canql 3.0.0 → 4.3.0

checksums.yaml

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data/CHANGELOG.md

@@ -1,6 +1,29 @@
 ## [Unreleased]
 *no unreleased changes*
 
+## 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
+
+## 4.0.0 / 2019-09-06
+### Changed
+* Added case filters for delivery and booking postcode fields and removed all simple postcode field filters (#36)
+
+### Added
+* Added fasp and fasp plus code groups (#37)
+
 ## 3.0.0 / 2019-06-04
 ### Changed
 * Added new branch of CANQL for querying all patient not just child patients - modifies DIR (#29)

data/README.md

@@ -1,4 +1,4 @@
-# CANQL [![Build Status](https://travis-ci.org/PublicHealthEngland/canql.svg?branch=master)](https://travis-ci.org/PublicHealthEngland/canql)
+# CANQL [![Build Status](https://travis-ci.org/PublicHealthEngland/canql.svg?branch=master)](https://travis-ci.org/PublicHealthEngland/canql) [![Gem Version](https://badge.fury.io/rb/canql.svg)](https://rubygems.org/gems/canql)
 
 Congenital Anomaly Natural Query Language (CANQL) is a [Treetop](http://treetop.rubyforge.org/) driven Domain Specific Language (DSL) used by the Public Health England (PHE) National Congenital Anomaly and Rare Disease Registration Service (NCARDRS) to identify cohorts of cases.
 

data/canql.gemspec

@@ -26,7 +26,7 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ['lib']
 
-  spec.add_dependency 'chronic', '~> 0.3.0'
+  spec.add_dependency 'chronic', '~> 0.3'
   spec.add_dependency 'ndr_support', '>= 3.0', '< 6'
   spec.add_dependency 'rails', '>= 4.1', '< 6'
   spec.add_dependency 'treetop', '>= 1.4.10'
@@ -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: 16abb8206a3d36c7532427cd7137df79d2733d1d
+    safe_revision: 8adb767031a19aa6b3cea3f1cb05b4a9bcc964f3
   CHANGELOG.md:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: ff70470e8fa9613a6968a7579b206b6107ef5312
+    safe_revision: 23852bc731fdf82a87fd06070a89ec81affe8155
   CODE_OF_CONDUCT.md:
     comments: 
     reviewed_by: drewthorp
@@ -35,7 +35,7 @@ file safety:
   README.md:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    safe_revision: 33feeeaa4b2089e33f563e4c766e91c38b108e36
   Rakefile:
     comments: 
     reviewed_by: timgentry
@@ -50,8 +50,8 @@ file safety:
     safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
   canql.gemspec:
     comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: 16abb8206a3d36c7532427cd7137df79d2733d1d
+    reviewed_by: timgentry
+    safe_revision: 6cb13f43b4353ab7c90ff0406ec13ac169b8e64c
   lib/canql.rb:
     comments: 
     reviewed_by: timgentry
@@ -73,7 +73,7 @@ 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: 73a7dac17b20fcc77bcbd9d38777c8aa4d524816
+    safe_revision: b7778ca1d536022a807420cc9fe0f1c2df7f73ef
   lib/canql/grammars/batch_types.treetop:
     comments: 
     reviewed_by: josh.pencheon
@@ -94,13 +94,13 @@ file safety:
   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: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    reviewed_by: timgentry
+    safe_revision: 05ccd47fcbba92bf5525c4d36118274696169d61
   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: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
   lib/canql/grammars/perinatal_hospital.treetop:
     comments: 
     reviewed_by: josh.pencheon
@@ -130,7 +130,7 @@ file safety:
   lib/canql/nodes/anomaly.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 73a7dac17b20fcc77bcbd9d38777c8aa4d524816
+    safe_revision: b7778ca1d536022a807420cc9fe0f1c2df7f73ef
   lib/canql/nodes/batch_types.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -154,7 +154,7 @@ file safety:
   lib/canql/nodes/patient.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 38369f1f26167f396d1705ec88611103d5262726
+    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
   lib/canql/nodes/perinatal_hospital.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -178,7 +178,7 @@ file safety:
   lib/canql/version.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: ff70470e8fa9613a6968a7579b206b6107ef5312
+    safe_revision: 23852bc731fdf82a87fd06070a89ec81affe8155
   test/anomaly_test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -202,11 +202,11 @@ file safety:
   test/nodes/case_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
   test/nodes/code_test.rb:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 695cec7ee61f36a9ef054a4079f290421d814666
+    reviewed_by: josh.pencheon
+    safe_revision: b7778ca1d536022a807420cc9fe0f1c2df7f73ef
   test/nodes/e_base_records_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -234,7 +234,7 @@ file safety:
   test/nodes/patient_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 33597126dbd2f720bd867fc357003634b73e6d0a
+    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
   test/nodes/perinatal_hospital_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -249,8 +249,8 @@ file safety:
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/parser_test.rb:
     comments: 
-    reviewed_by: josh.pencheon
-    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    reviewed_by: timgentry
+    safe_revision: 05ccd47fcbba92bf5525c4d36118274696169d61
   test/test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon

data/lib/canql/grammars/anomaly.treetop

@@ -43,7 +43,7 @@ module Canql
     end
 
     rule code_group
-      ('fasp' / 'structural' / 'trisomy') <Nodes::Anomaly::SingleCodeGroupNode>
+      ('fasp plus' / 'plus' / 'fasp' / 'structural' / 'trisomy') <Nodes::Anomaly::SingleCodeGroupNode>
     end
   end
 end

data/lib/canql/grammars/main.treetop

@@ -59,11 +59,11 @@ 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

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
@@ -42,15 +46,17 @@ module Canql
 
     rule case_field_names
       patient_field_name:(
-        'date of birth' / 'dob' / 'nhs number' / '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' / 'postcode' / 'sex'
+        'date of birth' / 'dob' / 'date of vital status' / 'nhs number' / 'sex'
       )
     end
 

data/lib/canql/nodes/anomaly.rb

@@ -25,6 +25,7 @@ module Canql #:nodoc: all
           end
           anomaly_hash['icd_codes'] = code_filter[:icd_code] if code_filter[:icd_code].present?
           return anomaly_hash if code_filter[:code_group].blank?
+
           anomaly_hash['code_groups'] = code_filter[:code_group]
           anomaly_hash
         end
@@ -48,11 +49,13 @@ module Canql #:nodoc: all
         def code_type(code)
           return :icd_code if code.respond_to?(:to_code) && code.to_code.present?
           return :code_group if code.respond_to?(:to_code_group) && code.to_code_group.present?
+
           raise 'Unable to find code type'
         end
 
         def code_value(code)
           return code.to_code if :icd_code == code_type(code)
+
           code.to_code_group
         end
 
@@ -67,6 +70,7 @@ module Canql #:nodoc: all
             code_filters[:icd_code] = { Canql::BEGINS => code_array[:icd_code] }
           end
           return code_filters if code_array[:code_group].blank?
+
           code_filters[:code_group] = { Canql::EQUALS => code_array[:code_group] }
           code_filters
         end
@@ -86,6 +90,7 @@ module Canql #:nodoc: all
       module AdditionalCodeNode
         def code_type
           return :icd_code if anomalies_icd_code.respond_to?(:to_code)
+
           :code_group
         end
 
@@ -106,7 +111,7 @@ module Canql #:nodoc: all
 
       module SingleCodeGroupNode
         def to_code_group
-          text_value.upcase
+          text_value.gsub(/( )/, '_').upcase
         end
       end
     end

data/lib/canql/nodes/patient.rb

@@ -21,20 +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' },
-          'postcode':               { patient: 'postcode',  mother: '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/version.rb

@@ -2,5 +2,5 @@
 
 # This stores the current version of the Canql gem
 module Canql
-  VERSION = '3.0.0'
+  VERSION = '4.3.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: canql
 version: !ruby/object:Gem::Version
-  version: 3.0.0
+  version: 4.3.0
 platform: ruby
 authors:
 - PHE NDR Development Team
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-06-04 00:00:00.000000000 Z
+date: 2020-06-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: chronic
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.3.0
+        version: '0.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.3.0
+        version: '0.3'
 - !ruby/object:Gem::Dependency
   name: ndr_support
   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