canql 4.3.0 → 5.2.0
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- 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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@@ -1,7 +1,7 @@
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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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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 767d7da5878ba53e624db9090a0bce25ee2b17c039b5ecce4bbb65126f0d32bc988851f7b31e41be235f9911919051a07a7e5478b54d11bc0aefdf7c6a939389
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7
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data.tar.gz: bd874eb46ba2641c84ba40d2a521db212b218879cf6e789777514d36bea0672fd9b38e24804ca4a86b54b722c62b5a7a89003d3040cd8179991b134ebb7543ab
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data/.github/CODEOWNERS
ADDED
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@@ -0,0 +1,23 @@
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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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@@ -0,0 +1,65 @@
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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
CHANGED
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@@ -1,11 +1 @@
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Rails:
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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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Style/FrozenStringLiteralComment:
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Enabled: true
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require: ndr_dev_support
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data/CHANGELOG.md
CHANGED
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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
CHANGED
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@@ -1,6 +1,6 @@
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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
CHANGED
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@@ -28,7 +28,7 @@ Gem::Specification.new do |spec|
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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 'bundler'
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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.
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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
CHANGED
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---
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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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comments:
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reviewed_by: timgentry
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reviewed_by: timgentry
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safe_revision: 0b34688f1198eace9310f47060aa8915f5b44985
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".rubocop.yml":
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comments:
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reviewed_by: timgentry
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safe_revision: 5bc563431f7822e2baf37bbeac9861c36675602d
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".travis.yml":
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comments:
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reviewed_by: josh.pencheon
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safe_revision:
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safe_revision: 146b255b240b0efc928d39dd1b70ab221ddc3138
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CHANGELOG.md:
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comments:
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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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comments:
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reviewed_by: drewthorp
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README.md:
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comments:
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reviewed_by: josh.pencheon
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safe_revision:
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safe_revision: 8c07968aa84db92b6f1cc528180f73530ddc6ff5
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Rakefile:
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comments:
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reviewed_by: timgentry
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safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
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canql.gemspec:
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safe_revision: 146b255b240b0efc928d39dd1b70ab221ddc3138
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lib/canql.rb:
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comments:
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reviewed_by: timgentry
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lib/canql/grammars.rb:
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safe_revision: c5f8f76b2c335a8554f39a14d6165bf5cd8f9b67
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lib/canql/grammars/age.treetop:
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comments: It is a known issue that this is potentially susceptible to certain
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kinds of DoS attack
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lib/canql/grammars/anomaly.treetop:
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comments: It is a known issue that this is potentially susceptible to certain
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kinds of DoS attack
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reviewed_by: ollietulloch
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safe_revision: e549c0dcafdd6004ec279bd256fae8b9964c9629
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lib/canql/grammars/batch_types.treetop:
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comments:
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lib/canql/grammars/main.treetop:
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comments: It is a known issue that this is potentially susceptible to certain
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safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
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lib/canql/grammars/patient.treetop:
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safe_revision: 7490099869e368dcd5c26ded11eb90229baf4cae
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lib/canql/grammars/perinatal_hospital.treetop:
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comments:
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comments: It is a known issue that this is potentially susceptible to certain
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safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
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lib/canql/grammars/test_result.treetop:
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comments: It is a known issue that this is potentially susceptible to certain
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reviewed_by: timgentry
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safe_revision: c39d24bb500719971969762e94545e82866bf92f
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lib/canql/grammars/test_result_group.treetop:
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comments:
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reviewed_by: josh.pencheon
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safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
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lib/canql/nodes.rb:
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comments:
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safe_revision: c5f8f76b2c335a8554f39a14d6165bf5cd8f9b67
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test/nodes/case_test.rb:
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test/nodes/genetic_tests_test.rb:
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test/nodes/registry_test.rb:
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|
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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
|