
|
-
require_relative './api/couchdb_api'
|
6
|
-
|
7
|
-
module Lab
|
8
|
-
module Lims
|
9
|
-
##
|
10
|
-
# Pull/Push orders from/to the LIMS queue (Oops meant CouchDB).
|
11
|
-
module Worker
|
12
|
-
def self.start
|
13
|
-
User.current = Utils.lab_user
|
14
|
-
|
15
|
-
fork(&method(:start_push_worker))
|
16
|
-
fork(&method(:start_pull_worker))
|
17
|
-
fork(&method(:start_realtime_pull_worker)) if realtime_updates_enabled?
|
18
|
-
|
19
|
-
Process.waitall
|
20
|
-
end
|
21
|
-
|
22
|
-
def self.start_push_worker
|
23
|
-
start_worker('push_worker') do
|
24
|
-
worker = PushWorker.new(lims_api)
|
25
|
-
|
26
|
-
worker.push_orders # (wait: true)
|
27
|
-
end
|
28
|
-
end
|
29
|
-
|
30
|
-
def self.start_pull_worker
|
31
|
-
start_worker('pull_worker') do
|
32
|
-
worker = PullWorker.new(lims_api)
|
33
|
-
|
34
|
-
worker.pull_orders
|
35
|
-
end
|
36
|
-
end
|
37
|
-
|
38
|
-
def self.start_realtime_pull_worker
|
39
|
-
start_worker('realtime_pull_worker') do
|
40
|
-
worker = PullWorker.new(Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket))
|
41
|
-
|
42
|
-
worker.pull_orders
|
43
|
-
end
|
44
|
-
end
|
45
|
-
|
46
|
-
LOG_FILES_TO_KEEP = 5
|
47
|
-
LOG_FILE_SIZE = 500.megabytes
|
48
|
-
|
49
|
-
def self.start_worker(worker_name)
|
50
|
-
Rails.logger = LoggerMultiplexor.new(file_logger(worker_name), $stdout)
|
51
|
-
ActiveRecord::Base.logger = Rails.logger
|
52
|
-
Rails.logger.level = :debug
|
53
|
-
|
54
|
-
File.open(log_path("#{worker_name}.lock"), File::RDWR | File::CREAT, 0o644) do |fout|
|
55
|
-
unless fout.flock(File::LOCK_EX | File::LOCK_NB)
|
56
|
-
Rails.logger.warn("Another process already holds lock #{worker_name} (#{fout.read}), exiting...")
|
57
|
-
break
|
58
|
-
end
|
59
|
-
|
60
|
-
fout.write("Locked by process ##{Process.pid} under process group ##{Process.ppid} at #{Time.now}")
|
61
|
-
fout.flush
|
62
|
-
yield
|
63
|
-
end
|
64
|
-
end
|
65
|
-
|
66
|
-
def self.file_logger(worker_name)
|
67
|
-
Logger.new(log_path("#{worker_name}.log"), LOG_FILES_TO_KEEP, LOG_FILE_SIZE)
|
68
|
-
end
|
69
|
-
|
70
|
-
def self.log_path(filename)
|
71
|
-
Lab::Lims::Utils::LIMS_LOG_PATH.join(filename)
|
72
|
-
end
|
73
|
-
|
74
|
-
def self.realtime_updates_enabled?
|
75
|
-
Lims::Config.updates_socket.key?('url')
|
76
|
-
rescue Lab::Lims::Config::ConfigNotFound => e
|
77
|
-
Rails.logger.warn("Check for realtime updates failed: #{e.message}")
|
78
|
-
false
|
79
|
-
end
|
80
|
-
|
81
|
-
def self.lims_api
|
82
|
-
Lab::Lims::ApiFactory.create_api
|
83
|
-
end
|
84
|
-
end
|
85
|
-
end
|
86
|
-
end
|
@@ -1,24 +0,0 @@
|
|
1
|
-
# frozen_string_literal: true
|
2
|
-
|
3
|
-
module Lab
|
4
|
-
module Metadata
|
5
|
-
# Concepts
|
6
|
-
REASON_FOR_TEST_CONCEPT_NAME = 'Reason for test'
|
7
|
-
REQUESTING_CLINICIAN_CONCEPT_NAME = 'Person making request'
|
8
|
-
SPECIMEN_TYPE_CONCEPT_NAME = 'Specimen type'
|
9
|
-
TARGET_LAB_CONCEPT_NAME = 'Lab'
|
10
|
-
TEST_RESULT_CONCEPT_NAME = 'Lab test result'
|
11
|
-
TEST_RESULT_INDICATOR_CONCEPT_NAME = 'Lab test result indicator'
|
12
|
-
TEST_TYPE_CONCEPT_NAME = 'Test type'
|
13
|
-
UNKNOWN_SPECIMEN = 'Unknown'
|
14
|
-
|
15
|
-
# Encounter
|
16
|
-
ENCOUNTER_TYPE_NAME = 'Lab'
|
17
|
-
|
18
|
-
# Order types
|
19
|
-
ORDER_TYPE_NAME = 'Lab'
|
20
|
-
|
21
|
-
# Programs
|
22
|
-
LAB_PROGRAM_NAME = 'Laboratory Program'
|
23
|
-
end
|
24
|
-
end
|
@@ -1,66 +0,0 @@
|
|
1
|
-
# frozen_string_literal: true
|
2
|
-
|
3
|
-
module Lab
|
4
|
-
# Search Lab orders.
|
5
|
-
module OrdersSearchService
|
6
|
-
class << self
|
7
|
-
def find_orders(filters)
|
8
|
-
extra_filters = pop_filters(filters, :date, :end_date, :status)
|
9
|
-
|
10
|
-
orders = Lab::LabOrder.prefetch_relationships
|
11
|
-
.where(filters)
|
12
|
-
.order(start_date: :desc)
|
13
|
-
|
14
|
-
orders = filter_orders_by_status(orders, pop_filters(extra_filters, :status))
|
15
|
-
orders = filter_orders_by_date(orders, extra_filters)
|
16
|
-
|
17
|
-
orders.map { |order| Lab::LabOrderSerializer.serialize_order(order) }
|
18
|
-
end
|
19
|
-
|
20
|
-
def find_orders_without_results(patient_id: nil)
|
21
|
-
results_query = Lab::LabResult.all
|
22
|
-
results_query = results_query.where(person_id: patient_id) if patient_id
|
23
|
-
|
24
|
-
query = Lab::LabOrder.where.not(order_id: results_query.select(:order_id))
|
25
|
-
query = query.where(patient_id: patient_id) if patient_id
|
26
|
-
|
27
|
-
query
|
28
|
-
end
|
29
|
-
|
30
|
-
def filter_orders_by_date(orders, date: nil, end_date: nil)
|
31
|
-
date = date&.to_date
|
32
|
-
end_date = end_date&.to_date
|
33
|
-
|
34
|
-
return orders.where('start_date BETWEEN ? AND ?', date, end_date + 1.day) if date && end_date
|
35
|
-
|
36
|
-
return orders.where('start_date BETWEEN ? AND ?', date, date + 1.day) if date
|
37
|
-
|
38
|
-
return orders.where('start_date < ?', end_date + 1.day) if end_date
|
39
|
-
|
40
|
-
orders
|
41
|
-
end
|
42
|
-
|
43
|
-
def filter_orders_by_status(orders, status: nil)
|
44
|
-
case status&.downcase
|
45
|
-
when 'ordered' then orders.where(concept_id: unknown_concept_id)
|
46
|
-
when 'drawn' then orders.where.not(concept_id: unknown_concept_id)
|
47
|
-
else orders
|
48
|
-
end
|
49
|
-
end
|
50
|
-
|
51
|
-
def unknown_concept_id
|
52
|
-
ConceptName.find_by_name!('Unknown').concept_id
|
53
|
-
end
|
54
|
-
|
55
|
-
def pop_filters(params, *filters)
|
56
|
-
filters.each_with_object({}) do |filter, popped_params|
|
57
|
-
next unless params.key?(filter)
|
58
|
-
|
59
|
-
popped_params[filter.to_sym] = params.delete(filter)
|
60
|
-
end
|
61
|
-
end
|
62
|
-
|
63
|
-
def fetch_results(order); end
|
64
|
-
end
|
65
|
-
end
|
66
|
-
end
|