his_emr_api_lab 0.0.7 → 0.0.12
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- checksums.yaml +4 -4
- data/app/services/lab/labelling_service/order_label.rb +27 -6
- data/app/services/lab/lims/failed_imports.rb +34 -0
- data/app/services/lab/lims/migrator.rb +1 -1
- data/app/services/lab/lims/order_dto.rb +4 -0
- data/app/services/lab/lims/utils.rb +2 -0
- data/app/services/lab/lims/worker.rb +3 -1
- data/lib/lab/version.rb +1 -1
- metadata +3 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
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: 38f48eba209b710d53ac07d89c95e335f9578a2b2b2137550b8b48f0032355f9
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4
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+
data.tar.gz: e6930b341721036f4aaeb8ab64551eb1ed4d35e6b80314d181488265e1cda0ba
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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: 2f9873af33a53537e59143efd1bf6b36fe5af1201be7cd463c42d14417babfb31640f3a46e12bd5dc73d709fa6075ea619a1faf868143f1f3f9a641341342c85
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7
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+
data.tar.gz: dbc656255bdb6c160a71771c06532d533ec90f38a6d7e37f5d1880564dcacf874097fe2c5ce424da60602117674135fec6859dda4380f3c4ef20cf4fd3235777
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@@ -27,7 +27,7 @@ module Lab
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27
27
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'',
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28
28
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drawer,
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29
29
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'',
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30
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-
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30
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+
tests,
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31
31
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reason_for_test,
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32
32
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order.accession_number,
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33
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order.accession_number)
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@@ -36,7 +36,7 @@ module Lab
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36
36
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def reason_for_test
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37
37
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return 'Unknown' unless order.reason_for_test
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38
38
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39
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-
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39
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+
short_concept_name(order.reason_for_test.value_coded) || 'Unknown'
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40
40
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end
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41
41
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42
42
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def patient
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@@ -60,11 +60,14 @@ module Lab
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60
60
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def drawer
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61
61
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return 'N/A' if order.concept_id == unknown_concept.concept_id
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62
62
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63
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-
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64
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-
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63
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+
drawer_id = order.discontinued_by || order.creator
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64
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+
draw_date = (order.discontinued_date || order.start_date).strftime('%d/%^b/%Y %H:%M:%S')
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65
65
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66
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-
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67
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-
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66
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+
name = PersonName.find_by_person_id(drawer_id)
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67
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+
return "#{name.given_name} #{name.family_name} #{draw_date}" if name
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68
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+
|
69
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+
user = User.find_by_user_id(drawer_id)
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70
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+
user ? "#{user.username} #{draw_date}" : 'N/A'
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68
71
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end
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69
72
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|
70
73
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def specimen
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@@ -73,6 +76,24 @@ module Lab
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73
76
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ConceptName.find_by_concept_id(order.concept_id)&.name || 'Unknown'
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74
77
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end
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75
78
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|
79
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+
def tests
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80
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+
tests = order.tests.map do |test|
|
81
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+
name = short_concept_name(test.value_coded) || 'Unknown'
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82
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+
|
83
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+
next 'VL' if name.match?(/Viral load/i)
|
84
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+
|
85
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+
name.size > 7 ? name[0..6] : name
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86
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+
end
|
87
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+
|
88
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+
tests.join(', ')
|
89
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end
|
90
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+
|
91
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+
def short_concept_name(concept_id)
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92
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+
ConceptName.where(concept_id: concept_id)
|
93
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.min_by { |concept| concept.name.size }
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94
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+
&.name
|
95
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+
end
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96
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+
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76
97
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def unknown_concept
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77
98
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ConceptName.find_by_name('Unknown')
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78
99
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end
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@@ -0,0 +1,34 @@
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1
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+
# frozen_string_literal: true
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2
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+
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3
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+
require_relative './api'
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4
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+
require_relative './order_dto'
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5
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+
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6
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+
module Lab
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7
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+
module Lims
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8
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+
##
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9
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+
# Manage LIMS orders that failed to import
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10
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+
module FailedImports
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11
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+
class << self
|
12
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+
##
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13
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+
# Retrieve all imports that failed
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14
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+
def failed_imports(start_id = 0, limit = 20)
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15
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Lab::LimsFailedImport.where('id >= ?', start_id).limit(limit)
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16
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end
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17
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+
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18
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##
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19
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# Forcefully imports a failed import into a patient
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20
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def force_import(failed_import_id, _patient_id)
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21
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failed_import = Lab::LimsFailedImport.find(failed_import_id)
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22
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order_dto = Lab::Lims::OrderDTO.new(lims_api.find_order(failed_import.lims_id))
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23
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byebug
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24
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+
end
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25
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+
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26
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private
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27
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+
|
28
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def lims_api
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29
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@lims_api ||= Lab::Lims::Api.new
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30
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end
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31
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end
|
32
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+
end
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33
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end
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34
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+
end
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@@ -66,6 +66,8 @@ module Lab
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66
66
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Date.strptime(str_date, '%d-%m-%Y').strftime('%Y-%m-%d')
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67
67
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elsif str_date.match?(/(\d{4}\d{2}\d{2})\d+/)
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68
68
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Date.strptime(str_date, '%Y%m%d').strftime('%Y-%m-%d')
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69
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+
elsif str_date.match?(%r{\d{2}/\d{2}/\d{4}})
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70
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+
str_date.to_date.to_s
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69
71
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else
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70
72
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Rails.logger.warn("Invalid date: #{str_date}")
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71
73
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parse_date(fallback_date)
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@@ -28,7 +28,9 @@ module Lab
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28
28
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fout.write("Worker ##{Process.pid} started at #{Time.now}")
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29
29
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worker = new(Api.new)
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30
30
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worker.pull_orders
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31
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-
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31
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+
# TODO: Verify that names being pushed to LIMS are of the correct format (ie matching
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32
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+
# LIMS naming conventions). Enable pushing when that is done
|
33
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+
# worker.push_orders
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32
34
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end
|
33
35
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end
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34
36
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data/lib/lab/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
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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
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-
version: 0.0.
|
4
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+
version: 0.0.12
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Elizabeth Glaser Pediatric Foundation Malawi
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8
8
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autorequire:
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9
9
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bindir: bin
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10
10
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cert_chain: []
|
11
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-
date: 2021-04-
|
11
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+
date: 2021-04-30 00:00:00.000000000 Z
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12
12
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dependencies:
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13
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- !ruby/object:Gem::Dependency
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14
14
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name: couchrest
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@@ -252,6 +252,7 @@ files:
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252
252
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- app/services/lab/lims/api.rb
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253
253
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- app/services/lab/lims/config.rb
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254
254
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- app/services/lab/lims/exceptions.rb
|
255
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+
- app/services/lab/lims/failed_imports.rb
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255
256
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- app/services/lab/lims/migrator.rb
|
256
257
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- app/services/lab/lims/order_dto.rb
|
257
258
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- app/services/lab/lims/order_serializer.rb
|