his_emr_api_lab 1.1.2 → 1.1.3
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checksums.yaml
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@@ -1,7 +1,7 @@
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metadata.gz:
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data.tar.gz:
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metadata.gz: eb21c8db8180a800fc69ebdfcfe9e2e804a96c698e73f28ae3c2c865a8853c16
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data.tar.gz: 2e2697ddeb327c79698ca229f9d625b6e6105e5621348df1c7d2d06d5c7b7cbb
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metadata.gz: 4440f3a2b7493335594206621cb2381207b59dfab73d841431d77ef8ba7f28f1bc033617378c7789f50e52dacdb0318b8e2ab1d93f3929b6a66601dbbfa1537c
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data.tar.gz: aacb8d43a4b71dc017a46d3f19791defc5f9f7b0562a96c8514d3d821f7d79124ce59719bcbf91f2042c7da61f61907bbab2b7e04b33b18443c0ea204b902f18
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@@ -11,15 +11,19 @@ module Lab
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class ConfigNotFound < RuntimeError; end
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class << self
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def preferred_api
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emr_api_application('lims_api', 'couchdb')
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end
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##
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# Returns LIMS' couchdb configuration file for the current environment (Rails.env)
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def couchdb
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config_path = begin
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find_config_path('couchdb.yml')
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rescue ConfigNotFound => e
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Rails.logger.error("Failed to find default LIMS couchdb config: #{e.message}")
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find_config_path('couchdb-lims.yml') # This can be placed in HIS-EMR-API/config
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end
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Rails.logger.debug("Using LIMS couchdb config: #{config_path}")
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@@ -64,9 +68,7 @@ module Lab
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@emr_api_application ||= YAML.load_file(Rails.root.join('config', 'application.yml'))
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@emr_api_application.fetch(param) do
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unless fallback
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raise ConfigNotFound, "Missing config param: #{param}"
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end
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raise ConfigNotFound, "Missing config param: #{param}" unless fallback
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fallback
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end
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@@ -83,9 +85,7 @@ module Lab
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Rails.root.parent.join("nlims_controller/config/#{filename}")
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]
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if filename == 'couchdb.yml'
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paths = [Rails.root.join('config/lims-couchdb.yml'), *paths]
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end
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paths = [Rails.root.join('config/lims-couchdb.yml'), *paths] if filename == 'couchdb.yml'
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paths.each do |path|
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Rails.logger.debug("Looking for LIMS couchdb config at: #{path}")
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@@ -69,9 +69,7 @@ module Lab
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end
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def start_date
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if self['date_created'].blank?
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raise LimsException, 'Order missing created date'
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end
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raise LimsException, 'Order missing created date' if self['date_created'].blank?
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Utils.parse_date(self['date_created'])
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end
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@@ -85,7 +83,7 @@ module Lab
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# Translates a LIMS sample priority to a concept_id
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def reason_for_test
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return
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return nil unless self['priority']
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name = case self['priority']
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when %r{Reapet / Missing}i then 'Repeat / Missing'
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@@ -2,6 +2,8 @@
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require 'logger_multiplexor'
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require_relative './api/couchdb_api'
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module Lab
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module Lims
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##
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def self.start_push_worker
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start_worker('push_worker') do
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-
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worker = PushWorker.new(api)
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worker = PushWorker.new(lims_api)
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worker.push_orders # (wait: true)
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end
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@@ -28,8 +29,7 @@ module Lab
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def self.start_pull_worker
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start_worker('pull_worker') do
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worker = PullWorker.new(api)
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worker = PullWorker.new(lims_api)
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worker.pull_orders
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end
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@@ -37,8 +37,7 @@ module Lab
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def self.start_realtime_pull_worker
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start_worker('realtime_pull_worker') do
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worker = PullWorker.new(api)
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worker = PullWorker.new(Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket))
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worker.pull_orders
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end
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Rails.logger.warn("Check for realtime updates failed: #{e.message}")
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false
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end
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def self.lims_api
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case Lims::Config.preferred_api
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when /couchdb/i then Api::CouchDbApi.new(config: Lab::Lims::Config.couchdb)
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when /rest/i then Api::RestApi.new(Lab::Lims::Config.rest_api)
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else raise "Invalid LIMS API in application.yml, expected 'rest' or 'couchdb'"
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end
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end
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end
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end
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end
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@@ -66,9 +66,7 @@ module Lab
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def update_order(order_id, params)
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specimen_id = params.dig(:specimen, :concept_id)
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unless specimen_id
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raise ::InvalidParameterError, 'Specimen concept_id is required'
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end
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raise ::InvalidParameterError, 'Specimen concept_id is required' unless specimen_id
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order = Lab::LabOrder.find(order_id)
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if order.concept_id != unknown_concept_id && !params[:force_update]&.casecmp?('true')
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discontinued_reason_non_coded: 'Sample drawn/updated')
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end
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if params
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if params[:reason_for_test_id]
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Rails.logger.debug("Updating reason for test on order ##{order.order_id}")
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update_reason_for_test(order, params[:reason_for_test_id])
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end
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# a 'Lab' encounter is created using the provided program_id and
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# patient_id.
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def find_encounter(order_params)
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if order_params[:encounter_id]
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return Encounter.find(order_params[:encounter_id])
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end
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return Encounter.find(order_params[:encounter_id]) if order_params[:encounter_id]
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unless order_params[:patient_id]
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raise InvalidParameterError, 'encounter_id or patient_id required'
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end
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raise InvalidParameterError, 'encounter_id or patient_id required' unless order_params[:patient_id]
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program_id = order_params[:program_id] || Program.find_by_name!(Lab::Metadata::LAB_PROGRAM_NAME).program_id
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end
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def update_reason_for_test(order, concept_id)
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if concept_id.blank?
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raise InvalidParameterError, "Reason for test can't be blank"
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end
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raise InvalidParameterError, "Reason for test can't be blank" if concept_id.blank?
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return if order.reason_for_test&.value_coded == concept_id
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raise InvalidParameterError, "Can't change reason for test once set"
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end
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raise InvalidParameterError, "Can't change reason for test once set" if order.reason_for_test&.value_coded
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order.reason_for_test
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order.reason_for_test&.delete
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add_reason_for_test(order, date: order.start_date, reason_for_test_id: concept_id)
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end
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end
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data/lib/lab/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: his_emr_api_lab
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version: !ruby/object:Gem::Version
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version: 1.1.
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version: 1.1.3
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platform: ruby
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authors:
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- Elizabeth Glaser Pediatric Foundation Malawi
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2021-07-
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date: 2021-07-19 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: couchrest
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