canql 4.3.0 → 5.2.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/.github/CODEOWNERS +2 -0
- data/.github/workflows/lint.yml +23 -0
- data/.github/workflows/test.yml +65 -0
- data/.rubocop.yml +1 -11
- data/CHANGELOG.md +27 -1
- data/README.md +2 -2
- data/canql.gemspec +2 -2
- data/code_safety.yml +54 -34
- data/lib/canql/grammars.rb +1 -0
- data/lib/canql/grammars/anomaly.treetop +5 -1
- data/lib/canql/grammars/main.treetop +4 -1
- data/lib/canql/grammars/patient.treetop +2 -1
- data/lib/canql/grammars/registry.treetop +41 -13
- data/lib/canql/grammars/test_result_group.treetop +28 -0
- data/lib/canql/nodes.rb +1 -0
- data/lib/canql/nodes/anomaly.rb +47 -12
- data/lib/canql/nodes/main.rb +28 -10
- data/lib/canql/nodes/patient.rb +3 -1
- data/lib/canql/nodes/test_result_group.rb +75 -0
- data/lib/canql/version.rb +1 -1
- metadata +11 -6
checksums.yaml
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: c11d88eb61eaebcc1fee8bbcf02c3528a26799b7a62800971c34517619b98668
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data.tar.gz: ac2d55b1fcf88636a1ccfdf3a2f11b4d4ef7e878ba886fceddd2dcdce26a6fb6
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metadata.gz:
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metadata.gz: 767d7da5878ba53e624db9090a0bce25ee2b17c039b5ecce4bbb65126f0d32bc988851f7b31e41be235f9911919051a07a7e5478b54d11bc0aefdf7c6a939389
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data.tar.gz: bd874eb46ba2641c84ba40d2a521db212b218879cf6e789777514d36bea0672fd9b38e24804ca4a86b54b722c62b5a7a89003d3040cd8179991b134ebb7543ab
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data/.github/CODEOWNERS
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name: Lint
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on: [pull_request]
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jobs:
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rubocop:
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name: RuboCop
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0 # fetch everything
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- name: Set up Ruby
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: 3.0
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- name: Install dependencies
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run: bundle install
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- name: Run RuboCop against BASE..HEAD changes
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run: bundle exec rake rubocop:diff origin/${GITHUB_BASE_REF#*/}
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name: Test
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on: [push, pull_request]
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jobs:
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test:
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strategy:
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matrix:
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ruby-version:
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- 2.6
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- 2.7
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- 3.0
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name: Ruby ${{ matrix.ruby-version }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Ruby
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uses: ruby/setup-ruby@v1
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with:
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ruby-version: ${{ matrix.ruby-version }}
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- name: Install dependencies
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run: bundle install
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- name: Run tests
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run: bundle exec rake
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# A utility job upon which Branch Protection can depend,
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# thus remaining agnostic of the matrix.
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test_matrix:
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if: ${{ always() }}
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runs-on: ubuntu-latest
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name: Matrix
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needs: test
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steps:
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- name: Check build matrix status
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if: ${{ needs.test.result != 'success' }}
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run: exit 1
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notify:
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# Run only on master, but regardless of whether tests past:
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if: ${{ always() && github.ref == 'refs/heads/master' }}
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needs: test_matrix
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runs-on: ubuntu-latest
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steps:
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- uses: 8398a7/action-slack@v3
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with:
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status: custom
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fields: workflow,commit,author
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custom_payload: |
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{
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channel: 'C7FQWGDHP',
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username: 'CI – ' + '${{ github.repository }}'.split('/')[1],
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icon_emoji: ':hammer_and_wrench:',
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attachments: [{
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color: '${{ needs.test_matrix.result }}' === 'success' ? 'good' : '${{ needs.test_matrix.result }}' === 'failure' ? 'danger' : 'warning',
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text: `${process.env.AS_WORKFLOW} against \`${{ github.ref }}\` (${process.env.AS_COMMIT}) for ${{ github.actor }} resulted in *${{ needs.test_matrix.result }}*.`
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}]
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}
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env:
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SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
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data/.rubocop.yml
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Enabled: false
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AllCops:
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TargetRailsVersion: 4.2
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TargetRubyVersion: 2.3
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Enabled: true
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require: ndr_dev_support
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data/CHANGELOG.md
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## [Unreleased]
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*no
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* no relevent changes
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## 5.2.0 / 2021-03-04
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* Added new FASP anomaly RAG rating filters (#63)
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## 5.1.0 / 2021-01-25
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### Added
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* Added new filters for test acceptance requirments (#59)
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## 5.0.0 / 2021-01-19
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### Changed
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* Changed the values of registry to use registry name rather than codes and added new supra-region options (#54)
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### Added
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* Added fetal medicine and dating options to the test group filter (#50)
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* Added new gestation at delivery and booking date to case field existance filter (#52)
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## 4.4.1 / 2021-01-13
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### Fixed
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* Relax constraints to support Rails 6.x
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## 4.4.0 / 2020-07-08
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### Added
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* Added filter for missing and supplied required test result groups (#47)
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## 4.3.0 / 2020-06-10
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### Added
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data/README.md
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# CANQL [](https://github.com/publichealthengland/canql/actions?query=workflow%3Atest) [](https://rubygems.org/gems/canql)
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Congenital Anomaly Natural Query Language (CANQL) is a [Treetop](http://treetop.rubyforge.org/)
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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.
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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.
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data/canql.gemspec
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spec.add_dependency 'chronic', '~> 0.3'
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spec.add_dependency 'ndr_support', '>= 3.0', '< 6'
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spec.add_dependency 'rails', '>= 4.1', '<
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spec.add_dependency 'rails', '>= 4.1', '< 7'
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spec.add_dependency 'treetop', '>= 1.4.10'
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spec.add_development_dependency 'guard-minitest'
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spec.add_development_dependency 'guard-rubocop'
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spec.add_development_dependency 'minitest'
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spec.add_development_dependency 'ndr_dev_support', '~> 5.9'
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spec.add_development_dependency 'pry'
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spec.add_development_dependency 'rake'
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spec.add_development_dependency 'terminal-notifier-guard' if RUBY_PLATFORM =~ /darwin/
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data/code_safety.yml
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file safety:
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".github/CODEOWNERS":
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comments:
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reviewed_by: josh.pencheon
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safe_revision: a964c47962d47724afd66ba59660589fc3c8b02c
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".github/workflows/lint.yml":
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comments:
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reviewed_by: josh.pencheon
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safe_revision: 71f6a631758a5a38814d3eafec407e0fde30101f
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".github/workflows/test.yml":
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comments:
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reviewed_by: josh.pencheon
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safe_revision: 865fc970554fee9207f8e3cd0247133c6a849b24
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".gitignore":
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reviewed_by: timgentry
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safe_revision: 0b34688f1198eace9310f47060aa8915f5b44985
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safe_revision: 146b255b240b0efc928d39dd1b70ab221ddc3138
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reviewed_by: ollietulloch
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safe_revision: 9af6ea0bcdac493fe5f31d62b504b285658867c4
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CODE_OF_CONDUCT.md:
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reviewed_by: drewthorp
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README.md:
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safe_revision: 8c07968aa84db92b6f1cc528180f73530ddc6ff5
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safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
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canql.gemspec:
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lib/canql.rb:
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lib/canql/grammars.rb:
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lib/canql/grammars/age.treetop:
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test/nodes/genetic_tests_test.rb:
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test/nodes/registry_test.rb:
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data/lib/canql/grammars.rb
CHANGED
|
@@ -9,6 +9,7 @@ Treetop.load File.expand_path('grammars/batch_types', File.dirname(__FILE__))
|
|
|
9
9
|
Treetop.load File.expand_path('grammars/e_base_records', File.dirname(__FILE__))
|
|
10
10
|
Treetop.load File.expand_path('grammars/genetic_test', File.dirname(__FILE__))
|
|
11
11
|
Treetop.load File.expand_path('grammars/test_result', File.dirname(__FILE__))
|
|
12
|
+
Treetop.load File.expand_path('grammars/test_result_group', File.dirname(__FILE__))
|
|
12
13
|
Treetop.load File.expand_path('grammars/patient', File.dirname(__FILE__))
|
|
13
14
|
Treetop.load File.expand_path('grammars/registry', File.dirname(__FILE__))
|
|
14
15
|
Treetop.load File.expand_path('grammars/provider', File.dirname(__FILE__))
|
|
@@ -35,7 +35,7 @@ module Canql
|
|
|
35
35
|
end
|
|
36
36
|
|
|
37
37
|
rule anomalies_icd_code
|
|
38
|
-
(icd_code_name / code_group)
|
|
38
|
+
(fasp_rating / icd_code_name / code_group)
|
|
39
39
|
end
|
|
40
40
|
|
|
41
41
|
rule icd_code_name
|
|
@@ -45,5 +45,9 @@ module Canql
|
|
|
45
45
|
rule code_group
|
|
46
46
|
('fasp plus' / 'plus' / 'fasp' / 'structural' / 'trisomy') <Nodes::Anomaly::SingleCodeGroupNode>
|
|
47
47
|
end
|
|
48
|
+
|
|
49
|
+
rule fasp_rating
|
|
50
|
+
('fasp red and amber' / 'fasp amber and red' / 'fasp red' / 'fasp amber' / 'fasp green') <Nodes::Anomaly::SingleFaspRatingNode>
|
|
51
|
+
end
|
|
48
52
|
end
|
|
49
53
|
end
|
|
@@ -5,6 +5,7 @@ grammar Canql
|
|
|
5
5
|
include Anomaly
|
|
6
6
|
include GeneticTest
|
|
7
7
|
include TestResult
|
|
8
|
+
include TestResultGroup
|
|
8
9
|
include Dates
|
|
9
10
|
include EBaseRecords
|
|
10
11
|
include BatchTypes
|
|
@@ -127,7 +128,9 @@ grammar Canql
|
|
|
127
128
|
end
|
|
128
129
|
|
|
129
130
|
rule case_with_conditions
|
|
130
|
-
anomalies / genetic_tests / test_results / perinatal_hospital /
|
|
131
|
+
anomalies / genetic_tests / test_results / perinatal_hospital /
|
|
132
|
+
case_field_existance / test_acceptance_existance / test_result_groups /
|
|
133
|
+
mother_conditions / action_or_ebr
|
|
131
134
|
end
|
|
132
135
|
|
|
133
136
|
rule patient_with_conditions
|
|
@@ -50,7 +50,8 @@ module Canql
|
|
|
50
50
|
'delivery postcode' / 'booking postcode' / 'birth weight' /
|
|
51
51
|
'place of delivery' / 'sex' / 'outcome' / 'edd' /
|
|
52
52
|
'expected delivery date' / 'booking hospital' / 'screening status' /
|
|
53
|
-
'number of fetuses at delivery' / 'malformed in set'
|
|
53
|
+
'number of fetuses at delivery' / 'malformed in set' / 'gestation at delivery' /
|
|
54
|
+
'booking date'
|
|
54
55
|
)
|
|
55
56
|
end
|
|
56
57
|
|
|
@@ -14,14 +14,15 @@ module Canql
|
|
|
14
14
|
|
|
15
15
|
rule registry_abbr
|
|
16
16
|
(england / east_mids / thames / east / yorkshire / north_east / north_west /
|
|
17
|
-
west_mids / south_west / wessex / london / limbo
|
|
17
|
+
west_mids / south_west_supra / south_west / wessex / london / limbo /
|
|
18
|
+
northern_supra / midlands_east_supra)
|
|
18
19
|
end
|
|
19
20
|
|
|
20
21
|
rule thames
|
|
21
22
|
('thames valley' / 'thames')
|
|
22
23
|
{
|
|
23
24
|
def to_registrycode
|
|
24
|
-
'
|
|
25
|
+
'thames'
|
|
25
26
|
end
|
|
26
27
|
}
|
|
27
28
|
end
|
|
@@ -30,7 +31,7 @@ module Canql
|
|
|
30
31
|
('east mids' / 'east midlands and south yorkshire' / 'east midlands')
|
|
31
32
|
{
|
|
32
33
|
def to_registrycode
|
|
33
|
-
'
|
|
34
|
+
'east_mids'
|
|
34
35
|
end
|
|
35
36
|
}
|
|
36
37
|
end
|
|
@@ -39,7 +40,7 @@ module Canql
|
|
|
39
40
|
'yorkshire'
|
|
40
41
|
{
|
|
41
42
|
def to_registrycode
|
|
42
|
-
'
|
|
43
|
+
'yorkshire'
|
|
43
44
|
end
|
|
44
45
|
}
|
|
45
46
|
end
|
|
@@ -48,7 +49,7 @@ module Canql
|
|
|
48
49
|
'north east'
|
|
49
50
|
{
|
|
50
51
|
def to_registrycode
|
|
51
|
-
'
|
|
52
|
+
'north_east'
|
|
52
53
|
end
|
|
53
54
|
}
|
|
54
55
|
end
|
|
@@ -57,7 +58,7 @@ module Canql
|
|
|
57
58
|
'north west'
|
|
58
59
|
{
|
|
59
60
|
def to_registrycode
|
|
60
|
-
'
|
|
61
|
+
'north_west'
|
|
61
62
|
end
|
|
62
63
|
}
|
|
63
64
|
end
|
|
@@ -66,7 +67,7 @@ module Canql
|
|
|
66
67
|
('west mids' / 'west midlands')
|
|
67
68
|
{
|
|
68
69
|
def to_registrycode
|
|
69
|
-
'
|
|
70
|
+
'west_mids'
|
|
70
71
|
end
|
|
71
72
|
}
|
|
72
73
|
end
|
|
@@ -75,7 +76,7 @@ module Canql
|
|
|
75
76
|
'south west'
|
|
76
77
|
{
|
|
77
78
|
def to_registrycode
|
|
78
|
-
'
|
|
79
|
+
'south_west'
|
|
79
80
|
end
|
|
80
81
|
}
|
|
81
82
|
end
|
|
@@ -84,7 +85,7 @@ module Canql
|
|
|
84
85
|
'wessex'
|
|
85
86
|
{
|
|
86
87
|
def to_registrycode
|
|
87
|
-
'
|
|
88
|
+
'wessex'
|
|
88
89
|
end
|
|
89
90
|
}
|
|
90
91
|
end
|
|
@@ -93,7 +94,7 @@ module Canql
|
|
|
93
94
|
('london and south east' / 'london')
|
|
94
95
|
{
|
|
95
96
|
def to_registrycode
|
|
96
|
-
'
|
|
97
|
+
'london'
|
|
97
98
|
end
|
|
98
99
|
}
|
|
99
100
|
end
|
|
@@ -102,7 +103,7 @@ module Canql
|
|
|
102
103
|
('east of england' / 'east')
|
|
103
104
|
{
|
|
104
105
|
def to_registrycode
|
|
105
|
-
'
|
|
106
|
+
'east'
|
|
106
107
|
end
|
|
107
108
|
}
|
|
108
109
|
end
|
|
@@ -111,7 +112,7 @@ module Canql
|
|
|
111
112
|
'limbo'
|
|
112
113
|
{
|
|
113
114
|
def to_registrycode
|
|
114
|
-
'
|
|
115
|
+
'limbo'
|
|
115
116
|
end
|
|
116
117
|
}
|
|
117
118
|
end
|
|
@@ -120,7 +121,34 @@ module Canql
|
|
|
120
121
|
'england'
|
|
121
122
|
{
|
|
122
123
|
def to_registrycode
|
|
123
|
-
'
|
|
124
|
+
'england'
|
|
125
|
+
end
|
|
126
|
+
}
|
|
127
|
+
end
|
|
128
|
+
|
|
129
|
+
rule northern_supra
|
|
130
|
+
('northern supra' / 'northern')
|
|
131
|
+
{
|
|
132
|
+
def to_registrycode
|
|
133
|
+
'northern_supra'
|
|
134
|
+
end
|
|
135
|
+
}
|
|
136
|
+
end
|
|
137
|
+
|
|
138
|
+
rule midlands_east_supra
|
|
139
|
+
('midlands & east supra' / 'midlands & east')
|
|
140
|
+
{
|
|
141
|
+
def to_registrycode
|
|
142
|
+
'midlands_east_supra'
|
|
143
|
+
end
|
|
144
|
+
}
|
|
145
|
+
end
|
|
146
|
+
|
|
147
|
+
rule south_west_supra
|
|
148
|
+
'south west supra'
|
|
149
|
+
{
|
|
150
|
+
def to_registrycode
|
|
151
|
+
'south_west_supra'
|
|
124
152
|
end
|
|
125
153
|
}
|
|
126
154
|
end
|
|
@@ -0,0 +1,28 @@
|
|
|
1
|
+
module Canql
|
|
2
|
+
grammar TestResultGroup
|
|
3
|
+
rule test_result_groups
|
|
4
|
+
and_keyword? existance_modifier:test_result_group_existance_keyword group:test_result_group_names <Nodes::TestResultGroup::WithCondition>
|
|
5
|
+
end
|
|
6
|
+
|
|
7
|
+
rule test_result_group_existance_keyword
|
|
8
|
+
# If in furture the reverse is needed use 'supplied require'
|
|
9
|
+
space ('missing required' / 'missing' / 'supplied required' / 'supplied') word_break
|
|
10
|
+
end
|
|
11
|
+
|
|
12
|
+
rule test_result_group_names
|
|
13
|
+
space ('screening' / 'anomaly scan' / 'fetal medicine' / 'dating') word_break
|
|
14
|
+
end
|
|
15
|
+
|
|
16
|
+
rule test_acceptance_existance
|
|
17
|
+
and_keyword? existance_modifier:test_acceptance_existance_keyword acceptance:test_acceptance_names <Nodes::TestAcceptanceExistamce::WithCondition>
|
|
18
|
+
end
|
|
19
|
+
|
|
20
|
+
rule test_acceptance_existance_keyword
|
|
21
|
+
space ('missing required' / 'missing' ) word_break
|
|
22
|
+
end
|
|
23
|
+
|
|
24
|
+
rule test_acceptance_names
|
|
25
|
+
space ('screening acceptance status' / 'anomaly scan acceptance status' ) word_break
|
|
26
|
+
end
|
|
27
|
+
end
|
|
28
|
+
end
|
data/lib/canql/nodes.rb
CHANGED
|
@@ -17,6 +17,7 @@ require 'canql/nodes/batch_types'
|
|
|
17
17
|
require 'canql/nodes/anomaly'
|
|
18
18
|
require 'canql/nodes/genetic_test'
|
|
19
19
|
require 'canql/nodes/test_result'
|
|
20
|
+
require 'canql/nodes/test_result_group'
|
|
20
21
|
require 'canql/nodes/patient'
|
|
21
22
|
require 'canql/nodes/main'
|
|
22
23
|
require 'canql/nodes/registry'
|
data/lib/canql/nodes/anomaly.rb
CHANGED
|
@@ -23,13 +23,21 @@ module Canql #:nodoc: all
|
|
|
23
23
|
if anomaly_screening_status_type.present?
|
|
24
24
|
anomaly_hash['screening_status'] = anomaly_screening_status_type_filter
|
|
25
25
|
end
|
|
26
|
-
anomaly_hash
|
|
27
|
-
return anomaly_hash if code_filter[:code_group].blank?
|
|
26
|
+
code_filters(anomaly_hash)
|
|
28
27
|
|
|
29
|
-
anomaly_hash['code_groups'] = code_filter[:code_group]
|
|
30
28
|
anomaly_hash
|
|
31
29
|
end
|
|
32
30
|
|
|
31
|
+
def code_filters(anomaly_hash)
|
|
32
|
+
anomaly_hash['icd_codes'] = code_filter[:icd_code] if code_filter[:icd_code].present?
|
|
33
|
+
if code_filter[:code_group].present?
|
|
34
|
+
anomaly_hash['code_groups'] = code_filter[:code_group]
|
|
35
|
+
end
|
|
36
|
+
return if code_filter[:fasp_rating].blank?
|
|
37
|
+
|
|
38
|
+
anomaly_hash['fasp_rating'] = code_filter[:fasp_rating]
|
|
39
|
+
end
|
|
40
|
+
|
|
33
41
|
def existance_filter
|
|
34
42
|
{ Canql::EQUALS => existance_modifier.text_value.strip != 'no' }
|
|
35
43
|
end
|
|
@@ -49,36 +57,50 @@ module Canql #:nodoc: all
|
|
|
49
57
|
def code_type(code)
|
|
50
58
|
return :icd_code if code.respond_to?(:to_code) && code.to_code.present?
|
|
51
59
|
return :code_group if code.respond_to?(:to_code_group) && code.to_code_group.present?
|
|
60
|
+
return :fasp_rating if code.respond_to?(:to_fasp_rating) && code.to_fasp_rating.present?
|
|
52
61
|
|
|
53
62
|
raise 'Unable to find code type'
|
|
54
63
|
end
|
|
55
64
|
|
|
56
65
|
def code_value(code)
|
|
57
66
|
return code.to_code if :icd_code == code_type(code)
|
|
67
|
+
return code.to_code_group if :code_group == code_type(code)
|
|
58
68
|
|
|
59
|
-
code.
|
|
69
|
+
code.to_fasp_rating
|
|
60
70
|
end
|
|
61
71
|
|
|
62
72
|
def prepare_code_filters(code_array)
|
|
63
|
-
code_array
|
|
64
|
-
code_array[:icd_code].delete_if(&:blank?)
|
|
65
|
-
code_array[:code_group].flatten!
|
|
66
|
-
code_array[:code_group].delete_if(&:blank?)
|
|
73
|
+
clean_code_array(code_array)
|
|
67
74
|
|
|
68
75
|
code_filters = {}
|
|
69
76
|
if code_array[:icd_code].any?
|
|
70
77
|
code_filters[:icd_code] = { Canql::BEGINS => code_array[:icd_code] }
|
|
71
78
|
end
|
|
72
|
-
return code_filters if code_array[:code_group].blank?
|
|
73
79
|
|
|
74
|
-
|
|
80
|
+
if code_array[:code_group].any?
|
|
81
|
+
code_filters[:code_group] = { Canql::EQUALS => code_array[:code_group] }
|
|
82
|
+
end
|
|
83
|
+
|
|
84
|
+
if code_array[:fasp_rating].any?
|
|
85
|
+
code_filters[:fasp_rating] = { Canql::EQUALS => code_array[:fasp_rating] }
|
|
86
|
+
end
|
|
87
|
+
|
|
75
88
|
code_filters
|
|
76
89
|
end
|
|
77
90
|
|
|
91
|
+
def clean_code_array(code_array)
|
|
92
|
+
code_array[:icd_code].flatten!
|
|
93
|
+
code_array[:icd_code].delete_if(&:blank?)
|
|
94
|
+
code_array[:code_group].flatten!
|
|
95
|
+
code_array[:code_group].delete_if(&:blank?)
|
|
96
|
+
code_array[:fasp_rating].flatten!
|
|
97
|
+
code_array[:fasp_rating].delete_if(&:blank?)
|
|
98
|
+
end
|
|
99
|
+
|
|
78
100
|
def code_filter
|
|
79
101
|
return {} if code_data.text_value.blank?
|
|
80
102
|
|
|
81
|
-
code_arrays = { icd_code: [], code_group: [] }
|
|
103
|
+
code_arrays = { icd_code: [], code_group: [], fasp_rating: [] }
|
|
82
104
|
code_arrays[code_type(code_data.first)] << code_value(code_data.first)
|
|
83
105
|
code_data.rest.elements.each do |code|
|
|
84
106
|
code_arrays[code_type(code)] << code_value(code)
|
|
@@ -90,8 +112,9 @@ module Canql #:nodoc: all
|
|
|
90
112
|
module AdditionalCodeNode
|
|
91
113
|
def code_type
|
|
92
114
|
return :icd_code if anomalies_icd_code.respond_to?(:to_code)
|
|
115
|
+
return :code_group if anomalies_icd_code.respond_to?(:to_code_group)
|
|
93
116
|
|
|
94
|
-
:
|
|
117
|
+
:fasp_rating
|
|
95
118
|
end
|
|
96
119
|
|
|
97
120
|
def to_code
|
|
@@ -101,6 +124,10 @@ module Canql #:nodoc: all
|
|
|
101
124
|
def to_code_group
|
|
102
125
|
anomalies_icd_code.to_code_group if :code_group == code_type
|
|
103
126
|
end
|
|
127
|
+
|
|
128
|
+
def to_fasp_rating
|
|
129
|
+
anomalies_icd_code.to_fasp_rating if :fasp_rating == code_type
|
|
130
|
+
end
|
|
104
131
|
end
|
|
105
132
|
|
|
106
133
|
module SingleIcdCodeNode
|
|
@@ -114,6 +141,14 @@ module Canql #:nodoc: all
|
|
|
114
141
|
text_value.gsub(/( )/, '_').upcase
|
|
115
142
|
end
|
|
116
143
|
end
|
|
144
|
+
|
|
145
|
+
module SingleFaspRatingNode
|
|
146
|
+
def to_fasp_rating
|
|
147
|
+
text_value.gsub(/( )/, '_').upcase.split('_AND_').map do |value|
|
|
148
|
+
value.start_with?('FASP_') ? value : "FASP_#{value}"
|
|
149
|
+
end
|
|
150
|
+
end
|
|
151
|
+
end
|
|
117
152
|
end
|
|
118
153
|
end
|
|
119
154
|
end
|
data/lib/canql/nodes/main.rb
CHANGED
|
@@ -29,20 +29,38 @@ module Canql #:nodoc: all
|
|
|
29
29
|
module WithConditions
|
|
30
30
|
def meta_data_item
|
|
31
31
|
conditions = {}
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
32
|
+
sub_clauses = build_sub_clauses
|
|
33
|
+
|
|
34
|
+
%i[
|
|
35
|
+
anomalies genetic_tests test_results test_result_groups test_acceptances
|
|
36
|
+
].each do |condition_key|
|
|
37
|
+
if sub_clauses[condition_key].present?
|
|
38
|
+
conditions[condition_key.to_s] = { Canql::ALL => sub_clauses[condition_key] }
|
|
39
|
+
end
|
|
40
|
+
end
|
|
41
|
+
conditions
|
|
42
|
+
end
|
|
43
|
+
|
|
44
|
+
def build_sub_clauses
|
|
45
|
+
sub_clauses = {}
|
|
35
46
|
|
|
36
47
|
post.elements.each do |element|
|
|
37
|
-
|
|
38
|
-
|
|
39
|
-
|
|
48
|
+
add_sub_clause(sub_clauses, element, :anomalies, :to_anomaly)
|
|
49
|
+
add_sub_clause(sub_clauses, element, :genetic_tests, :to_genetic_test)
|
|
50
|
+
add_sub_clause(sub_clauses, element, :test_results, :to_test_result)
|
|
51
|
+
add_sub_clause(
|
|
52
|
+
sub_clauses, element, :test_result_groups, :to_test_result_group
|
|
53
|
+
)
|
|
54
|
+
add_sub_clause(sub_clauses, element, :test_acceptances, :to_test_acceptance)
|
|
40
55
|
end
|
|
56
|
+
sub_clauses
|
|
57
|
+
end
|
|
41
58
|
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
|
|
45
|
-
|
|
59
|
+
def add_sub_clause(sub_clauses, element, key, condition)
|
|
60
|
+
return sub_clauses unless element.respond_to?(condition)
|
|
61
|
+
|
|
62
|
+
sub_clauses[key] ||= []
|
|
63
|
+
sub_clauses[key] << element.send(condition)
|
|
46
64
|
end
|
|
47
65
|
end
|
|
48
66
|
end
|
data/lib/canql/nodes/patient.rb
CHANGED
|
@@ -54,7 +54,9 @@ module Canql #:nodoc: all
|
|
|
54
54
|
'booking hospital': { patient: 'booking_hospital' },
|
|
55
55
|
'screening status': { patient: 'screeningstatus' },
|
|
56
56
|
'number of fetuses at delivery': { patient: 'numoffetusesatdelivery' },
|
|
57
|
-
'malformed in set': { patient: 'malformedinset' }
|
|
57
|
+
'malformed in set': { patient: 'malformedinset' },
|
|
58
|
+
'gestation at delivery': { patient: 'gestationallength' },
|
|
59
|
+
'booking date': { patient: 'firstbookingdate' }
|
|
58
60
|
}.freeze
|
|
59
61
|
|
|
60
62
|
def meta_data_item
|
|
@@ -0,0 +1,75 @@
|
|
|
1
|
+
# frozen_string_literal: true
|
|
2
|
+
|
|
3
|
+
module Canql #:nodoc: all
|
|
4
|
+
module Nodes
|
|
5
|
+
module TestResultGroup
|
|
6
|
+
module WithCondition
|
|
7
|
+
def test_result_group
|
|
8
|
+
group.text_value.strip.parameterize.underscore
|
|
9
|
+
end
|
|
10
|
+
|
|
11
|
+
def to_test_result_group
|
|
12
|
+
test_result_group_hash = { 'exists' => existance_filter }
|
|
13
|
+
test_result_group_hash['required'] = requirement_filter
|
|
14
|
+
test_result_group_hash['group'] = test_result_group_filter if test_result_group.present?
|
|
15
|
+
test_result_group_hash
|
|
16
|
+
end
|
|
17
|
+
|
|
18
|
+
def existance_filter
|
|
19
|
+
{
|
|
20
|
+
Canql::EQUALS => ['supplied required', 'supplied'].include?(
|
|
21
|
+
existance_modifier.text_value.strip
|
|
22
|
+
)
|
|
23
|
+
}
|
|
24
|
+
end
|
|
25
|
+
|
|
26
|
+
def requirement_filter
|
|
27
|
+
{
|
|
28
|
+
Canql::EQUALS => ['supplied required', 'missing required'].include?(
|
|
29
|
+
existance_modifier.text_value.strip
|
|
30
|
+
)
|
|
31
|
+
}
|
|
32
|
+
end
|
|
33
|
+
|
|
34
|
+
def test_result_group_filter
|
|
35
|
+
{ Canql::EQUALS => test_result_group }
|
|
36
|
+
end
|
|
37
|
+
end
|
|
38
|
+
end
|
|
39
|
+
|
|
40
|
+
module TestAcceptanceExistamce
|
|
41
|
+
module WithCondition
|
|
42
|
+
def test_acceptance
|
|
43
|
+
acceptance.text_value.strip.parameterize.underscore
|
|
44
|
+
end
|
|
45
|
+
|
|
46
|
+
def to_test_acceptance
|
|
47
|
+
test_acceptance_hash = { 'exists' => existance_filter }
|
|
48
|
+
test_acceptance_hash['required'] = requirement_filter
|
|
49
|
+
test_acceptance_hash['acceptance'] = test_acceptance_filter if test_acceptance.present?
|
|
50
|
+
test_acceptance_hash
|
|
51
|
+
end
|
|
52
|
+
|
|
53
|
+
def existance_filter
|
|
54
|
+
{
|
|
55
|
+
Canql::EQUALS => ['supplied required', 'supplied'].include?(
|
|
56
|
+
existance_modifier.text_value.strip
|
|
57
|
+
)
|
|
58
|
+
}
|
|
59
|
+
end
|
|
60
|
+
|
|
61
|
+
def requirement_filter
|
|
62
|
+
{
|
|
63
|
+
Canql::EQUALS => ['supplied required', 'missing required'].include?(
|
|
64
|
+
existance_modifier.text_value.strip
|
|
65
|
+
)
|
|
66
|
+
}
|
|
67
|
+
end
|
|
68
|
+
|
|
69
|
+
def test_acceptance_filter
|
|
70
|
+
{ Canql::EQUALS => test_acceptance }
|
|
71
|
+
end
|
|
72
|
+
end
|
|
73
|
+
end
|
|
74
|
+
end
|
|
75
|
+
end
|
data/lib/canql/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: canql
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version:
|
|
4
|
+
version: 5.2.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- PHE NDR Development Team
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: exe
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date:
|
|
11
|
+
date: 2021-03-04 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: chronic
|
|
@@ -53,7 +53,7 @@ dependencies:
|
|
|
53
53
|
version: '4.1'
|
|
54
54
|
- - "<"
|
|
55
55
|
- !ruby/object:Gem::Version
|
|
56
|
-
version: '
|
|
56
|
+
version: '7'
|
|
57
57
|
type: :runtime
|
|
58
58
|
prerelease: false
|
|
59
59
|
version_requirements: !ruby/object:Gem::Requirement
|
|
@@ -63,7 +63,7 @@ dependencies:
|
|
|
63
63
|
version: '4.1'
|
|
64
64
|
- - "<"
|
|
65
65
|
- !ruby/object:Gem::Version
|
|
66
|
-
version: '
|
|
66
|
+
version: '7'
|
|
67
67
|
- !ruby/object:Gem::Dependency
|
|
68
68
|
name: treetop
|
|
69
69
|
requirement: !ruby/object:Gem::Requirement
|
|
@@ -154,14 +154,14 @@ dependencies:
|
|
|
154
154
|
requirements:
|
|
155
155
|
- - "~>"
|
|
156
156
|
- !ruby/object:Gem::Version
|
|
157
|
-
version: '5.
|
|
157
|
+
version: '5.9'
|
|
158
158
|
type: :development
|
|
159
159
|
prerelease: false
|
|
160
160
|
version_requirements: !ruby/object:Gem::Requirement
|
|
161
161
|
requirements:
|
|
162
162
|
- - "~>"
|
|
163
163
|
- !ruby/object:Gem::Version
|
|
164
|
-
version: '5.
|
|
164
|
+
version: '5.9'
|
|
165
165
|
- !ruby/object:Gem::Dependency
|
|
166
166
|
name: pry
|
|
167
167
|
requirement: !ruby/object:Gem::Requirement
|
|
@@ -210,6 +210,9 @@ executables: []
|
|
|
210
210
|
extensions: []
|
|
211
211
|
extra_rdoc_files: []
|
|
212
212
|
files:
|
|
213
|
+
- ".github/CODEOWNERS"
|
|
214
|
+
- ".github/workflows/lint.yml"
|
|
215
|
+
- ".github/workflows/test.yml"
|
|
213
216
|
- ".gitignore"
|
|
214
217
|
- ".hound.yml"
|
|
215
218
|
- ".rubocop.yml"
|
|
@@ -238,6 +241,7 @@ files:
|
|
|
238
241
|
- lib/canql/grammars/provider.treetop
|
|
239
242
|
- lib/canql/grammars/registry.treetop
|
|
240
243
|
- lib/canql/grammars/test_result.treetop
|
|
244
|
+
- lib/canql/grammars/test_result_group.treetop
|
|
241
245
|
- lib/canql/nodes.rb
|
|
242
246
|
- lib/canql/nodes/age.rb
|
|
243
247
|
- lib/canql/nodes/anomaly.rb
|
|
@@ -250,6 +254,7 @@ files:
|
|
|
250
254
|
- lib/canql/nodes/perinatal_hospital.rb
|
|
251
255
|
- lib/canql/nodes/registry.rb
|
|
252
256
|
- lib/canql/nodes/test_result.rb
|
|
257
|
+
- lib/canql/nodes/test_result_group.rb
|
|
253
258
|
- lib/canql/parser.rb
|
|
254
259
|
- lib/canql/treetop/extensions.rb
|
|
255
260
|
- lib/canql/version.rb
|