canql 5.6.0 → 5.7.0
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- checksums.yaml +4 -4
- data/CHANGELOG.md +3 -1
- data/code_safety.yml +86 -86
- data/lib/canql/grammars/anomaly.treetop +1 -1
- data/lib/canql/grammars/batch_types.treetop +14 -1
- data/lib/canql/grammars/patient.treetop +3 -2
- data/lib/canql/nodes/batch_types.rb +19 -1
- data/lib/canql/nodes/patient.rb +7 -6
- data/lib/canql/version.rb +1 -1
- metadata +6 -6
checksums.yaml
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SHA256:
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metadata.gz:
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metadata.gz: 7b6c774649dcffa9c8948ce5635e0a383a5dbb3f909fbc58e2ae01e08f2e8ea2
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data.tar.gz: 77da684a8fe7ccfc0a8736c468a9f4c2baa438467baf5578054714c77da75c47
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SHA512:
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metadata.gz: 5d8464c8d1ebe51731ab9f3116fdb16e53f450a23a837a210d9b5cef6746c43c4b45095168bb9df7ce0e4c36ec4b27bf56feb594ff80699fa63c330aab2b7108
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data.tar.gz: 718b15cc009ef0a0830670bfcd29566c80a1fba33ca1741a2274a7ccc7b46ba6b82f29de9216d59e0e275846cff79a8076df0109627986c21889dc5189beea57
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data/CHANGELOG.md
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data/code_safety.yml
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file safety:
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LICENSE.txt:
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test/parser_test.rb:
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@@ -47,7 +47,7 @@ module Canql
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47
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end
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rule fasp_rating
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-
('fasp red and amber' / 'fasp amber and red' / 'fasp red' / 'fasp amber' / 'fasp green') <Nodes::Anomaly::SingleFaspRatingNode>
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+
('fasp amber and green' / 'fasp green and amber' / 'fasp red and amber' / 'fasp amber and red' / 'fasp red' / 'fasp amber' / 'fasp green') <Nodes::Anomaly::SingleFaspRatingNode>
|
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end
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end
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end
|
@@ -1,7 +1,8 @@
|
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1
1
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module Canql
|
2
2
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grammar BatchTypes
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3
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rule batch_type
|
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-
(paediatric / enote2 / badger / ucyto / nipt / rddeath /
|
4
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+
(paediatric / enote2 / badger / ucyto / nipt / rddeath /
|
5
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+
umum / ca_death / biochem / hes / uss) <Nodes::BatchTypeNode>
|
5
6
|
end
|
6
7
|
|
7
8
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rule paediatric
|
@@ -24,6 +25,18 @@ module Canql
|
|
24
25
|
'nipt' <Nodes::NiptNode>
|
25
26
|
end
|
26
27
|
|
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+
rule biochem
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+
'biochem' <Nodes::BiochemNode>
|
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+
end
|
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+
|
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+
rule hes
|
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|
+
'hes' <Nodes::HesNode>
|
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|
+
end
|
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+
|
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+
rule uss
|
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+
('uss' / 'ultrasound screening' ) <Nodes::UssNode>
|
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|
+
end
|
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+
|
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40
|
rule rddeath
|
28
41
|
('rddeath' / 'rd death' / 'rare disease death') <Nodes::RddeathNode>
|
29
42
|
end
|
@@ -16,8 +16,9 @@ module Canql
|
|
16
16
|
space category:('eurocat amber and green' /
|
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17
|
'eurocat red and amber' / 'eurocat red' / 'eurocat amber' /
|
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18
|
'eurocat green' / 'eurocat' /
|
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|
-
'fasp red and amber' / 'fasp amber and red' /
|
20
|
-
'fasp amber' / 'fasp green' / 'fasp
|
19
|
+
'fasp red and amber' / 'fasp amber and red' /
|
20
|
+
'fasp amber and green' / 'fasp green and amber' / 'fasp red' /
|
21
|
+
'fasp amber' / 'fasp green' / 'fasp excluded' / 'fasp'
|
21
22
|
) word_break <Nodes::Patient::CategoryNode>
|
22
23
|
end
|
23
24
|
|
@@ -1,6 +1,6 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
|
-
module Canql
|
3
|
+
module Canql # :nodoc: all
|
4
4
|
module Nodes
|
5
5
|
module BatchTypeNode
|
6
6
|
def to_type
|
@@ -39,6 +39,24 @@ module Canql #:nodoc: all
|
|
39
39
|
end
|
40
40
|
end
|
41
41
|
|
42
|
+
module BiochemNode
|
43
|
+
def normalise
|
44
|
+
'biochem'
|
45
|
+
end
|
46
|
+
end
|
47
|
+
|
48
|
+
module HesNode
|
49
|
+
def normalise
|
50
|
+
'hes'
|
51
|
+
end
|
52
|
+
end
|
53
|
+
|
54
|
+
module UssNode
|
55
|
+
def normalise
|
56
|
+
'uss'
|
57
|
+
end
|
58
|
+
end
|
59
|
+
|
42
60
|
module RddeathNode
|
43
61
|
def normalise
|
44
62
|
'rd_death'
|
data/lib/canql/nodes/patient.rb
CHANGED
@@ -1,6 +1,6 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
|
-
module Canql
|
3
|
+
module Canql # :nodoc: all
|
4
4
|
module Nodes
|
5
5
|
module Patient
|
6
6
|
module GenderNode
|
@@ -30,6 +30,7 @@ module Canql #:nodoc: all
|
|
30
30
|
if category.text_value.start_with?('eurocat ') || category.text_value.start_with?('fasp ')
|
31
31
|
filter_value = category.text_value.gsub(/( )/, '_').downcase.gsub(/(_and_)/, '_')
|
32
32
|
filter_value = 'fasp_red_amber' if filter_value == 'fasp_amber_red'
|
33
|
+
filter_value = 'fasp_amber_green' if filter_value == 'fasp_green_amber'
|
33
34
|
return filter_value
|
34
35
|
end
|
35
36
|
|
@@ -40,16 +41,16 @@ module Canql #:nodoc: all
|
|
40
41
|
module FieldExists
|
41
42
|
FIELDS = {
|
42
43
|
'date of birth': { patient: 'birthdate', mother: 'birthdate' },
|
43
|
-
|
44
|
+
dob: { patient: 'birthdate', mother: 'birthdate' },
|
44
45
|
'date of vital status': { patient: 'dateofvitalstatus', mother: 'dateofvitalstatus' },
|
45
46
|
'delivery postcode': { patient: 'delivery_postcode' },
|
46
47
|
'booking postcode': { patient: 'booking_postcode' },
|
47
48
|
'nhs number': { patient: 'nhsnumber', mother: 'nhsnumber' },
|
48
49
|
'birth weight': { patient: 'weight' },
|
49
50
|
'place of delivery': { patient: 'placeofdelivery' },
|
50
|
-
|
51
|
-
|
52
|
-
|
51
|
+
sex: { patient: 'sex' },
|
52
|
+
outcome: { patient: 'outcome' },
|
53
|
+
edd: { patient: 'expecteddeliverydate' },
|
53
54
|
'expected delivery date': { patient: 'expecteddeliverydate' },
|
54
55
|
'booking hospital': { patient: 'booking_hospital' },
|
55
56
|
'screening status': { patient: 'screeningstatus' },
|
@@ -65,7 +66,7 @@ module Canql #:nodoc: all
|
|
65
66
|
patient_field_list.text_values_for_marker(:patient_field_name), subject.to_sym
|
66
67
|
)
|
67
68
|
modifer = field_existance_modifier.text_value.strip
|
68
|
-
existance = modifer
|
69
|
+
existance = modifer == 'missing' ? 'fields_missing' : 'fields_populated'
|
69
70
|
{ "#{subject}.#{existance}" => { Canql::EQUALS => field_names } }
|
70
71
|
end
|
71
72
|
|
data/lib/canql/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: canql
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.
|
4
|
+
version: 5.7.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- PHE NDR Development Team
|
8
|
-
autorequire:
|
8
|
+
autorequire:
|
9
9
|
bindir: exe
|
10
10
|
cert_chain: []
|
11
|
-
date: 2021-
|
11
|
+
date: 2021-09-16 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: chronic
|
@@ -264,7 +264,7 @@ homepage: https://github.com/PublicHealthEngland/canql
|
|
264
264
|
licenses:
|
265
265
|
- MIT
|
266
266
|
metadata: {}
|
267
|
-
post_install_message:
|
267
|
+
post_install_message:
|
268
268
|
rdoc_options: []
|
269
269
|
require_paths:
|
270
270
|
- lib
|
@@ -279,8 +279,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
279
279
|
- !ruby/object:Gem::Version
|
280
280
|
version: '0'
|
281
281
|
requirements: []
|
282
|
-
rubygems_version: 3.
|
283
|
-
signing_key:
|
282
|
+
rubygems_version: 3.1.4
|
283
|
+
signing_key:
|
284
284
|
specification_version: 4
|
285
285
|
summary: Congenital Anomaly Natural Query Language
|
286
286
|
test_files: []
|