canql 4.4.0 → 5.3.0

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.
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@@ -0,0 +1,2 @@
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+ # Admins should have oversight of the version:
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+ lib/canql/version.rb @publichealthengland/ndr-admins
@@ -0,0 +1,23 @@
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+ name: Lint
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+
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+ on: [pull_request]
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+
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+ jobs:
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+ rubocop:
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+ name: RuboCop
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+
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+ runs-on: ubuntu-latest
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+
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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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+
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+ on: [push, pull_request]
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+
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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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+
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+ name: Ruby ${{ matrix.ruby-version }}
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+
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+ runs-on: ubuntu-latest
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+
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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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+
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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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+
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+ notify:
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+ # Run only on master, but regardless of whether tests past:
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+ if: ${{ always() && github.ref == 'refs/heads/master' }}
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+
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+ needs: test_matrix
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+
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+ runs-on: ubuntu-latest
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+
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+ steps:
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+ - uses: 8398a7/action-slack@v3
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+ with:
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+ status: custom
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+ fields: workflow,commit,author
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+ custom_payload: |
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+ {
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+ channel: 'C7FQWGDHP',
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+ username: 'CI – ' + '${{ 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 }}
data/.rubocop.yml CHANGED
@@ -1,11 +1 @@
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- inherit_from: 'https://raw.githubusercontent.com/PublicHealthEngland/ndr_dev_support/master/.rubocop.yml'
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-
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- Rails:
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- Enabled: false
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-
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- AllCops:
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- TargetRailsVersion: 4.2
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- TargetRubyVersion: 2.3
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-
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- Style/FrozenStringLiteralComment:
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- Enabled: true
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+ require: ndr_dev_support
data/CHANGELOG.md CHANGED
@@ -1,5 +1,32 @@
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  ## [Unreleased]
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- *no unreleased changes*
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+ * no relvent changes
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+
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+
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+ ## 5.3.0 / 2021-03-05
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+
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+ * Added new FASP case RAG rating filters (#66)
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+
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+ ## 5.2.0 / 2021-03-04
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+
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+ * Added new FASP anomaly RAG rating filters (#63)
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+
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+ ## 5.1.0 / 2021-01-25
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+
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+ ### Added
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+ * Added new filters for test acceptance requirments (#59)
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+
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+ ## 5.0.0 / 2021-01-19
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+
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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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+
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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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+
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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
data/README.md CHANGED
@@ -1,6 +1,6 @@
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- # 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)
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+ # 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)
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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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+ 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
@@ -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', '< 6'
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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'
@@ -36,7 +36,7 @@ Gem::Specification.new do |spec|
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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', '~> 5.6'
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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/
data/code_safety.yml CHANGED
@@ -1,5 +1,17 @@
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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
@@ -9,17 +21,13 @@ file safety:
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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: 8adb767031a19aa6b3cea3f1cb05b4a9bcc964f3
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+ safe_revision: 146b255b240b0efc928d39dd1b70ab221ddc3138
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  CHANGELOG.md:
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  comments:
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- reviewed_by: josh.pencheon
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- safe_revision: 7b5bc84b813b7ff156665a1a37cfe5dd5b53afe7
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+ reviewed_by: ollietulloch
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+ safe_revision: 64a8f1007fe57afd5bd886e6b02b17b7a6e874c4
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  CODE_OF_CONDUCT.md:
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  comments:
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  reviewed_by: drewthorp
@@ -35,7 +43,7 @@ file safety:
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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: 33feeeaa4b2089e33f563e4c766e91c38b108e36
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+ safe_revision: 8c07968aa84db92b6f1cc528180f73530ddc6ff5
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  Rakefile:
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  comments:
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  reviewed_by: timgentry
@@ -50,8 +58,8 @@ file safety:
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  safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
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  canql.gemspec:
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  comments:
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- reviewed_by: timgentry
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- safe_revision: 6cb13f43b4353ab7c90ff0406ec13ac169b8e64c
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+ reviewed_by: josh.pencheon
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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
@@ -72,8 +80,8 @@ file safety:
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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: josh.pencheon
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- safe_revision: b7778ca1d536022a807420cc9fe0f1c2df7f73ef
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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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  reviewed_by: josh.pencheon
@@ -95,12 +103,12 @@ file safety:
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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: josh.pencheon
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- safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
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+ safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
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  lib/canql/grammars/patient.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: josh.pencheon
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- safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
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+ reviewed_by: ollietulloch
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+ safe_revision: 481194575c30b48987f957a9cc5535d604ea0117
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  lib/canql/grammars/perinatal_hospital.treetop:
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  comments:
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  reviewed_by: josh.pencheon
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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: josh.pencheon
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- safe_revision: 4e26ac746098452b01dac88373e401e39f309b74
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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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  kinds of DoS attack
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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: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
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+ safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
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  lib/canql/nodes.rb:
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  comments:
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  reviewed_by: josh.pencheon
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  safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
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  lib/canql/nodes/anomaly.rb:
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  comments:
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- reviewed_by: josh.pencheon
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- safe_revision: b7778ca1d536022a807420cc9fe0f1c2df7f73ef
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+ reviewed_by: ollietulloch
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+ safe_revision: e549c0dcafdd6004ec279bd256fae8b9964c9629
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  lib/canql/nodes/batch_types.rb:
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  comments:
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  reviewed_by: josh.pencheon
@@ -154,11 +162,11 @@ file safety:
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  lib/canql/nodes/main.rb:
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  comments:
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  reviewed_by: josh.pencheon
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- safe_revision: c5f8f76b2c335a8554f39a14d6165bf5cd8f9b67
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+ safe_revision: 361dea5dc6d64bdb7b03434dd2878f8c3b128c95
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  lib/canql/nodes/patient.rb:
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  comments:
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- reviewed_by: josh.pencheon
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- safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
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+ reviewed_by: ollietulloch
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+ safe_revision: 481194575c30b48987f957a9cc5535d604ea0117
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  lib/canql/nodes/perinatal_hospital.rb:
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  comments:
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  reviewed_by: josh.pencheon
@@ -174,7 +182,7 @@ file safety:
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  lib/canql/nodes/test_result_group.rb:
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  comments:
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  reviewed_by: josh.pencheon
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- safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
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+ safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
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  lib/canql/parser.rb:
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  comments:
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  reviewed_by: timgentry
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  safe_revision: 6932d590299ad4a9d2ba24b425b158c67142bf74
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  lib/canql/version.rb:
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  comments:
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- reviewed_by: josh.pencheon
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- safe_revision: 7b5bc84b813b7ff156665a1a37cfe5dd5b53afe7
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+ reviewed_by: ollietulloch
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+ safe_revision: 64a8f1007fe57afd5bd886e6b02b17b7a6e874c4
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  test/anomaly_test_helper.rb:
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  comments:
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- reviewed_by: josh.pencheon
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- safe_revision: 73a7dac17b20fcc77bcbd9d38777c8aa4d524816
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+ reviewed_by: ollietulloch
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+ safe_revision: e549c0dcafdd6004ec279bd256fae8b9964c9629
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  test/canql_test.rb:
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  comments:
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  reviewed_by: timgentry
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  test/nodes/case_test.rb:
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  comments:
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  reviewed_by: josh.pencheon
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- safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
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+ safe_revision: 7490099869e368dcd5c26ded11eb90229baf4cae
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  test/nodes/code_test.rb:
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  comments:
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- reviewed_by: josh.pencheon
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- safe_revision: b7778ca1d536022a807420cc9fe0f1c2df7f73ef
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+ reviewed_by: ollietulloch
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+ safe_revision: e549c0dcafdd6004ec279bd256fae8b9964c9629
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  test/nodes/e_base_records_test.rb:
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  comments:
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  reviewed_by: josh.pencheon
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- safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
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+ safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
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  test/nodes/genetic_tests_test.rb:
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  comments:
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  reviewed_by: josh.pencheon
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  safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
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  test/nodes/patient_test.rb:
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  comments:
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- reviewed_by: josh.pencheon
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- safe_revision: 43425805d9ad4a99e63eeb5d50495fa14eaa053b
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+ reviewed_by: ollietulloch
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+ safe_revision: 481194575c30b48987f957a9cc5535d604ea0117
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  test/nodes/perinatal_hospital_test.rb:
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  comments:
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  reviewed_by: josh.pencheon
@@ -250,19 +258,19 @@ file safety:
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  test/nodes/registry_test.rb:
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  comments:
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  reviewed_by: josh.pencheon
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- safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
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+ safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
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  test/nodes/test_result_groups_test.rb:
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  comments:
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  reviewed_by: josh.pencheon
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- safe_revision: 42bb9bd177a761b9d04d728e53fcf0ebd0083ae4
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+ safe_revision: 9bb663b220e76e78f3f0f48e4bc6334fe9451925
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  test/nodes/test_results_test.rb:
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  comments:
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  reviewed_by: josh.pencheon
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  safe_revision: 511e4238f83eb5b32839c25d94ec2a59145539bb
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  test/parser_test.rb:
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  comments:
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- reviewed_by: timgentry
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- safe_revision: 05ccd47fcbba92bf5525c4d36118274696169d61
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+ reviewed_by: josh.pencheon
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+ safe_revision: 293248a17d087d7557a6aacdcb5bf3fbec946b87
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  test/test_helper.rb:
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  comments:
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  reviewed_by: josh.pencheon
@@ -35,7 +35,7 @@ module Canql
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  end
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  rule anomalies_icd_code
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- (icd_code_name / code_group)
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+ (fasp_rating / icd_code_name / code_group)
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  end
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  rule icd_code_name
@@ -45,5 +45,9 @@ module Canql
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  rule code_group
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  ('fasp plus' / 'plus' / 'fasp' / 'structural' / 'trisomy') <Nodes::Anomaly::SingleCodeGroupNode>
47
47
  end
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+
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+ rule fasp_rating
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+ ('fasp red and amber' / 'fasp amber and red' / 'fasp red' / 'fasp amber' / 'fasp green') <Nodes::Anomaly::SingleFaspRatingNode>
51
+ end
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  end
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  end
@@ -129,8 +129,8 @@ grammar Canql
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  rule case_with_conditions
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  anomalies / genetic_tests / test_results / perinatal_hospital /
132
- case_field_existance / test_result_groups / mother_conditions /
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- action_or_ebr
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+ case_field_existance / test_acceptance_existance / test_result_groups /
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+ mother_conditions / action_or_ebr
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  end
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  rule patient_with_conditions
@@ -13,7 +13,12 @@ module Canql
13
13
  end
14
14
 
15
15
  rule category
16
- space category:('eurocat amber and green' / 'eurocat red and amber' / 'eurocat red' / 'eurocat amber' / 'eurocat green' / 'eurocat') word_break <Nodes::Patient::CategoryNode>
16
+ space category:('eurocat amber and green' /
17
+ 'eurocat red and amber' / 'eurocat red' / 'eurocat amber' /
18
+ 'eurocat green' / 'eurocat' /
19
+ 'fasp red and amber' / 'fasp amber and red' / 'fasp red' /
20
+ 'fasp amber' / 'fasp green' / 'fasp excluded'
21
+ ) word_break <Nodes::Patient::CategoryNode>
17
22
  end
18
23
 
19
24
  rule expected_keyword
@@ -50,7 +55,8 @@ module Canql
50
55
  'delivery postcode' / 'booking postcode' / 'birth weight' /
51
56
  'place of delivery' / 'sex' / 'outcome' / 'edd' /
52
57
  'expected delivery date' / 'booking hospital' / 'screening status' /
53
- 'number of fetuses at delivery' / 'malformed in set'
58
+ 'number of fetuses at delivery' / 'malformed in set' / 'gestation at delivery' /
59
+ 'booking date'
54
60
  )
55
61
  end
56
62
 
@@ -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
- '68'
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
- '72'
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
- '93'
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
- '73'
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
- '94'
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
- '99'
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
- '84'
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
- '70'
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
- '95'
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
- '96'
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
- '01'
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
- '00'
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
@@ -10,7 +10,19 @@ module Canql
10
10
  end
11
11
 
12
12
  rule test_result_group_names
13
- space ('screening' / 'anomaly scan') word_break
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
14
26
  end
15
27
  end
16
28
  end
@@ -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['icd_codes'] = code_filter[:icd_code] if code_filter[:icd_code].present?
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.to_code_group
69
+ code.to_fasp_rating
60
70
  end
61
71
 
62
72
  def prepare_code_filters(code_array)
63
- code_array[:icd_code].flatten!
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
- code_filters[:code_group] = { Canql::EQUALS => code_array[:code_group] }
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
- :code_group
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
@@ -29,27 +29,38 @@ module Canql #:nodoc: all
29
29
  module WithConditions
30
30
  def meta_data_item
31
31
  conditions = {}
32
- anomalies = []
33
- genetic_tests = []
34
- test_results = []
35
- test_result_groups = []
32
+ sub_clauses = build_sub_clauses
36
33
 
37
- post.elements.each do |element|
38
- anomalies << element.to_anomaly if element.respond_to?(:to_anomaly)
39
- genetic_tests << element.to_genetic_test if element.respond_to?(:to_genetic_test)
40
- test_results << element.to_test_result if element.respond_to?(:to_test_result)
41
- if element.respond_to?(:to_test_result_group)
42
- test_result_groups << element.to_test_result_group
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] }
43
39
  end
44
40
  end
41
+ conditions
42
+ end
45
43
 
46
- conditions['anomalies'] = { Canql::ALL => anomalies } if anomalies.any?
47
- conditions['genetic_tests'] = { Canql::ALL => genetic_tests } if genetic_tests.any?
48
- conditions['test_results'] = { Canql::ALL => test_results } if test_results.any?
49
- if test_result_groups.any?
50
- conditions['test_result_groups'] = { Canql::ALL => test_result_groups }
44
+ def build_sub_clauses
45
+ sub_clauses = {}
46
+
47
+ post.elements.each do |element|
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)
51
55
  end
52
- conditions
56
+ sub_clauses
57
+ end
58
+
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)
53
64
  end
54
65
  end
55
66
  end
@@ -27,11 +27,11 @@ module Canql #:nodoc: all
27
27
  end
28
28
 
29
29
  def clean_category
30
- return 'eurocat_red' if 'eurocat red' == category.text_value
31
- return 'eurocat_amber' if 'eurocat amber' == category.text_value
32
- return 'eurocat_green' if 'eurocat green' == category.text_value
33
- return 'eurocat_amber_green' if 'eurocat amber and green' == category.text_value
34
- return 'eurocat_red_amber' if 'eurocat red and amber' == category.text_value
30
+ if category.text_value.start_with?('eurocat ') || category.text_value.start_with?('fasp ')
31
+ filter_value = category.text_value.gsub(/( )/, '_').downcase.gsub(/(_and_)/, '_')
32
+ filter_value = 'fasp_red_amber' if filter_value == 'fasp_amber_red'
33
+ return filter_value
34
+ end
35
35
 
36
36
  category.text_value
37
37
  end
@@ -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
@@ -36,5 +36,40 @@ module Canql #:nodoc: all
36
36
  end
37
37
  end
38
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
39
74
  end
40
75
  end
data/lib/canql/version.rb CHANGED
@@ -2,5 +2,5 @@
2
2
 
3
3
  # This stores the current version of the Canql gem
4
4
  module Canql
5
- VERSION = '4.4.0'
5
+ VERSION = '5.3.0'
6
6
  end
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: 4.4.0
4
+ version: 5.3.0
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: 2020-07-08 00:00:00.000000000 Z
11
+ date: 2021-03-08 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: '6'
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: '6'
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: '5.6'
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: '5.6'
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"