tnql 1.0.0

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Files changed (51) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +9 -0
  3. data/.hound.yml +10 -0
  4. data/.rubocop.yml +7 -0
  5. data/.travis.yml +11 -0
  6. data/CODE_OF_CONDUCT.md +13 -0
  7. data/Gemfile +4 -0
  8. data/Guardfile +15 -0
  9. data/LICENSE.txt +21 -0
  10. data/README.md +74 -0
  11. data/Rakefile +12 -0
  12. data/bin/console +10 -0
  13. data/bin/setup +7 -0
  14. data/code_safety.yml +272 -0
  15. data/lib/tnql.rb +4 -0
  16. data/lib/tnql/constants.rb +8 -0
  17. data/lib/tnql/grammars.rb +16 -0
  18. data/lib/tnql/grammars/age.treetop +63 -0
  19. data/lib/tnql/grammars/batch_types.treetop +65 -0
  20. data/lib/tnql/grammars/dates.treetop +35 -0
  21. data/lib/tnql/grammars/diagnosis.treetop +23 -0
  22. data/lib/tnql/grammars/e_base_records.treetop +86 -0
  23. data/lib/tnql/grammars/main.treetop +54 -0
  24. data/lib/tnql/grammars/patient.treetop +39 -0
  25. data/lib/tnql/grammars/provider.treetop +21 -0
  26. data/lib/tnql/grammars/registration_status.treetop +11 -0
  27. data/lib/tnql/grammars/registry.treetop +15 -0
  28. data/lib/tnql/grammars/staging.treetop +23 -0
  29. data/lib/tnql/grammars/treatment.treetop +35 -0
  30. data/lib/tnql/grammars/tumour_type.treetop +54 -0
  31. data/lib/tnql/grammars/vital_status.treetop +19 -0
  32. data/lib/tnql/nodes.rb +25 -0
  33. data/lib/tnql/nodes/age.rb +82 -0
  34. data/lib/tnql/nodes/batch_types.rb +52 -0
  35. data/lib/tnql/nodes/dates.rb +50 -0
  36. data/lib/tnql/nodes/diagnosis.rb +31 -0
  37. data/lib/tnql/nodes/e_base_records.rb +61 -0
  38. data/lib/tnql/nodes/main.rb +11 -0
  39. data/lib/tnql/nodes/patient.rb +9 -0
  40. data/lib/tnql/nodes/provider.rb +24 -0
  41. data/lib/tnql/nodes/registration_status.rb +27 -0
  42. data/lib/tnql/nodes/registry.rb +33 -0
  43. data/lib/tnql/nodes/staging.rb +17 -0
  44. data/lib/tnql/nodes/treatment.rb +45 -0
  45. data/lib/tnql/nodes/tumour_type.rb +74 -0
  46. data/lib/tnql/nodes/vital_status.rb +15 -0
  47. data/lib/tnql/parser.rb +56 -0
  48. data/lib/tnql/treetop/extensions.rb +20 -0
  49. data/lib/tnql/version.rb +4 -0
  50. data/tnql.gemspec +39 -0
  51. metadata +286 -0
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data/.gitignore ADDED
@@ -0,0 +1,9 @@
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+ /.bundle/
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+ /.yardoc
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+ /Gemfile.lock
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+ /_yardoc/
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+ /coverage/
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+ /doc/
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+ /pkg/
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+ /spec/reports/
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+ /tmp/
data/.hound.yml ADDED
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+ fail_on_violations: true
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+
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+ coffeescript:
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+ enabled: false
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+ javascript:
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+ enabled: false
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+ ruby:
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+ config_file: .rubocop.yml
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+ scss:
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+ enabled: false
data/.rubocop.yml ADDED
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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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+ TargetRubyVersion: 2.3
data/.travis.yml ADDED
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+ language: ruby
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+
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+ rvm:
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+ - 2.2.5
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+ - 2.3.1
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+
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+ sudo: false
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+
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+ cache: bundler
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+
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+ before_script: "bundle update"
data/CODE_OF_CONDUCT.md ADDED
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+ # Contributor Code of Conduct
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+
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+ As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.
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+
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+ We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
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+
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+ Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.
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+
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+ Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.
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+
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+ Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.
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+
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+ This Code of Conduct is adapted from the [Contributor Covenant](http://contributor-covenant.org), version 1.0.0, available at [http://contributor-covenant.org/version/1/0/0/](http://contributor-covenant.org/version/1/0/0/)
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in tnql.gemspec
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+ gemspec
data/Guardfile ADDED
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+ # A sample Guardfile
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+ # More info at https://github.com/guard/guard#readme
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+
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+ # automatically check Ruby code style with Rubocop when files are modified
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+ guard :rubocop, all_on_start: false, keep_failed: false do
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+ watch(/.+\.rb$/)
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+ watch(%r{(?:.+/)?\.rubocop\.yml$}) { |m| File.dirname(m[0]) }
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+ end
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+
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+ guard :minitest do
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+ watch(%r{^test/.+_test\.rb$})
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+ watch('test/test_helper.rb') { 'test' }
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+
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+ watch(%r{^lib/tnql/(.+)\.rb$}) { |m| "test/#{m[1]}_test.rb" }
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+ end
data/LICENSE.txt ADDED
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+ The MIT License (MIT)
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+
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+ Copyright (c) 2015 Public Health England
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in
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+ all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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+ THE SOFTWARE.
data/README.md ADDED
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+ # TNQL [![Build Status](https://travis-ci.org/PublicHealthEngland/tnql.svg?branch=master)](https://travis-ci.org/PublicHealthEngland/tnql)
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+
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+ Tumour Natural Query Language (TNQL) is a [Treetop](http://treetop.rubyforge.org/) driven Domain Specific Language (DSL) used by the Public Health England (PHE) National Cancer Registration and Analysis Service (NCRAS) to identify cohorts of tumours.
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+
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+ Used for analysis, research and day-to-day operations, it was first created in March 2011 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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+
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+ In moving it into a gem, TNQL is being further decoupled from the specifics of the NCRAS systems by producing an intermediate representation, known as Disease Intermediate Representation (DIR). This allows us to:
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+
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+ 1. implement separate DIR adapters for different datastores (e.g. SQL and NoSQL datastores);
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+ 2. utilize the same DIR adapters for different but over-lapping DSLs, starting with the Congenital Anomaly Natural Query Language (CANQL); and
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+ 3. pass DIR queries to non-ruby backend systems using any simple format like JSON.
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+
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+ ## Installation
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+
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+ Add this line to your application's Gemfile:
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+
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+ ```ruby
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+ gem 'tnql'
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+ ```
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+
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+ And then execute:
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+
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+ $ bundle
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+
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+ Or install it yourself as:
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+
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+ $ gem install tnql
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+
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+ ## Usage
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+
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+ Here is a simple example showing a TNQL query of all Colon tumours diagnosed at "Hello World" Hospital:
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+
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+ ```ruby
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+ require 'tnql'
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+ require 'json'
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+
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+ query = 'All C18 Tumours Diagnosed at Hello World Hospital'
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+ parser = Tnql::Parser.new(query)
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+
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+ if parser.valid?
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+ puts JSON.dump(parser.meta_data)
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+ end
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+ ```
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+
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+ would output:
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+
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+ ```json
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+ {"tumour.primarycode":{"begins":["C18"]},"diagnosis.providername":{"begins":"HELLO WORLD","interval":"29...49"}}
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+ ```
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+
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+ The parser is case insensitive. An example of an almost fully involved TNQL query is:
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+
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+ > First 27 Final Y0401 Non-invasive Stage 4 Head and Neck Tumours Diagnosed Between August 2010 and Oct 2010 at Hospital RGT01 Treated at Hospital RGN42 With Wait Action and Unprocessed PAS or Somerset Records for Dead Male Patients Who Were Born in 1999, Died Between May 2001 and Aug 2003, and Have no Death Certificate
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+
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+ Please see the tests for many more examples.
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+
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+ ## Development
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+
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+ After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake test` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
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+
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+ To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
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+
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+ PLEASE NOTE: A side-effect of decoupling TNQL from the NCRAS SQL adapter is that more of the grammar logic can be DRYed up, esp. in relation to providers. We plan to fix this and some internal namespacing in forthcoming releases.
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+
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+ ## Contributing
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+
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+ Bug reports and pull requests are welcome on GitHub at https://github.com/PublicHealthEngland/tnql.
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+
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+ This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
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+
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+ ## License
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+
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+ The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
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+
data/Rakefile ADDED
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+ require 'bundler/gem_tasks'
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+ require 'rake/testtask'
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+ require 'ndr_dev_support/tasks'
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+
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+ Rake::TestTask.new(:test) do |t|
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+ t.libs << 'test'
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+ t.test_files = FileList['test/**/*_test.rb']
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+ t.verbose = false
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+ t.warning = false
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+ end
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+
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+ task default: :test
data/bin/console ADDED
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+ #!/usr/bin/env ruby
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+
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+ require 'bundler/setup'
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+ require 'tnql'
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+
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+ # You can add fixtures and/or initialization code here to make experimenting
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+ # with your gem easier. You can also use a different console, if you like.
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+
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+ require 'pry'
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+ Pry.start
data/bin/setup ADDED
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+ #!/bin/bash
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+ set -euo pipefail
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+ IFS=$'\n\t'
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+
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+ bundle install
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+
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+ # Do any other automated setup that you need to do here
data/code_safety.yml ADDED
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+ ---
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+ file safety:
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+ ".gitignore":
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 065dcccb9db71374cea5aad104657a5c1f877d1c
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+ ".hound.yml":
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 1cf068b17559ed381e013fe71a481eb3db15f553
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+ ".rubocop.yml":
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: b85a30c6fd89eddc6597323f7afe7ea2859ae9ac
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+ ".travis.yml":
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: d4f2a88af5df3bde2a58185e8095821fafc599bf
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+ CODE_OF_CONDUCT.md:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 065dcccb9db71374cea5aad104657a5c1f877d1c
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+ Gemfile:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 065dcccb9db71374cea5aad104657a5c1f877d1c
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+ Guardfile:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ LICENSE.txt:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 065dcccb9db71374cea5aad104657a5c1f877d1c
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+ README.md:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: f47d9a806bce9a24ee538dae9674c7deba79a7a8
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+ Rakefile:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ bin/console:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: fdea3ed4f37453978857611724116f70dd08f1fd
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+ bin/setup:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 065dcccb9db71374cea5aad104657a5c1f877d1c
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+ lib/tnql.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
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+ lib/tnql/constants.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ lib/tnql/grammars.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
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+ lib/tnql/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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+ reviewed_by: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/batch_types.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/dates.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/diagnosis.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/e_base_records.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/main.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/provider.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/registration_status.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/registry.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/staging.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/treatment.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/tumour_type.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/grammars/vital_status.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: timgentry
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+ safe_revision: b3a8b33cbc5dd29822e0e6ded32500ccd7a15670
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+ lib/tnql/nodes.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
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+ lib/tnql/nodes/age.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ lib/tnql/nodes/batch_types.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
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+ lib/tnql/nodes/dates.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ lib/tnql/nodes/diagnosis.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ lib/tnql/nodes/e_base_records.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ lib/tnql/nodes/main.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
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+ lib/tnql/nodes/patient.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
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+ lib/tnql/nodes/provider.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ lib/tnql/nodes/registration_status.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
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+ lib/tnql/nodes/registry.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ lib/tnql/nodes/staging.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
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+ lib/tnql/nodes/treatment.rb:
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+ comments:
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+ reviewed_by: timgentry
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+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
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+ lib/tnql/nodes/tumour_type.rb:
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+ comments:
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+ reviewed_by: timgentry
188
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189
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190
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191
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192
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
193
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194
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195
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196
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197
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198
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199
+ reviewed_by: timgentry
200
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201
+ lib/tnql/version.rb:
202
+ comments:
203
+ reviewed_by: timgentry
204
+ safe_revision: 44b3b8fee3cf50c9fe614dbccc9eccc27f0c87a3
205
+ test/nodes/age_test.rb:
206
+ comments:
207
+ reviewed_by: timgentry
208
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
209
+ test/nodes/dates_test.rb:
210
+ comments:
211
+ reviewed_by: timgentry
212
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
213
+ test/nodes/diagnosis_test.rb:
214
+ comments:
215
+ reviewed_by: timgentry
216
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
217
+ test/nodes/e_base_records_test.rb:
218
+ comments:
219
+ reviewed_by: timgentry
220
+ safe_revision: 0749ad008871e286c6e0450a733599f0c86ced5f
221
+ test/nodes/main_test.rb:
222
+ comments:
223
+ reviewed_by: timgentry
224
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
225
+ test/nodes/patient_test.rb:
226
+ comments:
227
+ reviewed_by: timgentry
228
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
229
+ test/nodes/provider_test.rb:
230
+ comments:
231
+ reviewed_by: timgentry
232
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
233
+ test/nodes/registration_status_test.rb:
234
+ comments:
235
+ reviewed_by: timgentry
236
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
237
+ test/nodes/registry_test.rb:
238
+ comments:
239
+ reviewed_by: timgentry
240
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
241
+ test/nodes/staging_test.rb:
242
+ comments:
243
+ reviewed_by: timgentry
244
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
245
+ test/nodes/treatment_test.rb:
246
+ comments:
247
+ reviewed_by: timgentry
248
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
249
+ test/nodes/tumour_type_test.rb:
250
+ comments:
251
+ reviewed_by: timgentry
252
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
253
+ test/nodes/vital_status_test.rb:
254
+ comments:
255
+ reviewed_by: timgentry
256
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
257
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258
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259
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260
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261
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262
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263
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264
+ safe_revision: 2c3dd20879903b98f7f05d5d3e73b1478c275c93
265
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266
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267
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268
+ safe_revision: 61b0293f89d57118268e15fc49b529c64bbbe2b7
269
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270
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271
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272
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