canql 4.0.1 → 4.4.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,6 +1,26 @@
 ## [Unreleased]
 *no unreleased changes*
 
+## 4.4.1 / 2021-01-13
+### Fixed
+* Relax constraints to support Rails 6.x
+
+## 4.4.0 / 2020-07-08
+### Added
+* Added filter for missing and supplied required test result groups (#47)
+
+## 4.3.0 / 2020-06-10
+### Added
+* Added additional field existance options (#45)
+
+## 4.2.0 / 2020-03-25
+### Added
+* Added additional EUROCAT category filters for RAG combination
+
+## 4.1.0 / 2020-03-19
+### Added
+* Added filters for EUROCAT RAG rating (#39)
+
 ## 4.0.1 / 2019-10-29
 ### Fixed
 * Relax `chronic` dependency

data/canql.gemspec

@@ -28,7 +28,7 @@ Gem::Specification.new do |spec|
 
   spec.add_dependency 'chronic', '~> 0.3'
   spec.add_dependency 'ndr_support', '>= 3.0', '< 6'
-  spec.add_dependency 'rails', '>= 4.1', '< 6'
+  spec.add_dependency 'rails', '>= 4.1', '< 7'
   spec.add_dependency 'treetop', '>= 1.4.10'
 
   spec.add_development_dependency 'bundler'
@@ -36,7 +36,7 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency 'guard-minitest'
   spec.add_development_dependency 'guard-rubocop'
   spec.add_development_dependency 'minitest'
-  spec.add_development_dependency 'ndr_dev_support', '~> 3.1', '>= 3.1.3'
+  spec.add_development_dependency 'ndr_dev_support', '~> 5.6'
   spec.add_development_dependency 'pry'
   spec.add_development_dependency 'rake'
   spec.add_development_dependency 'terminal-notifier-guard' if RUBY_PLATFORM =~ /darwin/

data/code_safety.yml

@@ -15,11 +15,11 @@ file safety:
   ".travis.yml":
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 8adb767031a19aa6b3cea3f1cb05b4a9bcc964f3
+    safe_revision: bb0b75b6914deea03a7a520cd0827eaf5ecab92f
   CHANGELOG.md:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 03c6aaec256bc3b0500f422e0f97f84804bfeffa
+    safe_revision: 171f61eb19427e34aeb4d6e901260d447094b6d0
   CODE_OF_CONDUCT.md:
     comments: 
     reviewed_by: drewthorp
@@ -51,7 +51,7 @@ file safety:
   canql.gemspec:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: c3a0f7aae0658ce6236b82c715a4ace57e4bf513
+    safe_revision: bb0b75b6914deea03a7a520cd0827eaf5ecab92f
   lib/canql.rb:
     comments: 
     reviewed_by: timgentry
@@ -63,7 +63,7 @@ file safety:
   lib/canql/grammars.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
+    safe_revision: c5f8f76b2c335a8554f39a14d6165bf5cd8f9b67
   lib/canql/grammars/age.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
@@ -95,12 +95,12 @@ file safety:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
     reviewed_by: josh.pencheon
-    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
   lib/canql/grammars/patient.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
     reviewed_by: josh.pencheon
-    safe_revision: e258a1a403b7474f8919b1a76127f9ad71a640ad
+    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
   lib/canql/grammars/perinatal_hospital.treetop:
     comments: 
     reviewed_by: josh.pencheon
@@ -119,10 +119,14 @@ file safety:
       kinds of DoS attack
     reviewed_by: timgentry
     safe_revision: c39d24bb500719971969762e94545e82866bf92f
+  lib/canql/grammars/test_result_group.treetop:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
   lib/canql/nodes.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: c431b8a476b84d077e9c39a2a13c2b17a296773d
+    safe_revision: c5f8f76b2c335a8554f39a14d6165bf5cd8f9b67
   lib/canql/nodes/age.rb:
     comments: 
     reviewed_by: timgentry
@@ -150,11 +154,11 @@ file safety:
   lib/canql/nodes/main.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    safe_revision: c5f8f76b2c335a8554f39a14d6165bf5cd8f9b67
   lib/canql/nodes/patient.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: e258a1a403b7474f8919b1a76127f9ad71a640ad
+    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
   lib/canql/nodes/perinatal_hospital.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -167,6 +171,10 @@ file safety:
     comments: 
     reviewed_by: timgentry
     safe_revision: c39d24bb500719971969762e94545e82866bf92f
+  lib/canql/nodes/test_result_group.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
   lib/canql/parser.rb:
     comments: 
     reviewed_by: timgentry
@@ -178,7 +186,7 @@ file safety:
   lib/canql/version.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 03c6aaec256bc3b0500f422e0f97f84804bfeffa
+    safe_revision: 171f61eb19427e34aeb4d6e901260d447094b6d0
   test/anomaly_test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -202,7 +210,7 @@ file safety:
   test/nodes/case_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: e258a1a403b7474f8919b1a76127f9ad71a640ad
+    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
   test/nodes/code_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -234,7 +242,7 @@ file safety:
   test/nodes/patient_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: e258a1a403b7474f8919b1a76127f9ad71a640ad
+    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
   test/nodes/perinatal_hospital_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -243,15 +251,19 @@ file safety:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+  test/nodes/test_result_groups_test.rb:
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
   test/nodes/test_results_test.rb:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/parser_test.rb:
     comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: e258a1a403b7474f8919b1a76127f9ad71a640ad
+    reviewed_by: timgentry
+    safe_revision: 05ccd47fcbba92bf5525c4d36118274696169d61
   test/test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4

data/lib/canql/grammars.rb

@@ -9,6 +9,7 @@ Treetop.load File.expand_path('grammars/batch_types', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/e_base_records', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/genetic_test', File.dirname(__FILE__))
 Treetop.load File.expand_path('grammars/test_result', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/test_result_group', File.dirname(__FILE__))
 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__))

data/lib/canql/grammars/main.treetop

@@ -5,6 +5,7 @@ grammar Canql
   include Anomaly
   include GeneticTest
   include TestResult
+  include TestResultGroup
   include Dates
   include EBaseRecords
   include BatchTypes
@@ -59,11 +60,11 @@ grammar Canql
   end
 
   rule case_preconditions
-    registry / gender / outcome / primacy
+    registry / gender / outcome / primacy / category
   end
 
   rule patient_preconditions
-     gender / primacy
+     gender / primacy / category
   end
 
   rule case_additional_conditions
@@ -127,7 +128,9 @@ grammar Canql
   end
 
   rule case_with_conditions
-     anomalies / genetic_tests / test_results / perinatal_hospital / case_field_existance / mother_conditions / action_or_ebr
+     anomalies / genetic_tests / test_results / perinatal_hospital /
+     case_field_existance / test_result_groups / mother_conditions /
+     action_or_ebr
   end
 
   rule patient_with_conditions

data/lib/canql/grammars/patient.treetop

@@ -12,6 +12,10 @@ module Canql
       space primacy:('primary' / 'alias' ) word_break <Nodes::Patient::PrimacyNode>
     end
 
+    rule category
+      space category:('eurocat amber and green' / 'eurocat red and amber' / 'eurocat red' / 'eurocat amber' / 'eurocat green' / 'eurocat') word_break <Nodes::Patient::CategoryNode>
+    end
+
     rule expected_keyword
       space ('expected' / 'due') word_break
     end
@@ -42,16 +46,17 @@ module Canql
 
     rule case_field_names
       patient_field_name:(
-        'date of birth' / 'dob' / 'nhs number' / 'delivery postcode' /
-        'booking postcode' / 'birth weight' /
+        'date of birth' / 'dob' / 'date of vital status' / 'nhs number' /
+        'delivery postcode' / 'booking postcode' / 'birth weight' /
         'place of delivery' / 'sex' / 'outcome' / 'edd' /
-        'expected delivery date' / 'booking hospital' / 'screening status'
+        'expected delivery date' / 'booking hospital' / 'screening status' /
+        'number of fetuses at delivery' / 'malformed in set'
       )
     end
 
     rule patient_field_names
       patient_field_name:(
-        'date of birth' / 'dob' / 'nhs number' / 'sex'
+        'date of birth' / 'dob' / 'date of vital status' / 'nhs number' / 'sex'
       )
     end
 

data/lib/canql/grammars/test_result_group.treetop

@@ -0,0 +1,16 @@
+module Canql
+  grammar TestResultGroup
+    rule test_result_groups
+      and_keyword? existance_modifier:test_result_group_existance_keyword group:test_result_group_names <Nodes::TestResultGroup::WithCondition>
+    end
+
+    rule test_result_group_existance_keyword
+      # If in furture the reverse is needed use 'supplied require'
+      space ('missing required' / 'missing' / 'supplied required' / 'supplied') word_break
+    end
+
+    rule test_result_group_names
+      space ('screening' / 'anomaly scan') word_break
+    end
+  end
+end

data/lib/canql/nodes.rb

@@ -17,6 +17,7 @@ require 'canql/nodes/batch_types'
 require 'canql/nodes/anomaly'
 require 'canql/nodes/genetic_test'
 require 'canql/nodes/test_result'
+require 'canql/nodes/test_result_group'
 require 'canql/nodes/patient'
 require 'canql/nodes/main'
 require 'canql/nodes/registry'

data/lib/canql/nodes/main.rb

@@ -32,16 +32,23 @@ module Canql #:nodoc: all
         anomalies = []
         genetic_tests = []
         test_results = []
+        test_result_groups = []
 
         post.elements.each do |element|
           anomalies << element.to_anomaly if element.respond_to?(:to_anomaly)
           genetic_tests << element.to_genetic_test if element.respond_to?(:to_genetic_test)
           test_results << element.to_test_result if element.respond_to?(:to_test_result)
+          if element.respond_to?(:to_test_result_group)
+            test_result_groups << element.to_test_result_group
+          end
         end
 
         conditions['anomalies'] = { Canql::ALL => anomalies } if anomalies.any?
         conditions['genetic_tests'] = { Canql::ALL => genetic_tests } if genetic_tests.any?
         conditions['test_results'] = { Canql::ALL => test_results } if test_results.any?
+        if test_result_groups.any?
+          conditions['test_result_groups'] = { Canql::ALL => test_result_groups }
+        end
         conditions
       end
     end

data/lib/canql/nodes/patient.rb

@@ -21,21 +21,40 @@ module Canql #:nodoc: all
         end
       end
 
+      module CategoryNode
+        def meta_data_item
+          { 'patient.category' => { Canql::EQUALS => clean_category } }
+        end
+
+        def clean_category
+          return 'eurocat_red' if 'eurocat red' == category.text_value
+          return 'eurocat_amber' if 'eurocat amber' == category.text_value
+          return 'eurocat_green' if 'eurocat green' == category.text_value
+          return 'eurocat_amber_green' if 'eurocat amber and green' == category.text_value
+          return 'eurocat_red_amber' if 'eurocat red and amber' == category.text_value
+
+          category.text_value
+        end
+      end
+
       module FieldExists
         FIELDS = {
-          'date of birth':          { patient: 'birthdate', mother: 'birthdate' },
-          'dob':                    { patient: 'birthdate', mother: 'birthdate' },
-          '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' },
+          'date of birth': { 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' },
           'expected delivery date': { patient: 'expecteddeliverydate' },
-          'booking hospital':       { patient: 'booking_hospital' },
-          'screening status':       { patient: 'screeningstatus' }
+          'booking hospital': { patient: 'booking_hospital' },
+          'screening status': { patient: 'screeningstatus' },
+          'number of fetuses at delivery': { patient: 'numoffetusesatdelivery' },
+          'malformed in set': { patient: 'malformedinset' }
         }.freeze
 
         def meta_data_item

data/lib/canql/nodes/test_result_group.rb

@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+module Canql #:nodoc: all
+  module Nodes
+    module TestResultGroup
+      module WithCondition
+        def test_result_group
+          group.text_value.strip.parameterize.underscore
+        end
+
+        def to_test_result_group
+          test_result_group_hash = { 'exists' => existance_filter }
+          test_result_group_hash['required'] = requirement_filter
+          test_result_group_hash['group'] = test_result_group_filter if test_result_group.present?
+          test_result_group_hash
+        end
+
+        def existance_filter
+          {
+            Canql::EQUALS => ['supplied required', 'supplied'].include?(
+              existance_modifier.text_value.strip
+            )
+          }
+        end
+
+        def requirement_filter
+          {
+            Canql::EQUALS => ['supplied required', 'missing required'].include?(
+              existance_modifier.text_value.strip
+            )
+          }
+        end
+
+        def test_result_group_filter
+          { Canql::EQUALS => test_result_group }
+        end
+      end
+    end
+  end
+end

data/lib/canql/version.rb

@@ -2,5 +2,5 @@
 
 # This stores the current version of the Canql gem
 module Canql
-  VERSION = '4.0.1'
+  VERSION = '4.4.1'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: canql
 version: !ruby/object:Gem::Version
-  version: 4.0.1
+  version: 4.4.1
 platform: ruby
 authors:
 - PHE NDR Development Team
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-10-29 00:00:00.000000000 Z
+date: 2021-01-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: chronic
@@ -53,7 +53,7 @@ dependencies:
         version: '4.1'
     - - "<"
       - !ruby/object:Gem::Version
-        version: '6'
+        version: '7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -63,7 +63,7 @@ dependencies:
         version: '4.1'
     - - "<"
       - !ruby/object:Gem::Version
-        version: '6'
+        version: '7'
 - !ruby/object:Gem::Dependency
   name: treetop
   requirement: !ruby/object:Gem::Requirement
@@ -154,20 +154,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.1'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 3.1.3
+        version: '5.6'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.1'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 3.1.3
+        version: '5.6'
 - !ruby/object:Gem::Dependency
   name: pry
   requirement: !ruby/object:Gem::Requirement
@@ -244,6 +238,7 @@ files:
 - lib/canql/grammars/provider.treetop
 - lib/canql/grammars/registry.treetop
 - lib/canql/grammars/test_result.treetop
+- lib/canql/grammars/test_result_group.treetop
 - lib/canql/nodes.rb
 - lib/canql/nodes/age.rb
 - lib/canql/nodes/anomaly.rb
@@ -256,6 +251,7 @@ files:
 - lib/canql/nodes/perinatal_hospital.rb
 - lib/canql/nodes/registry.rb
 - lib/canql/nodes/test_result.rb
+- lib/canql/nodes/test_result_group.rb
 - lib/canql/parser.rb
 - lib/canql/treetop/extensions.rb
 - lib/canql/version.rb