his_emr_api_lab 1.1.1 → 1.1.2
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- checksums.yaml +4 -4
- data/app/jobs/lab/update_patient_orders_job.rb +16 -3
- data/app/services/lab/lims/api/rest_api.rb +89 -28
- data/app/services/lab/lims/order_dto.rb +10 -3
- data/app/services/lab/lims/order_serializer.rb +1 -0
- data/app/services/lab/lims/pull_worker.rb +2 -2
- data/app/services/lab/lims/push_worker.rb +2 -1
- data/app/services/lab/metadata.rb +1 -0
- data/app/services/lab/orders_search_service.rb +4 -2
- data/app/services/lab/orders_service.rb +32 -8
- data/lib/lab/version.rb +1 -1
- data/lib/tasks/loaders/data/reasons-for-test.csv +1 -0
- data/lib/tasks/loaders/data/tests.csv +0 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: e2202cc31522b4ae92847b3102841cfcf0c65a9e389fde480e3e787f1ef49ec7
|
4
|
+
data.tar.gz: a82291c66cdd6fb651e0917dc68e5b28b6dcedeb124973ab57f9f60187b4c920
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 7da2c231dba9fa4b013890becd128b0a8694fe797b510e9baa37638d1437133cc11e27e2479938eda921ccfe6c23583544092cb477372b5db298922913035c72
|
7
|
+
data.tar.gz: cb8fbf9e9c71d187e0085b42f0fe5299976dc4309d672c815c231cdb096548d9b53b9b0f222f453b66a41a8d18b759f2d8d295c46c899206d7c7ffcee500bb6c
|
@@ -12,9 +12,22 @@ module Lab
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|
12
12
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User.current = Lab::Lims::Utils.lab_user
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13
13
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Location.current = Location.find_by_name('ART clinic')
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14
14
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|
15
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-
|
16
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-
|
17
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-
|
15
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+
lockfile = Rails.root.join('tmp', "update-patient-orders-#{patient_id}.lock")
|
16
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+
|
17
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+
done = File.open(lockfile, File::RDWR | File::CREAT) do |lock|
|
18
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+
unless lock.flock(File::LOCK_NB | File::LOCK_EX)
|
19
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+
Rails.logger.info('Another update patient job is already running...')
|
20
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+
break false
|
21
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+
end
|
22
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+
|
23
|
+
lims_api = Lab::Lims::Api::RestApi.new(Lab::Lims::Config.rest_api)
|
24
|
+
worker = Lab::Lims::PullWorker.new(lims_api)
|
25
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+
worker.pull_orders(patient_id: patient_id)
|
26
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+
|
27
|
+
true
|
28
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+
end
|
29
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+
|
30
|
+
File.unlink(lockfile) if done
|
18
31
|
end
|
19
32
|
end
|
20
33
|
end
|
@@ -22,14 +22,13 @@ class Lab::Lims::Api::RestApi
|
|
22
22
|
end
|
23
23
|
end
|
24
24
|
|
25
|
-
|
26
|
-
|
27
|
-
data = JSON.parse(response.body)['data']
|
25
|
+
data = JSON.parse(response.body)
|
26
|
+
update_order_results(order_dto) unless data['message'].casecmp?('Order already available')
|
28
27
|
|
29
28
|
ActiveSupport::HashWithIndifferentAccess.new(
|
30
|
-
id:
|
29
|
+
id: order_dto.fetch(:_id, order_dto[:tracking_number]),
|
31
30
|
rev: 0,
|
32
|
-
tracking_number:
|
31
|
+
tracking_number: order_dto[:tracking_number]
|
33
32
|
)
|
34
33
|
end
|
35
34
|
|
@@ -44,21 +43,22 @@ class Lab::Lims::Api::RestApi
|
|
44
43
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end
|
45
44
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|
46
45
|
def consume_orders(*_args, patient_id: nil, **_kwargs)
|
47
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-
|
48
|
-
|
46
|
+
orders_pending_updates(patient_id).each do |order|
|
47
|
+
order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
|
49
48
|
|
50
|
-
|
51
|
-
|
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)
|
49
|
+
if order_dto['priority'].nil? || order_dto['sample_type'].casecmp?('not_specified')
|
50
|
+
patch_order_dto_with_lims_order!(order_dto, find_lims_order(order.accession_number))
|
54
51
|
end
|
55
52
|
|
56
|
-
|
57
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-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
53
|
+
if order_dto['test_results'].empty?
|
54
|
+
begin
|
55
|
+
patch_order_dto_with_lims_results!(order_dto, find_lims_results(order.accession_number))
|
56
|
+
rescue InvalidParameters => e # LIMS responds with a 401 when a result is not found :(
|
57
|
+
Rails.logger.error("Failed to fetch results for ##{order.accession_number}: #{e.message}")
|
58
|
+
end
|
59
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+
end
|
60
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+
|
61
|
+
yield order_dto, OpenStruct.new(last_seq: 0)
|
62
62
|
end
|
63
63
|
end
|
64
64
|
|
@@ -105,8 +105,8 @@ class Lab::Lims::Api::RestApi
|
|
105
105
|
self.authentication_token = nil
|
106
106
|
retry if (retries -= 1).positive?
|
107
107
|
rescue RestClient::ExceptionWithResponse => e
|
108
|
-
Rails.logger.error("LIMS Error: #{e.response
|
109
|
-
raise e unless e.response
|
108
|
+
Rails.logger.error("LIMS Error: #{e.response&.code} - #{e.response&.body}")
|
109
|
+
raise e unless e.response&.code == 401
|
110
110
|
|
111
111
|
self.authentication_token = nil
|
112
112
|
retry if (retries -= 1).positive?
|
@@ -117,7 +117,8 @@ class Lab::Lims::Api::RestApi
|
|
117
117
|
password = config.fetch(:password)
|
118
118
|
|
119
119
|
Rails.logger.debug("Authenticating with LIMS as: #{username}")
|
120
|
-
response = RestClient.get(expand_uri("re_authenticate/#{username}/#{password}"),
|
120
|
+
response = RestClient.get(expand_uri("re_authenticate/#{username}/#{password}"),
|
121
|
+
headers: { 'Content-type' => 'application/json' })
|
121
122
|
response_body = JSON.parse(response.body)
|
122
123
|
|
123
124
|
if response_body['status'] == 401
|
@@ -153,9 +154,7 @@ class Lab::Lims::Api::RestApi
|
|
153
154
|
|
154
155
|
Rails.logger.error("Lims Api Error: #{response.body}")
|
155
156
|
|
156
|
-
if body['status'] != 401
|
157
|
-
raise LimsApiError, "#{body['status']} - #{body['message']}"
|
158
|
-
end
|
157
|
+
raise LimsApiError, "#{body['status']} - #{body['message']}" if body['status'] != 401
|
159
158
|
|
160
159
|
if body['message'].match?(/token expired/i)
|
161
160
|
raise AuthenticationTokenExpired, "Authentication token expired: #{body['message']}"
|
@@ -255,11 +254,31 @@ class Lab::Lims::Api::RestApi
|
|
255
254
|
"#{orderer[:first_name]} #{orderer[:last_name]}"
|
256
255
|
end
|
257
256
|
|
257
|
+
def find_lims_order(tracking_number)
|
258
|
+
response = in_authenticated_session do |headers|
|
259
|
+
Rails.logger.info("Fetching order ##{tracking_number}")
|
260
|
+
RestClient.get(expand_uri("query_order_by_tracking_number/#{tracking_number}"), headers)
|
261
|
+
end
|
262
|
+
|
263
|
+
Rails.logger.info("Order ##{tracking_number} found... Parsing...")
|
264
|
+
JSON.parse(response).fetch('data')
|
265
|
+
end
|
266
|
+
|
267
|
+
def find_lims_results(tracking_number)
|
268
|
+
response = in_authenticated_session do |headers|
|
269
|
+
Rails.logger.info("Fetching results for order ##{tracking_number}")
|
270
|
+
RestClient.get(expand_uri("query_results_by_tracking_number/#{tracking_number}"), headers)
|
271
|
+
end
|
272
|
+
|
273
|
+
Rails.logger.info("Result for order ##{tracking_number} found... Parsing...")
|
274
|
+
JSON.parse(response).fetch('data').fetch('results')
|
275
|
+
end
|
276
|
+
|
258
277
|
##
|
259
278
|
# Make a copy of the order_dto with the results from LIMS parsed
|
260
279
|
# and appended to it.
|
261
|
-
def
|
262
|
-
order_dto.merge(
|
280
|
+
def patch_order_dto_with_lims_results!(order_dto, results)
|
281
|
+
order_dto.merge!(
|
263
282
|
'_id' => order_dto[:tracking_number],
|
264
283
|
'_rev' => 0,
|
265
284
|
'test_results' => results.each_with_object({}) do |result, formatted_results|
|
@@ -277,10 +296,16 @@ class Lab::Lims::Api::RestApi
|
|
277
296
|
)
|
278
297
|
end
|
279
298
|
|
299
|
+
def patch_order_dto_with_lims_order!(order_dto, lims_order)
|
300
|
+
order_dto.merge!(
|
301
|
+
'sample_type' => lims_order['other']['sample_type'],
|
302
|
+
'sample_status' => lims_order['other']['specimen_status'],
|
303
|
+
'priority' => lims_order['other']['priority']
|
304
|
+
)
|
305
|
+
end
|
306
|
+
|
280
307
|
def update_order_results(order_dto)
|
281
|
-
if order_dto['test_results'].nil? || order_dto['test_results'].empty?
|
282
|
-
return nil
|
283
|
-
end
|
308
|
+
return nil if order_dto['test_results'].nil? || order_dto['test_results'].empty?
|
284
309
|
|
285
310
|
order_dto['test_results'].each do |test_name, results|
|
286
311
|
Rails.logger.info("Pushing result for order ##{order_dto['tracking_number']}")
|
@@ -341,4 +366,40 @@ class Lab::Lims::Api::RestApi
|
|
341
366
|
test_status: 'voided'
|
342
367
|
}
|
343
368
|
end
|
369
|
+
|
370
|
+
def orders_pending_updates(patient_id = nil)
|
371
|
+
Rails.logger.info('Looking for orders that need to be updated...')
|
372
|
+
orders = {}
|
373
|
+
|
374
|
+
orders_without_specimen(patient_id).each { |order| orders[order.order_id] = order }
|
375
|
+
orders_without_results(patient_id).each { |order| orders[order.order_id] = order }
|
376
|
+
orders_without_reason(patient_id).each { |order| orders[order.order_id] = order }
|
377
|
+
|
378
|
+
orders.values
|
379
|
+
end
|
380
|
+
|
381
|
+
def orders_without_specimen(patient_id = nil)
|
382
|
+
Rails.logger.debug('Looking for orders without a specimen')
|
383
|
+
unknown_specimen = ConceptName.where(name: Lab::Metadata::UNKNOWN_SPECIMEN)
|
384
|
+
.select(:concept_id)
|
385
|
+
orders = Lab::LabOrder.where(concept_id: unknown_specimen)
|
386
|
+
orders = orders.where(patient_id: patient_id) if patient_id
|
387
|
+
|
388
|
+
orders
|
389
|
+
end
|
390
|
+
|
391
|
+
def orders_without_results(patient_id = nil)
|
392
|
+
Rails.logger.debug('Looking for orders without a result')
|
393
|
+
Lab::OrdersSearchService.find_orders_without_results(patient_id: patient_id)
|
394
|
+
end
|
395
|
+
|
396
|
+
def orders_without_reason(patient_id = nil)
|
397
|
+
Rails.logger.debug('Looking for orders without a reason for test')
|
398
|
+
orders = Lab::LabOrder.joins(:reason_for_test)
|
399
|
+
.merge(Observation.where(value_coded: nil, value_text: nil))
|
400
|
+
.limit(1000)
|
401
|
+
orders = orders.where(patient_id: patient_id) if patient_id
|
402
|
+
|
403
|
+
orders
|
404
|
+
end
|
344
405
|
end
|
@@ -22,7 +22,7 @@ module Lab
|
|
22
22
|
date: start_date,
|
23
23
|
target_lab: facility_name(self['receiving_facility']),
|
24
24
|
order_location: facility_name(self['sending_facility']),
|
25
|
-
|
25
|
+
reason_for_test_id: reason_for_test
|
26
26
|
)
|
27
27
|
end
|
28
28
|
|
@@ -69,7 +69,9 @@ module Lab
|
|
69
69
|
end
|
70
70
|
|
71
71
|
def start_date
|
72
|
-
|
72
|
+
if self['date_created'].blank?
|
73
|
+
raise LimsException, 'Order missing created date'
|
74
|
+
end
|
73
75
|
|
74
76
|
Utils.parse_date(self['date_created'])
|
75
77
|
end
|
@@ -85,7 +87,12 @@ module Lab
|
|
85
87
|
def reason_for_test
|
86
88
|
return unknown_concept.concept_id unless self['priority']
|
87
89
|
|
88
|
-
|
90
|
+
name = case self['priority']
|
91
|
+
when %r{Reapet / Missing}i then 'Repeat / Missing'
|
92
|
+
else self['priority']
|
93
|
+
end
|
94
|
+
|
95
|
+
ConceptName.find_by_name!(name).concept_id
|
89
96
|
end
|
90
97
|
|
91
98
|
def lab_program
|
@@ -16,6 +16,7 @@ module Lab
|
|
16
16
|
serialized_order = Lims::Utils.structify(Lab::LabOrderSerializer.serialize_order(order))
|
17
17
|
|
18
18
|
Lims::OrderDTO.new(
|
19
|
+
_id: Lab::LimsOrderMapping.find_by(order: order)&.lims_id || serialized_order.accession_number,
|
19
20
|
tracking_number: serialized_order.accession_number,
|
20
21
|
sending_facility: current_facility_name,
|
21
22
|
receiving_facility: serialized_order.target_lab,
|
@@ -176,7 +176,7 @@ module Lab
|
|
176
176
|
def update_order(patient, order_id, order_dto)
|
177
177
|
logger.debug("Updating order ##{order_dto['_id']}")
|
178
178
|
order = OrdersService.update_order(order_id, order_dto.to_order_service_params(patient_id: patient.patient_id)
|
179
|
-
.merge(force_update: true))
|
179
|
+
.merge(force_update: 'true'))
|
180
180
|
unless order_dto['test_results'].empty?
|
181
181
|
update_results(order, order_dto['test_results'])
|
182
182
|
end
|
@@ -194,7 +194,7 @@ module Lab
|
|
194
194
|
next
|
195
195
|
end
|
196
196
|
|
197
|
-
next
|
197
|
+
next if test.result || test_results['results'].blank?
|
198
198
|
|
199
199
|
measures = test_results['results'].map do |indicator, value|
|
200
200
|
measure = find_measure(order, indicator, value)
|
@@ -56,7 +56,8 @@ module Lab
|
|
56
56
|
else
|
57
57
|
Rails.logger.info("Creating order ##{order_dto['accession_number']} in LIMS")
|
58
58
|
update = lims_api.create_order(order_dto)
|
59
|
-
Lab::LimsOrderMapping.create!(order: order, lims_id: update['id'], revision: update['rev'],
|
59
|
+
Lab::LimsOrderMapping.create!(order: order, lims_id: update['id'], revision: update['rev'],
|
60
|
+
pushed_at: Time.now)
|
60
61
|
end
|
61
62
|
end
|
62
63
|
|
@@ -26,8 +26,10 @@ module Lab
|
|
26
26
|
end
|
27
27
|
|
28
28
|
def find_orders_without_results(patient_id: nil)
|
29
|
-
|
30
|
-
|
29
|
+
results_query = Lab::LabResult.all
|
30
|
+
results_query = results_query.where(person_id: patient_id) if patient_id
|
31
|
+
|
32
|
+
query = Lab::LabOrder.where.not(order_id: results_query.select(:order_id))
|
31
33
|
query = query.where(patient_id: patient_id) if patient_id
|
32
34
|
|
33
35
|
query
|
@@ -71,15 +71,24 @@ module Lab
|
|
71
71
|
end
|
72
72
|
|
73
73
|
order = Lab::LabOrder.find(order_id)
|
74
|
-
|
75
|
-
raise ::UnprocessableEntityError
|
74
|
+
if order.concept_id != unknown_concept_id && !params[:force_update]&.casecmp?('true')
|
75
|
+
raise ::UnprocessableEntityError, "Can't change order specimen once set"
|
76
|
+
end
|
77
|
+
|
78
|
+
if specimen_id.to_i != order.concept_id
|
79
|
+
Rails.logger.debug("Updating order ##{order.order_id}")
|
80
|
+
order.update!(concept_id: specimen_id,
|
81
|
+
discontinued: true,
|
82
|
+
discontinued_by: User.current.user_id,
|
83
|
+
discontinued_date: params[:date]&.to_date || Time.now,
|
84
|
+
discontinued_reason_non_coded: 'Sample drawn/updated')
|
85
|
+
end
|
86
|
+
|
87
|
+
if params.key?(:reason_for_test_id)
|
88
|
+
Rails.logger.debug("Updating reason for test on order ##{order.order_id}")
|
89
|
+
update_reason_for_test(order, params[:reason_for_test_id])
|
76
90
|
end
|
77
91
|
|
78
|
-
order.update!(concept_id: specimen_id,
|
79
|
-
discontinued: true,
|
80
|
-
discontinued_by: User.current.user_id,
|
81
|
-
discontinued_date: params[:date]&.to_date || Time.now,
|
82
|
-
discontinued_reason_non_coded: 'Sample drawn/updated')
|
83
92
|
Lab::LabOrderSerializer.serialize_order(order)
|
84
93
|
end
|
85
94
|
|
@@ -159,7 +168,7 @@ module Lab
|
|
159
168
|
order,
|
160
169
|
Lab::Metadata::REASON_FOR_TEST_CONCEPT_NAME,
|
161
170
|
params[:date],
|
162
|
-
value_coded: params[
|
171
|
+
value_coded: params[:reason_for_test_id]
|
163
172
|
)
|
164
173
|
end
|
165
174
|
|
@@ -192,6 +201,21 @@ module Lab
|
|
192
201
|
def unknown_concept_id
|
193
202
|
ConceptName.find_by_name!('Unknown').concept_id
|
194
203
|
end
|
204
|
+
|
205
|
+
def update_reason_for_test(order, concept_id)
|
206
|
+
if concept_id.blank?
|
207
|
+
raise InvalidParameterError, "Reason for test can't be blank"
|
208
|
+
end
|
209
|
+
|
210
|
+
return if order.reason_for_test&.value_coded == concept_id
|
211
|
+
|
212
|
+
unless order.reason_for_test&.value_coded.nil?
|
213
|
+
raise InvalidParameterError, "Can't change reason for test once set"
|
214
|
+
end
|
215
|
+
|
216
|
+
order.reason_for_test.delete
|
217
|
+
add_reason_for_test(order, date: order.start_date, reason_for_test_id: concept_id)
|
218
|
+
end
|
195
219
|
end
|
196
220
|
end
|
197
221
|
end
|
data/lib/lab/version.rb
CHANGED
@@ -86,8 +86,6 @@ Blood,HbA1c,"2019-11-19 14:05:31"
|
|
86
86
|
Blood,Microalbumin,"2019-11-19 14:05:31"
|
87
87
|
Blood,Microprotein,"2019-11-19 14:05:31"
|
88
88
|
Blood,"Von Willebrand Factor","2019-11-19 14:05:31"
|
89
|
-
Blood,"HIV_viral_load","2021-04-13 00:00:00"
|
90
|
-
Blood,"Viral laod","2021-04-11 00:00:00"
|
91
89
|
Blood,"Viral Load","2019-11-19 14:05:31"
|
92
90
|
Blood,"Urine Lam","2019-11-19 14:05:31"
|
93
91
|
Blood,"Protein and Sugar","2021-04-16"
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: his_emr_api_lab
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.1.
|
4
|
+
version: 1.1.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Elizabeth Glaser Pediatric Foundation Malawi
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2021-07-
|
11
|
+
date: 2021-07-15 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: couchrest
|