his_emr_api_lab 0.0.3 → 0.0.4
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- checksums.yaml +4 -4
- data/app/services/lab/lims/api.rb +0 -5
- data/app/services/lab/lims/migrator.rb +10 -19
- data/app/services/lab/lims/order_serializer.rb +3 -1
- data/app/services/lab/lims/utils.rb +12 -0
- data/app/services/lab/lims/worker.rb +24 -6
- data/lib/couch_bum/couch_bum.rb +10 -5
- data/lib/lab/version.rb +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: f53ca7acc69718ba31cf2ae278b6fdbdc4996d3ad6a28db0a08d3945d1463998
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4
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+
data.tar.gz: 77b2cfdc430706b9864e9ec71b2f4b64c2ec11a5695b45b81984c86a8fefefd4
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 19f53f3c471dd4552f64bf1200a6bbd8051e7bc7bc7e0670b2079bea4af61621575a9c0e7f5cdc06c43ac7b80c2534e6ca704fd06e43b0deed3475ea66690017
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7
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+
data.tar.gz: cbe4e02964f635b60e7e7b0c6b53ac3b406ab9bff55da582371a3de38a8d65901bcca1771a7b3cf0d8be83e31ac8bf0a15e9c752f7131bb631f1011df95fa713
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@@ -29,16 +29,11 @@ module Lab
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# given block until the queue is empty or connection is terminated
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# by calling method +choke+.
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def consume_orders(from: 0, limit: 30)
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32
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-
last_seq = { value: 0 }
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-
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bum.binge_changes(since: from, limit: limit, include_docs: true) do |change|
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next unless change['doc']['type']&.casecmp?('Order')
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yield OrderDTO.new(change['doc']), self
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-
last_seq[:value] = self.last_seq
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end
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-
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-
last_seq[:value]
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end
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def create_order(order)
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@@ -29,6 +29,7 @@ require 'lab/lab_test'
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require 'lab/lims_order_mapping'
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require 'lab/lims_failed_import'
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+
require_relative './worker'
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require_relative '../orders_service'
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require_relative '../results_service'
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require_relative '../tests_service'
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@@ -47,14 +48,16 @@ module Lab
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attr_reader :rejections
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50
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-
def consume_orders(from: nil,
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51
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+
def consume_orders(from: nil, **_kwargs)
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52
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+
limit = 50_000
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53
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+
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51
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Parallel.each(read_orders(from, limit),
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in_processes: MAX_THREADS,
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finish: order_pmap_post_processor(from)) do |row|
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next unless row['doc']['type']&.casecmp?('Order')
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-
User.current =
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-
yield OrderDTO.new(row['doc']), OpenStruct.new(last_seq: from)
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+
User.current = Utils.lab_user
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+
yield OrderDTO.new(row['doc']), OpenStruct.new(last_seq: (from || 0) + limit, current_seq: from)
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end
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end
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@@ -70,7 +73,7 @@ module Lab
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private
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def last_seq_path
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-
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+
LIMS_LOG_PATH.join('migration-last-id.dat')
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end
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def order_pmap_post_processor(last_seq)
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@@ -129,18 +132,6 @@ module Lab
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def update_last_seq(_last_seq); end
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end
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-
def self.lab_user
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-
user = User.find_by_username('lab_daemon')
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-
return user if user
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-
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-
god_user = User.first
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-
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-
person = Person.create!(creator: god_user.user_id)
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-
PersonName.create!(person: person, given_name: 'Lab', family_name: 'Daemon', creator: god_user.user_id)
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-
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-
User.create!(username: 'lab_daemon', person: person, creator: god_user.user_id)
|
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-
end
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143
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-
|
144
135
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def self.save_csv(filename, rows:, headers: nil)
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CSV.open(filename, File::WRONLY | File::CREAT) do |csv|
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csv << headers if headers
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@@ -148,7 +139,7 @@ module Lab
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end
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end
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150
141
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151
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-
MIGRATION_REJECTIONS_CSV_PATH =
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142
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+
MIGRATION_REJECTIONS_CSV_PATH = LIMS_LOG_PATH.join('migration-rejections.csv')
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152
143
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153
144
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def self.export_rejections(rejections)
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154
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headers = ['Accession number', 'NHID', 'First name', 'Last name', 'Reason']
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@@ -165,7 +156,7 @@ module Lab
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save_csv(MIGRATION_REJECTIONS_CSV_PATH, headers: headers, rows: rows)
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end
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-
MIGRATION_FAILURES_CSV_PATH =
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+
MIGRATION_FAILURES_CSV_PATH = LIMS_LOG_PATH.join('migration-failures.csv')
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def self.export_failures
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headers = ['Accession number', 'NHID', 'Reason', 'Difference']
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@@ -181,7 +172,7 @@ module Lab
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save_csv(MIGRATION_FAILURES_CSV_PATH, headers: headers, rows: rows)
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end
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MIGRATION_LOG_PATH =
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+
MIGRATION_LOG_PATH = LIMS_LOG_PATH.join('migration.log')
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def self.start_migration
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log_dir = Rails.root.join('log/lims')
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@@ -97,7 +97,9 @@ module Lab
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end
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99
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def format_test_results(order)
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100
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-
order.tests
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100
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order.tests&.each_with_object({}) do |test, results|
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101
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next unless test.result
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102
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+
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results[test.name] = {
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results: test.result.each_with_object({}) do |measure, measures|
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measures[measure.indicator.name] = { result_value: "#{measure.value_modifier}#{measure.value}" }
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@@ -39,6 +39,18 @@ module Lab
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end
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end
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def self.lab_user
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user = User.find_by_username('lab_daemon')
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return user if user
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+
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god_user = User.first
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person = Person.create!(creator: god_user.user_id)
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PersonName.create!(person: person, given_name: 'Lab', family_name: 'Daemon', creator: god_user.user_id)
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+
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User.create!(username: 'lab_daemon', person: person, creator: god_user.user_id)
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end
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+
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def self.parse_date(str_date, fallback_date = nil)
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if str_date.blank? && fallback_date.blank?
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raise "Can't parse blank date"
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@@ -2,12 +2,16 @@
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require 'cgi/util'
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require_relative './api'
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require_relative './exceptions'
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require_relative './order_serializer'
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require_relative './utils'
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module Lab
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module Lims
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12
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LIMS_LOG_PATH = Rails.root.join('log/lims')
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Dir.mkdir(LIMS_LOG_PATH) unless File.exist?(LIMS_LOG_PATH)
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##
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# Pull/Push orders from/to the LIMS queue (Oops meant CouchDB).
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class Worker
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@@ -15,6 +19,19 @@ module Lab
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attr_reader :lims_api
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def self.start
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File.open(LIMS_LOG_PATH.join('worker.lock'), File::WRONLY | File::CREAT, 0o644) do |fout|
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fout.flock(File::LOCK_EX)
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+
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User.current = Utils.lab_user
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fout.write("Worker ##{Process.pid} started at #{Time.now}")
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worker = new(Api.new)
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worker.pull_orders
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worker.push_orders
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end
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end
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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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@@ -52,8 +69,8 @@ module Lab
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lims_api.update_order(mapping.lims_id, order_dto)
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mapping.update(pushed_at: Time.now)
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else
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-
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-
LimsOrderMapping.create!(order: order, lims_id:
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+
update = lims_api.create_order(order_dto)
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LimsOrderMapping.create!(order: order, lims_id: update['id'], revision: update['rev'], pushed_at: Time.now)
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end
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end
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@@ -64,7 +81,8 @@ module Lab
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# Pulls orders from the LIMS queue and writes them to the local database
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def pull_orders
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66
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logger.info("Retrieving LIMS orders starting from #{last_seq}")
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-
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+
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lims_api.consume_orders(from: last_seq, limit: 100) do |order_dto, context|
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logger.debug("Retrieved order ##{order_dto[:tracking_number]}: #{order_dto}")
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69
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patient = find_patient_by_nhid(order_dto[:patient][:id])
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@@ -80,6 +98,8 @@ module Lab
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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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+
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[:accepted, "Patient NPID, '#{order_dto[:patient][:id]}', matched"]
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rescue DuplicateNHID
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logger.warn("Failed to import order due to duplicate patient NHID: #{order_dto[:patient][:id]}")
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@@ -90,8 +110,6 @@ module Lab
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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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-
ensure
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update_last_seq(context.last_seq)
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end
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end
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@@ -303,7 +321,7 @@ module Lab
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end
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def last_seq_path
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306
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-
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+
LIMS_LOG_PATH.join('last_seq.dat')
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end
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end
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end
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data/lib/couch_bum/couch_bum.rb
CHANGED
@@ -24,18 +24,21 @@ class CouchBum
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# within the passed block.
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def binge_changes(since: 0, limit: nil, include_docs: nil, &block)
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catch(:choke) do
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-
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+
logger.debug("Binging #{limit} changes from '#{since}'")
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+
params = stringify_params(limit: limit, include_docs: include_docs)
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+
params = "since=#{since}&#{params}" unless since.blank?
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29
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-
changes = couch_rest(:get, "_changes
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+
changes = couch_rest(:get, "_changes?#{params}")
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context = BingeContext.new(changes)
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-
changes['results'].each
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+
changes['results'].each do |change|
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context.current_seq = change['seq']
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+
context.instance_exec(change, &block)
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+
end
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end
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end
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def couch_rest(method, route, *args, **kwargs)
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36
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url = expand_route(route)
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-
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-
logger.debug("CouchBum: Executing #{method} #{url}")
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CouchRest.send(method, url, *args, **kwargs)
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rescue CouchRest::Exception => e
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logger.error("Failed to communicate with CouchDB: Status: #{e.http_code} - #{e.http_body}")
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@@ -46,6 +49,8 @@ class CouchBum
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47
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# Context under which the callback passed to binge_changes is executed.
|
48
51
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class BingeContext
|
52
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+
attr_accessor :current_seq
|
53
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+
|
49
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def initialize(changes)
|
50
55
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@changes = changes
|
51
56
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end
|
data/lib/lab/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: his_emr_api_lab
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
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+
version: 0.0.4
|
5
5
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platform: ruby
|
6
6
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authors:
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- Elizabeth Glaser Pediatric Foundation Malawi
|
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autorequire:
|
9
9
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bindir: bin
|
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cert_chain: []
|
11
|
-
date: 2021-04-
|
11
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+
date: 2021-04-20 00:00:00.000000000 Z
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12
12
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dependencies:
|
13
13
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- !ruby/object:Gem::Dependency
|
14
14
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name: couchrest
|