his_emr_api_lab 1.0.5 → 1.1.0
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/README.md +20 -1
- data/app/jobs/lab/update_patient_orders_job.rb +20 -0
- data/app/jobs/lab/void_order_job.rb +18 -0
- data/app/models/lab/lab_order.rb +4 -0
- data/app/serializers/lab/lab_order_serializer.rb +7 -1
- data/app/services/lab/lims/api/rest_api.rb +344 -0
- data/app/services/lab/lims/api/ws_api.rb +121 -0
- data/app/services/lab/lims/config.rb +45 -8
- data/app/services/lab/lims/migrator.rb +12 -9
- data/app/services/lab/lims/order_serializer.rb +31 -8
- data/app/services/lab/lims/pull_worker.rb +295 -0
- data/app/services/lab/lims/push_worker.rb +103 -0
- data/app/services/lab/lims/utils.rb +6 -1
- data/app/services/lab/lims/worker.rb +40 -317
- data/app/services/lab/orders_search_service.rb +18 -0
- data/app/services/lab/orders_service.rb +4 -2
- data/lib/lab/version.rb +1 -1
- metadata +22 -3
- data/app/services/lab/lims/failed_imports.rb +0 -33
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 69ffcbf9ab0cea24c83a5e18f9298af7599090009eea8f17f111c37333902b64
|
4
|
+
data.tar.gz: 2e4dab1daa94bfa9af75510691c40505468bfb4faaa5410eaaf6cf43ee47e8f8
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 951f366fed5cc8ac190a7b73bcf958a9f93eb233d724fb9b30d42b9f4b5de78985cd20a01cc262fa85a795fb4fdf86d3d8e912e11256b25b980605493319f736
|
7
|
+
data.tar.gz: da971e7cb0f69ea705fcf2b8f9a52d2101959183b20004c0330c2103ec49d03a3c16492b8e3908d3f8ffd13f128a444f6b011c54fdfd37fb982ab392b840a0f0
|
data/README.md
CHANGED
@@ -43,9 +43,28 @@ Finally run:
|
|
43
43
|
$ bundle exec rails lab:install
|
44
44
|
```
|
45
45
|
|
46
|
+
## Configuration
|
47
|
+
|
48
|
+
This module in most cases should work without any configuration, however to enable
|
49
|
+
certain features some configuration may be required. Visit the
|
50
|
+
[configuration](./docs/configuration.md) page to learn how to configure the
|
51
|
+
application.
|
52
|
+
|
46
53
|
## Contributing
|
47
54
|
|
48
|
-
|
55
|
+
Fork this application create a branch for the contribution you want to make,
|
56
|
+
push your changes to the branch and then issue a pull request. You may want
|
57
|
+
to create a new first on our repository, so that your pull request references
|
58
|
+
this issue.
|
59
|
+
|
60
|
+
If you are fixing a bug, it will be nice to add a unit test that exposes
|
61
|
+
the bug. Although this is not a requirement in most cases.
|
62
|
+
|
63
|
+
Be sure to follow [this](https://github.com/rubocop/ruby-style-guide) Ruby
|
64
|
+
style guide. We don't necessarily look for strict adherence to the guidelines
|
65
|
+
but too much a departure from it is frowned upon. For example, you will be forgiven
|
66
|
+
for writing a method with 15 to 20 lines if you clearly justify why you couldn't
|
67
|
+
break that method into multiple smaller methods.
|
49
68
|
|
50
69
|
## License
|
51
70
|
|
@@ -0,0 +1,20 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
module Lab
|
4
|
+
##
|
5
|
+
# Fetches updates on a patient's orders from external sources.
|
6
|
+
class UpdatePatientOrdersJob < ApplicationJob
|
7
|
+
queue_as :default
|
8
|
+
|
9
|
+
def perform(patient_id)
|
10
|
+
Rails.logger.info('Initialising LIMS REST API...')
|
11
|
+
|
12
|
+
User.current = Lab::Lims::Utils.lab_user
|
13
|
+
Location.current = Location.find_by_name('ART clinic')
|
14
|
+
|
15
|
+
lims_api = Lab::Lims::Api::RestApi.new
|
16
|
+
worker = Lab::Lims::Worker.new(lims_api)
|
17
|
+
worker.pull_orders(patient_id: patient_id)
|
18
|
+
end
|
19
|
+
end
|
20
|
+
end
|
@@ -0,0 +1,18 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
module Lab
|
4
|
+
class VoidOrderJob < ApplicationJob
|
5
|
+
queue_as :default
|
6
|
+
|
7
|
+
def perform(order_id)
|
8
|
+
Rails.logger.info("Voiding order ##{order_id} in LIMS")
|
9
|
+
|
10
|
+
User.current = Lab::Lims::Utils.lab_user
|
11
|
+
Location.current = Location.find_by_name('ART clinic')
|
12
|
+
|
13
|
+
lims_api = Lab::Lims::Api::RestApi.new
|
14
|
+
worker = Lab::Lims::Worker.new(lims_api)
|
15
|
+
worker.push_order(Lab::LabOrder.unscoped.find(order_id))
|
16
|
+
end
|
17
|
+
end
|
18
|
+
end
|
data/app/models/lab/lab_order.rb
CHANGED
@@ -41,6 +41,10 @@ module Lab
|
|
41
41
|
.where.not(concept_id: ConceptName.where(name: 'Tests ordered').select(:concept_id))
|
42
42
|
end
|
43
43
|
|
44
|
+
scope :drawn, -> { where.not(concept_id: ConceptName.where(name: 'Unknown').select(:concept_id)) }
|
45
|
+
|
46
|
+
scope :not_drawn, -> { where(concept_id: ConceptName.where(name: 'Unknown').select(:concept_id)) }
|
47
|
+
|
44
48
|
def self.prefetch_relationships
|
45
49
|
includes(:reason_for_test,
|
46
50
|
:requesting_clinician,
|
@@ -3,7 +3,7 @@
|
|
3
3
|
module Lab
|
4
4
|
module LabOrderSerializer
|
5
5
|
def self.serialize_order(order, tests: nil, requesting_clinician: nil, reason_for_test: nil, target_lab: nil)
|
6
|
-
tests ||= order.tests
|
6
|
+
tests ||= order.voided == 1 ? voided_tests(order) : order.tests
|
7
7
|
requesting_clinician ||= order.requesting_clinician
|
8
8
|
reason_for_test ||= order.reason_for_test
|
9
9
|
target_lab ||= order.target_lab
|
@@ -45,5 +45,11 @@ module Lab
|
|
45
45
|
|
46
46
|
ConceptName.select(:name).find_by_concept_id(concept_id)&.name
|
47
47
|
end
|
48
|
+
|
49
|
+
def self.voided_tests(order)
|
50
|
+
concept = ConceptName.where(name: Lab::Metadata::TEST_TYPE_CONCEPT_NAME)
|
51
|
+
.select(:concept_id)
|
52
|
+
LabTest.unscoped.where(concept: concept, order: order, voided: true)
|
53
|
+
end
|
48
54
|
end
|
49
55
|
end
|
@@ -0,0 +1,344 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
class Lab::Lims::Api::RestApi
|
4
|
+
class LimsApiError < GatewayError; end
|
5
|
+
|
6
|
+
class AuthenticationTokenExpired < LimsApiError; end
|
7
|
+
|
8
|
+
class InvalidParameters < LimsApiError; end
|
9
|
+
|
10
|
+
def initialize(config)
|
11
|
+
@config = config
|
12
|
+
end
|
13
|
+
|
14
|
+
def create_order(order_dto)
|
15
|
+
response = in_authenticated_session do |headers|
|
16
|
+
Rails.logger.info("Pushing order ##{order_dto[:tracking_number]} to LIMS")
|
17
|
+
|
18
|
+
if order_dto['sample_type'].casecmp?('not_specified')
|
19
|
+
RestClient.post(expand_uri('request_order', api_version: 'v2'), make_create_params(order_dto), headers)
|
20
|
+
else
|
21
|
+
RestClient.post(expand_uri('create_order'), make_create_params(order_dto), headers)
|
22
|
+
end
|
23
|
+
end
|
24
|
+
|
25
|
+
update_order_results(order_dto)
|
26
|
+
|
27
|
+
data = JSON.parse(response.body)['data']
|
28
|
+
|
29
|
+
ActiveSupport::HashWithIndifferentAccess.new(
|
30
|
+
id: data['tracking_number'],
|
31
|
+
rev: 0,
|
32
|
+
tracking_number: data['tracking_number']
|
33
|
+
)
|
34
|
+
end
|
35
|
+
|
36
|
+
def update_order(_id, order_dto)
|
37
|
+
in_authenticated_session do |headers|
|
38
|
+
RestClient.post(expand_uri('update_order'), make_update_params(order_dto), headers)
|
39
|
+
end
|
40
|
+
|
41
|
+
update_order_results(order_dto)
|
42
|
+
|
43
|
+
{ tracking_number: order_dto[:tracking_number] }
|
44
|
+
end
|
45
|
+
|
46
|
+
def consume_orders(*_args, patient_id: nil, **_kwargs)
|
47
|
+
Rails.logger.info('Looking for orders without results...')
|
48
|
+
orders = Lab::OrdersSearchService.find_orders_without_results(patient_id: patient_id)
|
49
|
+
|
50
|
+
orders.each do |order|
|
51
|
+
response = in_authenticated_session do |headers|
|
52
|
+
Rails.logger.info("Fetching results for order ##{order.accession_number}")
|
53
|
+
RestClient.get(expand_uri("query_results_by_tracking_number/#{order.accession_number}"), headers)
|
54
|
+
end
|
55
|
+
|
56
|
+
Rails.logger.info("Result for order ##{order.accession_number} found... Parsing...")
|
57
|
+
results = JSON.parse(response).fetch('data').fetch('results')
|
58
|
+
order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
|
59
|
+
yield lims_results_to_order_dto(results, order_dto), OpenStruct.new(last_seq: 0)
|
60
|
+
rescue InvalidParameters => e # LIMS responds with a 401 when a result is not found :(
|
61
|
+
Rails.logger.error("Failed to fetch results for ##{order.accession_number}: #{e.message}")
|
62
|
+
end
|
63
|
+
end
|
64
|
+
|
65
|
+
def delete_order(_id, order_dto)
|
66
|
+
tracking_number = order_dto.fetch('tracking_number')
|
67
|
+
|
68
|
+
order_dto['tests'].each do |test|
|
69
|
+
Rails.logger.info("Voiding test '#{test}' (#{tracking_number}) in LIMS")
|
70
|
+
in_authenticated_session do |headers|
|
71
|
+
date_voided, voided_status = find_test_status(order_dto, test, 'Voided')
|
72
|
+
params = make_void_test_params(tracking_number, test, voided_status['updated_by'], date_voided)
|
73
|
+
RestClient.post(expand_uri('update_test'), params, headers)
|
74
|
+
end
|
75
|
+
end
|
76
|
+
end
|
77
|
+
|
78
|
+
private
|
79
|
+
|
80
|
+
attr_reader :config
|
81
|
+
|
82
|
+
MAX_LIMS_RETRIES = 5 # LIMS API Calls can only fail this number of times before we give up on it
|
83
|
+
|
84
|
+
##
|
85
|
+
# Execute LIMS API calls within an authenticated session.
|
86
|
+
#
|
87
|
+
# Method automatically checks authenticates with LIMS if necessary and passes
|
88
|
+
# down the necessary headers for authentication to the REST call being made.
|
89
|
+
#
|
90
|
+
# Example:
|
91
|
+
#
|
92
|
+
# response = in_authenticated_session do |headers|
|
93
|
+
# RestClient.get(expand_uri('query_results_by_tracking_number/XXXXXX'), headers)
|
94
|
+
# end
|
95
|
+
#
|
96
|
+
# pp JSON.parse(response.body) if response.code == 200
|
97
|
+
def in_authenticated_session
|
98
|
+
retries ||= MAX_LIMS_RETRIES
|
99
|
+
|
100
|
+
self.authentication_token = authenticate unless authentication_token
|
101
|
+
|
102
|
+
response = yield 'token' => authentication_token, 'Content-type' => 'application/json'
|
103
|
+
check_response!(response)
|
104
|
+
rescue AuthenticationTokenExpired => e
|
105
|
+
self.authentication_token = nil
|
106
|
+
retry if (retries -= 1).positive?
|
107
|
+
rescue RestClient::ExceptionWithResponse => e
|
108
|
+
Rails.logger.error("LIMS Error: #{e.response.code} - #{e.response.body}")
|
109
|
+
raise e unless e.response.code == 401
|
110
|
+
|
111
|
+
self.authentication_token = nil
|
112
|
+
retry if (retries -= 1).positive?
|
113
|
+
end
|
114
|
+
|
115
|
+
def authenticate
|
116
|
+
username = config.fetch(:username)
|
117
|
+
password = config.fetch(:password)
|
118
|
+
|
119
|
+
Rails.logger.debug("Authenticating with LIMS as: #{username}")
|
120
|
+
response = RestClient.get(expand_uri("re_authenticate/#{username}/#{password}"), headers: { 'Content-type' => 'application/json' })
|
121
|
+
response_body = JSON.parse(response.body)
|
122
|
+
|
123
|
+
if response_body['status'] == 401
|
124
|
+
Rails.logger.error("Failed to authenticate with LIMS as #{config.fetch(:username)}: #{response_body['message']}")
|
125
|
+
raise LimsApiError, 'LIMS authentication failed'
|
126
|
+
end
|
127
|
+
|
128
|
+
response_body['data']['token']
|
129
|
+
end
|
130
|
+
|
131
|
+
def authentication_token=(token)
|
132
|
+
Thread.current[:lims_authentication_token] = token
|
133
|
+
end
|
134
|
+
|
135
|
+
def authentication_token
|
136
|
+
Thread.current[:lims_authentication_token]
|
137
|
+
end
|
138
|
+
|
139
|
+
##
|
140
|
+
# Examines a response from LIMS to check if token has expired.
|
141
|
+
#
|
142
|
+
# LIMS' doesn't properly use HTTP status codes; the codes are embedded in the
|
143
|
+
# response body. 200 is used for success responses and 401 for everything else.
|
144
|
+
# We have this work around to examine the response body and
|
145
|
+
# throw errors accordingly. The following are the errors thrown:
|
146
|
+
#
|
147
|
+
# Lims::AuthenticationTokenExpired
|
148
|
+
# Lims::InvalidParameters
|
149
|
+
# Lims::ApiError - Thrown when we couldn't make sense of the error
|
150
|
+
def check_response!(response)
|
151
|
+
body = JSON.parse(response.body)
|
152
|
+
return response if body['status'] == 200
|
153
|
+
|
154
|
+
Rails.logger.error("Lims Api Error: #{response.body}")
|
155
|
+
|
156
|
+
if body['status'] != 401
|
157
|
+
raise LimsApiError, "#{body['status']} - #{body['message']}"
|
158
|
+
end
|
159
|
+
|
160
|
+
if body['message'].match?(/token expired/i)
|
161
|
+
raise AuthenticationTokenExpired, "Authentication token expired: #{body['message']}"
|
162
|
+
end
|
163
|
+
|
164
|
+
raise InvalidParameters, body['message']
|
165
|
+
end
|
166
|
+
|
167
|
+
##
|
168
|
+
# Takes a LIMS API relative URI and converts it to a full URL.
|
169
|
+
def expand_uri(uri, api_version: 'v1')
|
170
|
+
protocol = config.fetch(:protocol)
|
171
|
+
host = config.fetch(:host)
|
172
|
+
port = config.fetch(:port)
|
173
|
+
uri = uri.gsub(%r{^/+}, '')
|
174
|
+
|
175
|
+
"#{protocol}://#{host}:#{port}/api/#{api_version}/#{uri}"
|
176
|
+
end
|
177
|
+
|
178
|
+
##
|
179
|
+
# Converts an OrderDTO to parameters for POST /create_order
|
180
|
+
def make_create_params(order_dto)
|
181
|
+
{
|
182
|
+
tracking_number: order_dto.fetch(:tracking_number),
|
183
|
+
district: current_district,
|
184
|
+
health_facility_name: order_dto.fetch(:sending_facility),
|
185
|
+
first_name: order_dto.fetch(:patient).fetch(:first_name),
|
186
|
+
last_name: order_dto.fetch(:patient).fetch(:last_name),
|
187
|
+
phone_number: order_dto.fetch(:patient).fetch(:phone_number),
|
188
|
+
gender: order_dto.fetch(:patient).fetch(:gender),
|
189
|
+
national_patient_id: order_dto.fetch(:patient).fetch(:id),
|
190
|
+
requesting_clinician: requesting_clinician(order_dto),
|
191
|
+
sample_type: order_dto.fetch(:sample_type),
|
192
|
+
tests: order_dto.fetch(:tests),
|
193
|
+
date_sample_drawn: sample_drawn_date(order_dto),
|
194
|
+
sample_priority: order_dto.fetch(:priority) || 'Routine',
|
195
|
+
sample_status: order_dto.fetch(:sample_status),
|
196
|
+
target_lab: order_dto.fetch(:receiving_facility),
|
197
|
+
order_location: order_dto.fetch(:order_location) || 'Unknown',
|
198
|
+
who_order_test_first_name: order_dto.fetch(:who_order_test).fetch(:first_name),
|
199
|
+
who_order_test_last_name: order_dto.fetch(:who_order_test).fetch(:last_name)
|
200
|
+
}
|
201
|
+
end
|
202
|
+
|
203
|
+
##
|
204
|
+
# Converts an OrderDTO to parameters for POST /update_order
|
205
|
+
def make_update_params(order_dto)
|
206
|
+
date_updated, status = sample_drawn_status(order_dto)
|
207
|
+
|
208
|
+
{
|
209
|
+
tracking_number: order_dto.fetch(:tracking_number),
|
210
|
+
who_updated: status.fetch(:updated_by),
|
211
|
+
date_updated: date_updated,
|
212
|
+
specimen_type: order_dto.fetch(:sample_type),
|
213
|
+
status: 'specimen_collected'
|
214
|
+
}
|
215
|
+
end
|
216
|
+
|
217
|
+
def current_district
|
218
|
+
health_centre = Location.current_health_center
|
219
|
+
raise 'Current health centre not set' unless health_centre
|
220
|
+
|
221
|
+
district = health_centre.district || Lab::Lims::Config.application['district']
|
222
|
+
|
223
|
+
unless district
|
224
|
+
health_centre_name = "##{health_centre.id} - #{health_centre.name}"
|
225
|
+
raise "Current health centre district not set: #{health_centre_name}"
|
226
|
+
end
|
227
|
+
|
228
|
+
district
|
229
|
+
end
|
230
|
+
|
231
|
+
##
|
232
|
+
# Extracts sample drawn status from an OrderDTO
|
233
|
+
def sample_drawn_status(order_dto)
|
234
|
+
order_dto[:sample_statuses].each do |trail_entry|
|
235
|
+
date, status = trail_entry.each_pair.find { |_date, status| status['status'].casecmp?('Drawn') }
|
236
|
+
next unless date
|
237
|
+
|
238
|
+
return Date.strptime(date, '%Y%m%d%H%M%S').strftime('%Y-%m-%d'), status
|
239
|
+
end
|
240
|
+
|
241
|
+
[order_dto['date_created'], nil]
|
242
|
+
end
|
243
|
+
|
244
|
+
##
|
245
|
+
# Extracts a sample drawn date from a LIMS OrderDTO.
|
246
|
+
def sample_drawn_date(order_dto)
|
247
|
+
sample_drawn_status(order_dto).first
|
248
|
+
end
|
249
|
+
|
250
|
+
##
|
251
|
+
# Extracts the requesting clinician from a LIMS OrderDTO
|
252
|
+
def requesting_clinician(order_dto)
|
253
|
+
orderer = order_dto[:who_order_test]
|
254
|
+
|
255
|
+
"#{orderer[:first_name]} #{orderer[:last_name]}"
|
256
|
+
end
|
257
|
+
|
258
|
+
##
|
259
|
+
# Make a copy of the order_dto with the results from LIMS parsed
|
260
|
+
# and appended to it.
|
261
|
+
def lims_results_to_order_dto(results, order_dto)
|
262
|
+
order_dto.merge(
|
263
|
+
'_id' => order_dto[:tracking_number],
|
264
|
+
'_rev' => 0,
|
265
|
+
'test_results' => results.each_with_object({}) do |result, formatted_results|
|
266
|
+
test_name, measures = result
|
267
|
+
result_date = measures.delete('result_date')
|
268
|
+
|
269
|
+
formatted_results[test_name] = {
|
270
|
+
results: measures.each_with_object({}) do |measure, processed_measures|
|
271
|
+
processed_measures[measure[0]] = { 'result_value' => measure[1] }
|
272
|
+
end,
|
273
|
+
result_date: result_date,
|
274
|
+
result_entered_by: {}
|
275
|
+
}
|
276
|
+
end
|
277
|
+
)
|
278
|
+
end
|
279
|
+
|
280
|
+
def update_order_results(order_dto)
|
281
|
+
if order_dto['test_results'].nil? || order_dto['test_results'].empty?
|
282
|
+
return nil
|
283
|
+
end
|
284
|
+
|
285
|
+
order_dto['test_results'].each do |test_name, results|
|
286
|
+
Rails.logger.info("Pushing result for order ##{order_dto['tracking_number']}")
|
287
|
+
in_authenticated_session do |headers|
|
288
|
+
params = make_update_test_params(order_dto['tracking_number'], test_name, results)
|
289
|
+
|
290
|
+
RestClient.post(expand_uri('update_test'), params, headers)
|
291
|
+
end
|
292
|
+
end
|
293
|
+
end
|
294
|
+
|
295
|
+
def make_update_test_params(tracking_number, test_name, results, test_status = 'Drawn')
|
296
|
+
{
|
297
|
+
tracking_number: tracking_number,
|
298
|
+
test_name: test_name,
|
299
|
+
result_date: results['result_date'],
|
300
|
+
time_updated: results['result_date'],
|
301
|
+
who_updated: {
|
302
|
+
first_name: results[:result_entered_by][:first_name],
|
303
|
+
last_name: results[:result_entered_by][:last_name],
|
304
|
+
id_number: results[:result_entered_by][:id]
|
305
|
+
},
|
306
|
+
test_status: test_status,
|
307
|
+
results: results['results']&.each_with_object({}) do |measure, formatted_results|
|
308
|
+
measure_name, measure_value = measure
|
309
|
+
|
310
|
+
formatted_results[measure_name] = measure_value['result_value']
|
311
|
+
end
|
312
|
+
}
|
313
|
+
end
|
314
|
+
|
315
|
+
def find_test_status(order_dto, target_test, target_status)
|
316
|
+
order_dto['test_statuses'].each do |test, statuses|
|
317
|
+
next unless test.casecmp?(target_test)
|
318
|
+
|
319
|
+
statuses.each do |date, status|
|
320
|
+
next unless status['status'].casecmp?(target_status)
|
321
|
+
|
322
|
+
return [Date.strptime(date, '%Y%m%d%H%M%S'), status]
|
323
|
+
end
|
324
|
+
end
|
325
|
+
|
326
|
+
nil
|
327
|
+
end
|
328
|
+
|
329
|
+
def make_void_test_params(tracking_number, test_name, voided_by, void_date = nil)
|
330
|
+
void_date ||= Time.now
|
331
|
+
|
332
|
+
{
|
333
|
+
tracking_number: tracking_number,
|
334
|
+
test_name: test_name,
|
335
|
+
time_updated: void_date,
|
336
|
+
who_updated: {
|
337
|
+
first_name: voided_by[:first_name],
|
338
|
+
last_name: voided_by[:last_name],
|
339
|
+
id_number: voided_by[:id]
|
340
|
+
},
|
341
|
+
test_status: 'voided'
|
342
|
+
}
|
343
|
+
end
|
344
|
+
end
|