canql 5.6.0 → 5.7.0

checksums.yaml

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data/CHANGELOG.md

@@ -1,5 +1,7 @@
 ## [Unreleased]
-* no relevant changes
+## 5.7.0 / 2021-09-16
+* Added new 'fasp' and 'fasp amber and green' case / patient / anomaly categoryfilters (#78)
+* Added new HES, BIOCHEM and USS unprocessed record filters (#79)
 
 ## 5.6.0 / 2021-03-16
 ### Added

data/code_safety.yml

@@ -1,75 +1,75 @@
 ---
 file safety:
   ".github/CODEOWNERS":
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: a964c47962d47724afd66ba59660589fc3c8b02c
   ".github/workflows/lint.yml":
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 71f6a631758a5a38814d3eafec407e0fde30101f
   ".github/workflows/test.yml":
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: a3f5265f1d20a6dcb8c45ab5f09207ca7d1e255c
   ".gitignore":
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: cbb48a04cbac04a6dce845110928f69492e152a1
   ".hound.yml":
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 0b34688f1198eace9310f47060aa8915f5b44985
   ".rubocop.yml":
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 146b255b240b0efc928d39dd1b70ab221ddc3138
   CHANGELOG.md:
-    comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: 29d2a4accc6fbe9305b01e79cb285e5bf8531cbc
+    comments:
+    reviewed_by: kenny.lee
+    safe_revision: 1f6f0da156ec3d26bfa9b77547646dae1c352b85
   CODE_OF_CONDUCT.md:
-    comments: 
+    comments:
     reviewed_by: drewthorp
     safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
   Gemfile:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   LICENSE.txt:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: ee80c4bbd5e990d38b5fc954f4fd037177672db2
   README.md:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   Rakefile:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   bin/console:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
   bin/setup:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
   canql.gemspec:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 146b255b240b0efc928d39dd1b70ab221ddc3138
   lib/canql.rb:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   lib/canql/constants.rb:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
   lib/canql/grammars.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/grammars/age.treetop:
@@ -80,27 +80,27 @@ file safety:
   lib/canql/grammars/anomaly.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
-    reviewed_by: ollietulloch
-    safe_revision: b0b092613c94a8c2f04191dbe2a1a347c8e14d16
+    reviewed_by: kenny.lee
+    safe_revision: 7580eb6b1196dec1fb778ee345d2bce50ef0f7c7
   lib/canql/grammars/batch_types.treetop:
-    comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: df64f58ac3cc8dbd70d1792d24071ef013f9ae42
+    comments:
+    reviewed_by: kenny.lee
+    safe_revision: 5bd6ccd1951140ab01b701583af94f414188b299
   lib/canql/grammars/dates.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
     reviewed_by: timgentry
     safe_revision: 2346abb4435bf95cbe9b4d8c124123b9fefe60d6
   lib/canql/grammars/e_base_records.treetop:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 4e26ac746098452b01dac88373e401e39f309b74
   lib/canql/grammars/genetic_test.treetop:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 526dbe8a3dc3334b4174928e6f51d07e48ed9247
   lib/canql/grammars/hes_event.treetop:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/grammars/main.treetop:
@@ -111,14 +111,14 @@ file safety:
   lib/canql/grammars/patient.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
-    reviewed_by: ollietulloch
-    safe_revision: 481194575c30b48987f957a9cc5535d604ea0117
+    reviewed_by: kenny.lee
+    safe_revision: a69bbd63d71d5fb2ba46d6a84589915b1120763b
   lib/canql/grammars/perinatal_hospital.treetop:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/grammars/provider.treetop:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/grammars/registry.treetop:
@@ -132,162 +132,162 @@ file safety:
     reviewed_by: timgentry
     safe_revision: c39d24bb500719971969762e94545e82866bf92f
   lib/canql/grammars/test_result_group.treetop:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
   lib/canql/nodes.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/nodes/age.rb:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   lib/canql/nodes/anomaly.rb:
-    comments: 
+    comments:
     reviewed_by: ollietulloch
     safe_revision: e549c0dcafdd6004ec279bd256fae8b9964c9629
   lib/canql/nodes/batch_types.rb:
-    comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: df64f58ac3cc8dbd70d1792d24071ef013f9ae42
+    comments:
+    reviewed_by: kenny.lee
+    safe_revision: 49d17e254a95d50dea1448ca59fd45c44937d661
   lib/canql/nodes/dates.rb:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   lib/canql/nodes/e_base_records.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 4805609963f75639e2444df8f42d2d6d65005b7c
   lib/canql/nodes/genetic_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 526dbe8a3dc3334b4174928e6f51d07e48ed9247
   lib/canql/nodes/hes_event.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/nodes/main.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/nodes/patient.rb:
-    comments: 
-    reviewed_by: ollietulloch
-    safe_revision: 481194575c30b48987f957a9cc5535d604ea0117
+    comments:
+    reviewed_by: kenny.lee
+    safe_revision: 49d17e254a95d50dea1448ca59fd45c44937d661
   lib/canql/nodes/perinatal_hospital.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
   lib/canql/nodes/registry.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 4e26ac746098452b01dac88373e401e39f309b74
   lib/canql/nodes/test_result.rb:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: c39d24bb500719971969762e94545e82866bf92f
   lib/canql/nodes/test_result_group.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
   lib/canql/parser.rb:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   lib/canql/treetop/extensions.rb:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   lib/canql/version.rb:
-    comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: 29d2a4accc6fbe9305b01e79cb285e5bf8531cbc
+    comments:
+    reviewed_by: kenny.lee
+    safe_revision: 1f6f0da156ec3d26bfa9b77547646dae1c352b85
   test/anomaly_test_helper.rb:
-    comments: 
+    comments:
     reviewed_by: ollietulloch
     safe_revision: e549c0dcafdd6004ec279bd256fae8b9964c9629
   test/canql_test.rb:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   test/hes_event_test_helper.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   test/minitest_helper.rb:
-    comments: 
+    comments:
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
   test/nodes/anomaly_test.rb:
-    comments: 
+    comments:
     reviewed_by: ollietulloch
     safe_revision: b0b092613c94a8c2f04191dbe2a1a347c8e14d16
   test/nodes/case_age_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/case_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 7490099869e368dcd5c26ded11eb90229baf4cae
   test/nodes/code_test.rb:
-    comments: 
-    reviewed_by: ollietulloch
-    safe_revision: e549c0dcafdd6004ec279bd256fae8b9964c9629
+    comments:
+    reviewed_by: kenny.lee
+    safe_revision: 7580eb6b1196dec1fb778ee345d2bce50ef0f7c7
   test/nodes/e_base_records_test.rb:
-    comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: df64f58ac3cc8dbd70d1792d24071ef013f9ae42
+    comments:
+    reviewed_by: kenny.lee
+    safe_revision: 5bd6ccd1951140ab01b701583af94f414188b299
   test/nodes/genetic_tests_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/hes_event_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   test/nodes/main_case_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/main_patient_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/mother_e_base_records_test.rb:
-    comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: 4805609963f75639e2444df8f42d2d6d65005b7c
+    comments:
+    reviewed_by: kenny.lee
+    safe_revision: 99ef15c6610409a1562e6a03b015569d087b045f
   test/nodes/patient_age_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/patient_test.rb:
-    comments: 
-    reviewed_by: ollietulloch
-    safe_revision: 481194575c30b48987f957a9cc5535d604ea0117
+    comments:
+    reviewed_by: kenny.lee
+    safe_revision: a69bbd63d71d5fb2ba46d6a84589915b1120763b
   test/nodes/perinatal_hospital_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/registry_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
   test/nodes/test_result_groups_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
   test/nodes/test_results_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/parser_test.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   test/test_helper.rb:
-    comments: 
+    comments:
     reviewed_by: josh.pencheon
     safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4

data/lib/canql/grammars/anomaly.treetop

@@ -47,7 +47,7 @@ module Canql
     end
 
     rule fasp_rating
-      ('fasp red and amber' / 'fasp amber and red' / 'fasp red' / 'fasp amber' / 'fasp green') <Nodes::Anomaly::SingleFaspRatingNode>
+      ('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>
     end
   end
 end

data/lib/canql/grammars/batch_types.treetop

@@ -1,7 +1,8 @@
 module Canql
   grammar BatchTypes
     rule batch_type
-      (paediatric / enote2 / badger / ucyto / nipt / rddeath / umum / ca_death) <Nodes::BatchTypeNode>
+      (paediatric / enote2 / badger / ucyto / nipt / rddeath /
+      umum / ca_death / biochem / hes / uss) <Nodes::BatchTypeNode>
     end
 
     rule paediatric
@@ -24,6 +25,18 @@ module Canql
       'nipt' <Nodes::NiptNode>
     end
 
+    rule biochem
+      'biochem' <Nodes::BiochemNode>
+    end
+
+    rule hes
+      'hes' <Nodes::HesNode>
+    end
+
+    rule uss
+      ('uss' / 'ultrasound screening' ) <Nodes::UssNode>
+    end
+
     rule rddeath
       ('rddeath' / 'rd death' / 'rare disease death') <Nodes::RddeathNode>
     end

data/lib/canql/grammars/patient.treetop

@@ -16,8 +16,9 @@ module Canql
       space category:('eurocat amber and green' /
         'eurocat red and amber' / 'eurocat red' / 'eurocat amber' /
         'eurocat green' / 'eurocat' /
-        'fasp red and amber' / 'fasp amber and red' / 'fasp red' /
-        'fasp amber' / 'fasp green' / 'fasp excluded'
+        'fasp red and amber' / 'fasp amber and red' /
+        'fasp amber and green' / 'fasp green and amber' / 'fasp red' /
+        'fasp amber' / 'fasp green' / 'fasp excluded' / 'fasp'
       ) word_break <Nodes::Patient::CategoryNode>
     end
 

data/lib/canql/nodes/batch_types.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-module Canql #:nodoc: all
+module Canql # :nodoc: all
   module Nodes
     module BatchTypeNode
       def to_type
@@ -39,6 +39,24 @@ module Canql #:nodoc: all
       end
     end
 
+    module BiochemNode
+      def normalise
+        'biochem'
+      end
+    end
+
+    module HesNode
+      def normalise
+        'hes'
+      end
+    end
+
+    module UssNode
+      def normalise
+        'uss'
+      end
+    end
+
     module RddeathNode
       def normalise
         'rd_death'

data/lib/canql/nodes/patient.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-module Canql #:nodoc: all
+module Canql # :nodoc: all
   module Nodes
     module Patient
       module GenderNode
@@ -30,6 +30,7 @@ module Canql #:nodoc: all
           if category.text_value.start_with?('eurocat ') || category.text_value.start_with?('fasp ')
             filter_value = category.text_value.gsub(/( )/, '_').downcase.gsub(/(_and_)/, '_')
             filter_value = 'fasp_red_amber' if filter_value == 'fasp_amber_red'
+            filter_value = 'fasp_amber_green' if filter_value == 'fasp_green_amber'
             return filter_value
           end
 
@@ -40,16 +41,16 @@ module Canql #:nodoc: all
       module FieldExists
         FIELDS = {
           'date of birth': { patient: 'birthdate', mother: 'birthdate' },
-          'dob': { patient: 'birthdate', mother: 'birthdate' },
+          dob: { patient: 'birthdate', mother: 'birthdate' },
           'date of vital status': { patient: 'dateofvitalstatus', mother: 'dateofvitalstatus' },
           'delivery postcode': { patient: 'delivery_postcode' },
           'booking postcode': { patient: 'booking_postcode' },
           'nhs number': { patient: 'nhsnumber', mother: 'nhsnumber' },
           'birth weight': { patient: 'weight' },
           'place of delivery': { patient: 'placeofdelivery' },
-          'sex': { patient: 'sex' },
-          'outcome': { patient: 'outcome' },
-          'edd': { patient: 'expecteddeliverydate' },
+          sex: { patient: 'sex' },
+          outcome: { patient: 'outcome' },
+          edd: { patient: 'expecteddeliverydate' },
           'expected delivery date': { patient: 'expecteddeliverydate' },
           'booking hospital': { patient: 'booking_hospital' },
           'screening status': { patient: 'screeningstatus' },
@@ -65,7 +66,7 @@ module Canql #:nodoc: all
             patient_field_list.text_values_for_marker(:patient_field_name), subject.to_sym
           )
           modifer = field_existance_modifier.text_value.strip
-          existance = modifer != 'missing' ? 'fields_populated' : 'fields_missing'
+          existance = modifer == 'missing' ? 'fields_missing' : 'fields_populated'
           { "#{subject}.#{existance}" => { Canql::EQUALS => field_names } }
         end
 

data/lib/canql/version.rb

@@ -2,5 +2,5 @@
 
 # This stores the current version of the Canql gem
 module Canql
-  VERSION = '5.6.0'
+  VERSION = '5.7.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: canql
 version: !ruby/object:Gem::Version
-  version: 5.6.0
+  version: 5.7.0
 platform: ruby
 authors:
 - PHE NDR Development Team
-autorequire: 
+autorequire:
 bindir: exe
 cert_chain: []
-date: 2021-03-16 00:00:00.000000000 Z
+date: 2021-09-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: chronic
@@ -264,7 +264,7 @@ homepage: https://github.com/PublicHealthEngland/canql
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -279,8 +279,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
-signing_key: 
+rubygems_version: 3.1.4
+signing_key:
 specification_version: 4
 summary: Congenital Anomaly Natural Query Language
 test_files: []