canql 5.4.0 → 5.7.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/.github/workflows/test.yml

@@ -1,6 +1,6 @@
 name: Test
 
-on: [push, pull_request]
+on: [push]
 
 jobs:
   test:

data/CHANGELOG.md

@@ -1,25 +1,39 @@
 ## [Unreleased]
-* no relevant changes
+*no unreleased changes*
 
-## 5.4.0 / 2021-03-08
+## 5.7.1 / 2021-10-11
+### Patched
+* Corrected issue where date related tests failed on some ruby version (#83)
+
+## 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
+* Add new CA Death option to the unprocessed record filter (#75)
 
+## 5.5.0 / 2021-03-16
+### Added
+* Add HES event filter (#72)
+
+## 5.4.0 / 2021-03-08
+### Added
 * Add 'pending data' option to the anomaly screening status filter (#69)
 
 ## 5.3.0 / 2021-03-05
-
+### Added
 * Added new FASP case RAG rating filters (#66)
 
 ## 5.2.0 / 2021-03-04
-
+### Added
 * Added new FASP anomaly RAG rating filters (#63)
 
 ## 5.1.0 / 2021-01-25
-
 ### Added
 * Added new filters for test acceptance requirments (#59)
 
 ## 5.0.0 / 2021-01-19
-
 ### Changed
 * Changed the values of registry to use registry name rather than codes and added new supra-region options (#54)
 

data/README.md

@@ -50,7 +50,7 @@ would output:
       and booking at hospital RGT01 and delivery at addenbrookes trust
 The parser is case insensitive. An example of an almost fully involved CANQL query is:
 
-> First 27 Male Liveborn Thames Primary Cases Due between 20/06/2015 and 25/06/2015 and Born on 22/06/2015 and that Died on 07/07/2015 with Suspected Prenatal Q20 Anomalies and Booking at hospital RGT01 and Delivery at addenbrookes trust and Postnatal Tests and Missing Postcode and Date of Birth and QA Action and Unprocessed paediatric records and Mother Born between 01/10/1990 and 10/01/1999 and who Died on 01/08/2015 with Populated Postcode and NHS Number
+> First 27 Male Liveborn Thames Primary Cases Due between 20/06/2015 and 25/06/2015 and Born on 22/06/2015 and that Died on 07/07/2015 with Suspected Prenatal Q20 Anomalies and Booking at hospital RGT01 and Delivery at addenbrookes trust and Postnatal Tests and Missing Postcode and Date of Birth and QA Action and Unprocessed paediatric records and hes records and Mother Born between 01/10/1990 and 10/01/1999 and who Died on 01/08/2015 with Populated Postcode and NHS Number
 
 Please see the tests for many more examples.
 

data/code_safety.yml

@@ -11,7 +11,7 @@ file safety:
   ".github/workflows/test.yml":
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 865fc970554fee9207f8e3cd0247133c6a849b24
+    safe_revision: a3f5265f1d20a6dcb8c45ab5f09207ca7d1e255c
   ".gitignore":
     comments: 
     reviewed_by: timgentry
@@ -27,7 +27,7 @@ file safety:
   CHANGELOG.md:
     comments: 
     reviewed_by: ollietulloch
-    safe_revision: 8e66f9ea2d880e368446969c3b0e63a1660cb427
+    safe_revision: 80a300b5aeadf74ca952d4adc4a7a49595e3cc6d
   CODE_OF_CONDUCT.md:
     comments: 
     reviewed_by: drewthorp
@@ -43,7 +43,7 @@ file safety:
   README.md:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 8c07968aa84db92b6f1cc528180f73530ddc6ff5
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   Rakefile:
     comments: 
     reviewed_by: timgentry
@@ -71,7 +71,7 @@ file safety:
   lib/canql/grammars.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: c5f8f76b2c335a8554f39a14d6165bf5cd8f9b67
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/grammars/age.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
@@ -80,12 +80,12 @@ 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: 1892161f3c300f3b199aa318b3fe23a54dd80829
+    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
@@ -99,16 +99,20 @@ file safety:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: 526dbe8a3dc3334b4174928e6f51d07e48ed9247
+  lib/canql/grammars/hes_event.treetop:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/grammars/main.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
     reviewed_by: josh.pencheon
-    safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   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: 
     reviewed_by: josh.pencheon
@@ -134,7 +138,7 @@ file safety:
   lib/canql/nodes.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: c5f8f76b2c335a8554f39a14d6165bf5cd8f9b67
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/nodes/age.rb:
     comments: 
     reviewed_by: timgentry
@@ -145,8 +149,8 @@ file safety:
     safe_revision: e549c0dcafdd6004ec279bd256fae8b9964c9629
   lib/canql/nodes/batch_types.rb:
     comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: 1892161f3c300f3b199aa318b3fe23a54dd80829
+    reviewed_by: kenny.lee
+    safe_revision: 49d17e254a95d50dea1448ca59fd45c44937d661
   lib/canql/nodes/dates.rb:
     comments: 
     reviewed_by: timgentry
@@ -159,14 +163,18 @@ file safety:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: 526dbe8a3dc3334b4174928e6f51d07e48ed9247
+  lib/canql/nodes/hes_event.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/nodes/main.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 361dea5dc6d64bdb7b03434dd2878f8c3b128c95
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   lib/canql/nodes/patient.rb:
     comments: 
-    reviewed_by: ollietulloch
-    safe_revision: 481194575c30b48987f957a9cc5535d604ea0117
+    reviewed_by: kenny.lee
+    safe_revision: 49d17e254a95d50dea1448ca59fd45c44937d661
   lib/canql/nodes/perinatal_hospital.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -194,7 +202,7 @@ file safety:
   lib/canql/version.rb:
     comments: 
     reviewed_by: ollietulloch
-    safe_revision: 8e66f9ea2d880e368446969c3b0e63a1660cb427
+    safe_revision: 80a300b5aeadf74ca952d4adc4a7a49595e3cc6d
   test/anomaly_test_helper.rb:
     comments: 
     reviewed_by: ollietulloch
@@ -203,6 +211,10 @@ file safety:
     comments: 
     reviewed_by: timgentry
     safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
+  test/hes_event_test_helper.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   test/minitest_helper.rb:
     comments: 
     reviewed_by: timgentry
@@ -221,16 +233,20 @@ file safety:
     safe_revision: 7490099869e368dcd5c26ded11eb90229baf4cae
   test/nodes/code_test.rb:
     comments: 
-    reviewed_by: ollietulloch
-    safe_revision: e549c0dcafdd6004ec279bd256fae8b9964c9629
+    reviewed_by: kenny.lee
+    safe_revision: 7580eb6b1196dec1fb778ee345d2bce50ef0f7c7
   test/nodes/e_base_records_test.rb:
     comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
+    reviewed_by: ollietulloch
+    safe_revision: bdbff32b03f27a487a68f72f8663215282bf62b6
   test/nodes/genetic_tests_test.rb:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+  test/nodes/hes_event_test.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   test/nodes/main_case_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -241,16 +257,16 @@ file safety:
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/mother_e_base_records_test.rb:
     comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: 4805609963f75639e2444df8f42d2d6d65005b7c
+    reviewed_by: kenny.lee
+    safe_revision: 99ef15c6610409a1562e6a03b015569d087b045f
   test/nodes/patient_age_test.rb:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/nodes/patient_test.rb:
     comments: 
-    reviewed_by: ollietulloch
-    safe_revision: 481194575c30b48987f957a9cc5535d604ea0117
+    reviewed_by: kenny.lee
+    safe_revision: a69bbd63d71d5fb2ba46d6a84589915b1120763b
   test/nodes/perinatal_hospital_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -270,7 +286,7 @@ file safety:
   test/parser_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
+    safe_revision: 3ace8794c1c545b47898da1fbee49af8afdbf521
   test/test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon

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) <Nodes::BatchTypeNode>
+      (paediatric / enote2 / badger / ucyto / nipt / rddeath /
+      umum / ca_death / biochem / hes / uss) <Nodes::BatchTypeNode>
     end
 
     rule paediatric
@@ -24,12 +25,28 @@ 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' / 'rare disease death') <Nodes::RddeathNode>
+      ('rddeath' / 'rd death' / 'rare disease death') <Nodes::RddeathNode>
     end
 
     rule umum
       ('umum' / 'mum') <Nodes::UmumNode>
     end
+
+    rule ca_death
+     ('cadeath' / 'ca death' / 'congenital anomaly death') <Nodes::CADeathNode>
+    end
   end
 end

data/lib/canql/grammars/hes_event.treetop

@@ -0,0 +1,15 @@
+module Canql
+  grammar HesEvent
+    rule hes_events
+      and_keyword? existance_modifier:hes_no_keyword? hes_keyword <Nodes::HesEvent::WithCondition>
+    end
+
+    rule hes_no_keyword
+      space ('no' / 'some') word_break
+    end
+
+    rule hes_keyword
+      space ('hes events' / 'hes records') word_break
+    end
+  end
+end

data/lib/canql/grammars/main.treetop

@@ -6,6 +6,7 @@ grammar Canql
   include GeneticTest
   include TestResult
   include TestResultGroup
+  include HesEvent
   include Dates
   include EBaseRecords
   include BatchTypes
@@ -130,10 +131,11 @@ grammar Canql
   rule case_with_conditions
      anomalies / genetic_tests / test_results / perinatal_hospital /
      case_field_existance / test_acceptance_existance / test_result_groups /
-     mother_conditions / action_or_ebr
+     mother_conditions / action_or_ebr / hes_events
   end
 
   rule patient_with_conditions
-     anomalies / genetic_tests / test_results / patient_field_existance / action_or_ebr
+     anomalies / genetic_tests / test_results / patient_field_existance /
+     action_or_ebr / hes_events
   end
 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/grammars.rb

@@ -14,4 +14,5 @@ Treetop.load File.expand_path('grammars/patient', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/registry', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/provider', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/perinatal_hospital', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/hes_event', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/main', File.dirname(__FILE__))

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'
@@ -50,5 +68,11 @@ module Canql #:nodoc: all
         'umum'
       end
     end
+
+    module CADeathNode
+      def normalise
+        'ca_death'
+      end
+    end
   end
 end

data/lib/canql/nodes/hes_event.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+module Canql #:nodoc: all
+  module Nodes
+    module HesEvent
+      module WithCondition
+        def to_hes
+          { 'exists' => existance_filter }
+        end
+
+        def existance_filter
+          { Canql::EQUALS => existance_modifier.text_value.strip != 'no' }
+        end
+      end
+    end
+  end
+end

data/lib/canql/nodes/main.rb

@@ -32,7 +32,7 @@ module Canql #:nodoc: all
         sub_clauses = build_sub_clauses
 
         %i[
-          anomalies genetic_tests test_results test_result_groups test_acceptances
+          anomalies genetic_tests test_results test_result_groups test_acceptances hes_events
         ].each do |condition_key|
           if sub_clauses[condition_key].present?
             conditions[condition_key.to_s] = { Canql::ALL => sub_clauses[condition_key] }
@@ -52,6 +52,7 @@ module Canql #:nodoc: all
             sub_clauses, element, :test_result_groups, :to_test_result_group
           )
           add_sub_clause(sub_clauses, element, :test_acceptances, :to_test_acceptance)
+          add_sub_clause(sub_clauses, element, :hes_events, :to_hes)
         end
         sub_clauses
       end

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/nodes.rb

@@ -22,3 +22,4 @@ require 'canql/nodes/patient'
 require 'canql/nodes/main'
 require 'canql/nodes/registry'
 require 'canql/nodes/perinatal_hospital'
+require 'canql/nodes/hes_event'

data/lib/canql/version.rb

@@ -2,5 +2,5 @@
 
 # This stores the current version of the Canql gem
 module Canql
-  VERSION = '5.4.0'
+  VERSION = '5.7.1'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: canql
 version: !ruby/object:Gem::Version
-  version: 5.4.0
+  version: 5.7.1
 platform: ruby
 authors:
 - PHE NDR Development Team
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2021-03-08 00:00:00.000000000 Z
+date: 2021-10-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: chronic
@@ -235,6 +235,7 @@ files:
 - lib/canql/grammars/dates.treetop
 - lib/canql/grammars/e_base_records.treetop
 - lib/canql/grammars/genetic_test.treetop
+- lib/canql/grammars/hes_event.treetop
 - lib/canql/grammars/main.treetop
 - lib/canql/grammars/patient.treetop
 - lib/canql/grammars/perinatal_hospital.treetop
@@ -249,6 +250,7 @@ files:
 - lib/canql/nodes/dates.rb
 - lib/canql/nodes/e_base_records.rb
 - lib/canql/nodes/genetic_test.rb
+- lib/canql/nodes/hes_event.rb
 - lib/canql/nodes/main.rb
 - lib/canql/nodes/patient.rb
 - lib/canql/nodes/perinatal_hospital.rb