canql 4.4.1 → 5.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 54b9bc4e7dcb9f8952d07784089ab4c28d747bcc9f9c367e2ead3f91c4c74cdc
+  metadata.gz: 99a2f7ebbb5ae3c1cbdd8368b020f8eb7c54d969278db3bdd90277f113095ce9
+  data.tar.gz: fb4f6561d61cc9da30dd9a30562c7374a95e52d615b014bc16e5e282529c4975
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-  data.tar.gz: 2d56d8da5357e9b66f8f486dec03887f1d31ec0f6c405c34ae8e66ada36cb51e520a89808821b0b308dfdc7581eb39c2d4f17c3d1987e9dadf7540ad2feadd50
+  metadata.gz: 93cc26e76a35a5b47600368d7208f81c6cd6457c416f942be852536952d54b9a1bbcb49df7c17f95fb09b5bdaa4581fda91b70e36ad229aae5213914d9d7db39
+  data.tar.gz: 2a8bf966e8a0b93411117a09f790f20825c6b27850f1903cea53fd636855d920ec4fdc5dc9bb903b11ec0c2e34275af88ca2e49e4c09b3ea206a6ff2620d626b

data/.github/CODEOWNERS

@@ -0,0 +1,2 @@
+# Admins should have oversight of the version:
+lib/canql/version.rb      @publichealthengland/ndr-admins

data/.github/workflows/lint.yml

@@ -0,0 +1,23 @@
+name: Lint
+
+on: [pull_request]
+
+jobs:
+  rubocop:
+    name: RuboCop
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0 # fetch everything
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: 3.0
+    - name: Install dependencies
+      run: bundle install
+    - name: Run RuboCop against BASE..HEAD changes
+      run: bundle exec rake rubocop:diff origin/${GITHUB_BASE_REF#*/}
+

data/.github/workflows/test.yml

@@ -0,0 +1,65 @@
+name: Test
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        ruby-version:
+          - 2.6
+          - 2.7
+          - 3.0
+
+    name: Ruby ${{ matrix.ruby-version }}
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: ${{ matrix.ruby-version }}
+    - name: Install dependencies
+      run: bundle install
+    - name: Run tests
+      run: bundle exec rake
+
+  # A utility job upon which Branch Protection can depend,
+  # thus remaining agnostic of the matrix.
+  test_matrix:
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    name: Matrix
+    needs: test
+    steps:
+    - name: Check build matrix status
+      if: ${{ needs.test.result != 'success' }}
+      run: exit 1
+
+  notify:
+    # Run only on master, but regardless of whether tests past:
+    if: ${{ always() && github.ref == 'refs/heads/master' }}
+
+    needs: test_matrix
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: 8398a7/action-slack@v3
+      with:
+        status: custom
+        fields: workflow,commit,author
+        custom_payload: |
+          {
+            channel: 'C7FQWGDHP',
+            username: 'CI – ' + '${{ github.repository }}'.split('/')[1],
+            icon_emoji: ':hammer_and_wrench:',
+            attachments: [{
+              color: '${{ needs.test_matrix.result }}' === 'success' ? 'good' : '${{ needs.test_matrix.result }}' === 'failure' ? 'danger' : 'warning',
+              text: `${process.env.AS_WORKFLOW} against \`${{ github.ref }}\` (${process.env.AS_COMMIT}) for ${{ github.actor }} resulted in *${{ needs.test_matrix.result }}*.`
+            }]
+          }
+      env:
+        SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}

data/.rubocop.yml

@@ -1,11 +1 @@
-inherit_from: 'https://raw.githubusercontent.com/PublicHealthEngland/ndr_dev_support/master/.rubocop.yml'
-
-Rails:
-  Enabled: false
-
-AllCops:
-  TargetRailsVersion: 4.2
-  TargetRubyVersion: 2.3
-
-Style/FrozenStringLiteralComment:
-  Enabled: true
+require: ndr_dev_support

data/CHANGELOG.md

@@ -1,6 +1,15 @@
 ## [Unreleased]
 *no unreleased changes*
 
+## 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)
+
+### Added
+* Added fetal medicine and dating options to the test group filter (#50)
+* Added new gestation at delivery and booking date to case field existance filter (#52)
+
 ## 4.4.1 / 2021-01-13
 ### Fixed
 * Relax constraints to support Rails 6.x

data/README.md

@@ -1,6 +1,6 @@
-# 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)
+# CANQL [![Build Status](https://github.com/publichealthengland/canql/workflows/Test/badge.svg)](https://github.com/publichealthengland/canql/actions?query=workflow%3Atest) [![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.
+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.
 
 Used for analysis, research and day-to-day operations to empower non-technical users to write sophisticated human readable queries without the need to know or understand the underlying datastore and/or schema.
 

data/canql.gemspec

@@ -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', '~> 5.6'
+  spec.add_development_dependency 'ndr_dev_support', '~> 5.9'
   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

@@ -1,5 +1,17 @@
 ---
 file safety:
+  ".github/CODEOWNERS":
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: a964c47962d47724afd66ba59660589fc3c8b02c
+  ".github/workflows/lint.yml":
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 71f6a631758a5a38814d3eafec407e0fde30101f
+  ".github/workflows/test.yml":
+    comments: 
+    reviewed_by: josh.pencheon
+    safe_revision: 865fc970554fee9207f8e3cd0247133c6a849b24
   ".gitignore":
     comments: 
     reviewed_by: timgentry
@@ -9,17 +21,13 @@ file safety:
     reviewed_by: timgentry
     safe_revision: 0b34688f1198eace9310f47060aa8915f5b44985
   ".rubocop.yml":
-    comments: 
-    reviewed_by: timgentry
-    safe_revision: 5bc563431f7822e2baf37bbeac9861c36675602d
-  ".travis.yml":
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: bb0b75b6914deea03a7a520cd0827eaf5ecab92f
+    safe_revision: 146b255b240b0efc928d39dd1b70ab221ddc3138
   CHANGELOG.md:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 171f61eb19427e34aeb4d6e901260d447094b6d0
+    safe_revision: f84cb2190f46ee550db796a17455980ab00d3187
   CODE_OF_CONDUCT.md:
     comments: 
     reviewed_by: drewthorp
@@ -35,7 +43,7 @@ file safety:
   README.md:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 33feeeaa4b2089e33f563e4c766e91c38b108e36
+    safe_revision: 8c07968aa84db92b6f1cc528180f73530ddc6ff5
   Rakefile:
     comments: 
     reviewed_by: timgentry
@@ -51,7 +59,7 @@ file safety:
   canql.gemspec:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: bb0b75b6914deea03a7a520cd0827eaf5ecab92f
+    safe_revision: 146b255b240b0efc928d39dd1b70ab221ddc3138
   lib/canql.rb:
     comments: 
     reviewed_by: timgentry
@@ -100,7 +108,7 @@ 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: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
+    safe_revision: 7490099869e368dcd5c26ded11eb90229baf4cae
   lib/canql/grammars/perinatal_hospital.treetop:
     comments: 
     reviewed_by: josh.pencheon
@@ -113,7 +121,7 @@ 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: 4e26ac746098452b01dac88373e401e39f309b74
+    safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
   lib/canql/grammars/test_result.treetop:
     comments: It is a known issue that this is potentially susceptible to certain
       kinds of DoS attack
@@ -122,7 +130,7 @@ file safety:
   lib/canql/grammars/test_result_group.treetop:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
+    safe_revision: 8ea906ca663b98edee2592fc5b0731881573f06b
   lib/canql/nodes.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -158,7 +166,7 @@ file safety:
   lib/canql/nodes/patient.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
+    safe_revision: 7490099869e368dcd5c26ded11eb90229baf4cae
   lib/canql/nodes/perinatal_hospital.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -186,7 +194,7 @@ file safety:
   lib/canql/version.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 171f61eb19427e34aeb4d6e901260d447094b6d0
+    safe_revision: cfe2f76a07880e268e1f29fbac5f6cd380202ce3
   test/anomaly_test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -210,7 +218,7 @@ file safety:
   test/nodes/case_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
+    safe_revision: 7490099869e368dcd5c26ded11eb90229baf4cae
   test/nodes/code_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -218,7 +226,7 @@ file safety:
   test/nodes/e_base_records_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
   test/nodes/genetic_tests_test.rb:
     comments: 
     reviewed_by: josh.pencheon
@@ -250,19 +258,19 @@ file safety:
   test/nodes/registry_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
+    safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
   test/nodes/test_result_groups_test.rb:
     comments: 
     reviewed_by: josh.pencheon
-    safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
+    safe_revision: 8ea906ca663b98edee2592fc5b0731881573f06b
   test/nodes/test_results_test.rb:
     comments: 
     reviewed_by: josh.pencheon
     safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
   test/parser_test.rb:
     comments: 
-    reviewed_by: timgentry
-    safe_revision: 05ccd47fcbba92bf5525c4d36118274696169d61
+    reviewed_by: josh.pencheon
+    safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
   test/test_helper.rb:
     comments: 
     reviewed_by: josh.pencheon

data/lib/canql/grammars/patient.treetop

@@ -50,7 +50,8 @@ module Canql
         'delivery postcode' / 'booking postcode' / 'birth weight' /
         'place of delivery' / 'sex' / 'outcome' / 'edd' /
         'expected delivery date' / 'booking hospital' / 'screening status' /
-        'number of fetuses at delivery' / 'malformed in set'
+        'number of fetuses at delivery' / 'malformed in set' / 'gestation at delivery' /
+        'booking date'
       )
     end
 

data/lib/canql/grammars/registry.treetop

@@ -14,14 +14,15 @@ module Canql
 
     rule registry_abbr
       (england / east_mids / thames / east / yorkshire / north_east / north_west /
-        west_mids / south_west / wessex / london / limbo)
+        west_mids / south_west_supra / south_west / wessex / london / limbo /
+        northern_supra / midlands_east_supra)
     end
 
     rule thames
       ('thames valley' / 'thames')
       {
         def to_registrycode
-          '68'
+          'thames'
         end
       }
     end
@@ -30,7 +31,7 @@ module Canql
       ('east mids' / 'east midlands and south yorkshire' / 'east midlands')
       {
         def to_registrycode
-          '72'
+          'east_mids'
         end
       }
     end
@@ -39,7 +40,7 @@ module Canql
       'yorkshire'
       {
         def to_registrycode
-          '93'
+          'yorkshire'
         end
       }
     end
@@ -48,7 +49,7 @@ module Canql
       'north east'
       {
         def to_registrycode
-          '73'
+          'north_east'
         end
       }
     end
@@ -57,7 +58,7 @@ module Canql
       'north west'
       {
         def to_registrycode
-          '94'
+          'north_west'
         end
       }
     end
@@ -66,7 +67,7 @@ module Canql
       ('west mids' / 'west midlands')
       {
         def to_registrycode
-          '99'
+          'west_mids'
         end
       }
     end
@@ -75,7 +76,7 @@ module Canql
       'south west'
       {
         def to_registrycode
-          '84'
+          'south_west'
         end
       }
     end
@@ -84,7 +85,7 @@ module Canql
       'wessex'
       {
         def to_registrycode
-          '70'
+          'wessex'
         end
       }
     end
@@ -93,7 +94,7 @@ module Canql
       ('london and south east' / 'london')
       {
         def to_registrycode
-          '95'
+          'london'
         end
       }
     end
@@ -102,7 +103,7 @@ module Canql
       ('east of england' / 'east')
       {
         def to_registrycode
-          '96'
+          'east'
         end
       }
     end
@@ -111,7 +112,7 @@ module Canql
       'limbo'
       {
         def to_registrycode
-          '01'
+          'limbo'
         end
       }
     end
@@ -120,7 +121,34 @@ module Canql
       'england'
       {
         def to_registrycode
-          '00'
+          'england'
+        end
+      }
+    end
+
+    rule northern_supra
+      ('northern supra' / 'northern')
+      {
+        def to_registrycode
+          'northern_supra'
+        end
+      }
+    end
+
+    rule midlands_east_supra
+      ('midlands & east supra' / 'midlands & east')
+      {
+        def to_registrycode
+          'midlands_east_supra'
+        end
+      }
+    end
+
+    rule south_west_supra
+      'south west supra'
+      {
+        def to_registrycode
+          'south_west_supra'
         end
       }
     end

data/lib/canql/grammars/test_result_group.treetop

@@ -10,7 +10,7 @@ module Canql
     end
 
     rule test_result_group_names
-      space ('screening' / 'anomaly scan') word_break
+      space ('screening' / 'anomaly scan' / 'fetal medicine' / 'dating') word_break
     end
   end
 end

data/lib/canql/nodes/patient.rb

@@ -54,7 +54,9 @@ module Canql #:nodoc: all
           'booking hospital': { patient: 'booking_hospital' },
           'screening status': { patient: 'screeningstatus' },
           'number of fetuses at delivery': { patient: 'numoffetusesatdelivery' },
-          'malformed in set': { patient: 'malformedinset' }
+          'malformed in set': { patient: 'malformedinset' },
+          'gestation at delivery': { patient: 'gestationallength' },
+          'booking date': { patient: 'firstbookingdate' }
         }.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 = '4.4.1'
+  VERSION = '5.0.0'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: canql
 version: !ruby/object:Gem::Version
-  version: 4.4.1
+  version: 5.0.0
 platform: ruby
 authors:
 - PHE NDR Development Team
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2021-01-13 00:00:00.000000000 Z
+date: 2021-01-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: chronic
@@ -154,14 +154,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5.6'
+        version: '5.9'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5.6'
+        version: '5.9'
 - !ruby/object:Gem::Dependency
   name: pry
   requirement: !ruby/object:Gem::Requirement
@@ -210,6 +210,9 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- ".github/CODEOWNERS"
+- ".github/workflows/lint.yml"
+- ".github/workflows/test.yml"
 - ".gitignore"
 - ".hound.yml"
 - ".rubocop.yml"