his_emr_api_lab 1.1.2 → 1.1.6
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- checksums.yaml +4 -4
- data/app/services/lab/lims/api/couchdb_api.rb +3 -0
- data/app/services/lab/lims/api/rest_api.rb +3 -0
- data/app/services/lab/lims/config.rb +11 -11
- data/app/services/lab/lims/order_dto.rb +2 -4
- data/app/services/lab/lims/order_serializer.rb +2 -4
- data/app/services/lab/lims/push_worker.rb +6 -1
- data/app/services/lab/lims/worker.rb +13 -6
- data/app/services/lab/orders_service.rb +7 -17
- data/db/migrate/20210807111531_add_default_to_lims_order_mapping.rb +7 -0
- 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: ec3adbde37c8f4213c049a83371cd30deb35a4833e3f95d5ace57bf9e2344e02
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4
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+
data.tar.gz: 2b676b2060b642493906794747160939e9d5cec15e94f87cb35e486434e4a7cd
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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: 232dbd10ff1f15f18432d3421e99ecce64ab5855c30fc0d6f028bfe3cce291f29d5954453c0f7bc6f9d9c27a5990ac16299677721188d4d0b981734ba23d283f
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7
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+
data.tar.gz: 2f823d4b6edc2494f405002dc6681eb895ec7e961c817dd7c02b6688e286edf9a72b9467651d39d743d74a4bee094a4590150020002c3028a69d8534696af8de
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@@ -11,15 +11,19 @@ module Lab
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11
11
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class ConfigNotFound < RuntimeError; end
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12
12
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13
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class << self
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14
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+
def preferred_api
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15
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+
emr_api_application('lims_api', 'couchdb')
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16
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+
end
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17
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+
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14
18
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##
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15
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# Returns LIMS' couchdb configuration file for the current environment (Rails.env)
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16
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def couchdb
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17
21
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config_path = begin
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18
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-
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19
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-
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20
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-
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21
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-
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22
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-
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22
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+
find_config_path('couchdb.yml')
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+
rescue ConfigNotFound => e
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24
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+
Rails.logger.error("Failed to find default LIMS couchdb config: #{e.message}")
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25
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+
find_config_path('couchdb-lims.yml') # This can be placed in HIS-EMR-API/config
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26
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+
end
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23
27
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24
28
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Rails.logger.debug("Using LIMS couchdb config: #{config_path}")
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25
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@@ -64,9 +68,7 @@ module Lab
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64
68
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@emr_api_application ||= YAML.load_file(Rails.root.join('config', 'application.yml'))
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65
69
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66
70
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@emr_api_application.fetch(param) do
|
67
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-
unless fallback
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68
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-
raise ConfigNotFound, "Missing config param: #{param}"
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69
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-
end
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71
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+
raise ConfigNotFound, "Missing config param: #{param}" unless fallback
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70
72
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fallback
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72
74
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end
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@@ -83,9 +85,7 @@ module Lab
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85
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Rails.root.parent.join("nlims_controller/config/#{filename}")
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84
86
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]
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85
87
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|
86
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-
if filename == 'couchdb.yml'
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87
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-
paths = [Rails.root.join('config/lims-couchdb.yml'), *paths]
|
88
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-
end
|
88
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+
paths = [Rails.root.join('config/lims-couchdb.yml'), *paths] if filename == 'couchdb.yml'
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89
89
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90
90
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paths.each do |path|
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91
91
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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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69
69
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end
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70
70
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71
71
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def start_date
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72
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-
if self['date_created'].blank?
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73
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-
raise LimsException, 'Order missing created date'
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74
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-
end
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72
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+
raise LimsException, 'Order missing created date' if self['date_created'].blank?
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75
73
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76
74
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Utils.parse_date(self['date_created'])
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77
75
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end
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@@ -85,7 +83,7 @@ module Lab
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85
83
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86
84
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# Translates a LIMS sample priority to a concept_id
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85
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def reason_for_test
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88
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-
return
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86
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+
return nil unless self['priority']
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89
87
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|
90
88
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name = case self['priority']
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when %r{Reapet / Missing}i then 'Repeat / Missing'
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@@ -64,7 +64,7 @@ module Lab
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64
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first_name: name&.given_name,
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65
65
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last_name: name&.family_name,
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66
66
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id: national_id&.identifier,
|
67
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-
phone_number: phone_number&.value,
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67
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+
phone_number: phone_number&.value || 'Unknown',
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68
68
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gender: person.gender,
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69
69
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email: nil
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}
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@@ -83,9 +83,7 @@ module Lab
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83
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end
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84
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85
85
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def format_sample_status_trail(order)
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86
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-
if order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
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87
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-
return []
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88
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-
end
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86
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+
return [] if order.concept_id == ConceptName.find_by_name!('Unknown').concept_id
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89
87
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90
88
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user = User.find(order.discontinued_by || order.creator)
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91
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drawn_by = PersonName.find_by_person_id(user.user_id)
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@@ -17,7 +17,12 @@ module Lab
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17
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loop do
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logger.info('Looking for new orders to push to LIMS...')
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19
19
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orders = orders_pending_sync(batch_size).all
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20
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-
orders.each
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20
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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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+
sleep(Lab::Lims::Config.updates_poll_frequency)
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25
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+
end
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# Doing this after .each above to stop ActiveRecord from executing
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# an extra request to the database (ActiveRecord's lazy evaluation
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@@ -2,6 +2,8 @@
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2
2
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3
3
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require 'logger_multiplexor'
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4
4
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5
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+
require_relative './api/couchdb_api'
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6
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+
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5
7
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module Lab
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6
8
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module Lims
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7
9
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##
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@@ -19,8 +21,7 @@ module Lab
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19
21
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20
22
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def self.start_push_worker
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21
23
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start_worker('push_worker') do
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22
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-
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23
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-
worker = PushWorker.new(api)
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24
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+
worker = PushWorker.new(lims_api)
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24
25
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|
25
26
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worker.push_orders # (wait: true)
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26
27
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end
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@@ -28,8 +29,7 @@ module Lab
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29
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29
30
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def self.start_pull_worker
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30
31
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start_worker('pull_worker') do
|
31
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-
|
32
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-
worker = PullWorker.new(api)
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32
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+
worker = PullWorker.new(lims_api)
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33
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34
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worker.pull_orders
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35
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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
|
40
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-
|
41
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-
worker = PullWorker.new(api)
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40
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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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@@ -71,6 +70,14 @@ module Lab
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Rails.logger.warn("Check for realtime updates failed: #{e.message}")
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false
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73
72
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end
|
73
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+
|
74
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+
def self.lims_api
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75
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+
case Lims::Config.preferred_api
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76
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+
when /couchdb/i then Api::CouchDbApi.new(config: Lab::Lims::Config.couchdb)
|
77
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+
when /rest/i then Api::RestApi.new(Lab::Lims::Config.rest_api)
|
78
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+
else raise "Invalid LIMS API in application.yml, expected 'rest' or 'couchdb'"
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79
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+
end
|
80
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+
end
|
74
81
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end
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75
82
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end
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76
83
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end
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@@ -66,9 +66,7 @@ module Lab
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66
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67
67
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def update_order(order_id, params)
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68
68
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specimen_id = params.dig(:specimen, :concept_id)
|
69
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-
unless specimen_id
|
70
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-
raise ::InvalidParameterError, 'Specimen concept_id is required'
|
71
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-
end
|
69
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+
raise ::InvalidParameterError, 'Specimen concept_id is required' unless specimen_id
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72
70
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73
71
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order = Lab::LabOrder.find(order_id)
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74
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if order.concept_id != unknown_concept_id && !params[:force_update]&.casecmp?('true')
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@@ -84,7 +82,7 @@ module Lab
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84
82
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discontinued_reason_non_coded: 'Sample drawn/updated')
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85
83
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end
|
86
84
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|
87
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-
if params
|
85
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+
if params[:reason_for_test_id]
|
88
86
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Rails.logger.debug("Updating reason for test on order ##{order.order_id}")
|
89
87
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update_reason_for_test(order, params[:reason_for_test_id])
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90
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end
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@@ -116,13 +114,9 @@ module Lab
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116
114
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# a 'Lab' encounter is created using the provided program_id and
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117
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# patient_id.
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118
116
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def find_encounter(order_params)
|
119
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-
if order_params[:encounter_id]
|
120
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-
return Encounter.find(order_params[:encounter_id])
|
121
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-
end
|
117
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+
return Encounter.find(order_params[:encounter_id]) if order_params[:encounter_id]
|
122
118
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|
123
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-
unless order_params[:patient_id]
|
124
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-
raise InvalidParameterError, 'encounter_id or patient_id required'
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125
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-
end
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119
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+
raise InvalidParameterError, 'encounter_id or patient_id required' unless order_params[:patient_id]
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126
120
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|
127
121
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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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128
122
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@@ -203,17 +197,13 @@ module Lab
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203
197
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end
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204
198
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205
199
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def update_reason_for_test(order, concept_id)
|
206
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-
if concept_id.blank?
|
207
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-
raise InvalidParameterError, "Reason for test can't be blank"
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208
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-
end
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200
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+
raise InvalidParameterError, "Reason for test can't be blank" if concept_id.blank?
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209
201
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|
210
202
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return if order.reason_for_test&.value_coded == concept_id
|
211
203
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|
212
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-
|
213
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-
raise InvalidParameterError, "Can't change reason for test once set"
|
214
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-
end
|
204
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+
raise InvalidParameterError, "Can't change reason for test once set" if order.reason_for_test&.value_coded
|
215
205
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|
216
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-
order.reason_for_test
|
206
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+
order.reason_for_test&.delete
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217
207
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add_reason_for_test(order, date: order.start_date, reason_for_test_id: concept_id)
|
218
208
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end
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219
209
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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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1
1
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--- !ruby/object:Gem::Specification
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2
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name: his_emr_api_lab
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3
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version: !ruby/object:Gem::Version
|
4
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-
version: 1.1.
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4
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+
version: 1.1.6
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platform: ruby
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authors:
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7
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- Elizabeth Glaser Pediatric Foundation Malawi
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autorequire:
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9
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bindir: bin
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10
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cert_chain: []
|
11
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-
date: 2021-07
|
11
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+
date: 2021-08-07 00:00:00.000000000 Z
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
|
14
14
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name: couchrest
|
@@ -290,6 +290,7 @@ files:
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290
290
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- db/migrate/20210326195504_add_order_revision_to_lims_order_mapping.rb
|
291
291
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- db/migrate/20210407071728_create_lab_lims_failed_imports.rb
|
292
292
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- db/migrate/20210610095024_fix_numeric_results_value_type.rb
|
293
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+
- db/migrate/20210807111531_add_default_to_lims_order_mapping.rb
|
293
294
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- lib/auto12epl.rb
|
294
295
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- lib/couch_bum/couch_bum.rb
|
295
296
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- lib/generators/lab/install/USAGE
|