canql 1.3.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: fcf2d37654027295939edf58f998fcc355b899da
+  data.tar.gz: 5f13b67d937e9e5f7517f06a7cd7d296d82e87df
+SHA512:
+  metadata.gz: d8adc584f9bc0c2a66c80217875d838591b38838e2a9a1ef1da96b42445877db37f4b3a829f2b67601e1a3d6d616592738d62844a1b2f9e91ff6b29e714bb6ae
+  data.tar.gz: 0d591c714d021a59182f9fbd129734fd59e07496c9bfeb24f586614f894ae9ce655fbb5559294e3d75ab83a9bcc6b971a299f77c340fe1f37bbf7cb5c4986255

data/.gitignore

@@ -0,0 +1,10 @@
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+.rubocop-https---raw-githubusercontent-com-PublicHealthEngland-ndr-dev-support-master--rubocop-yml

data/.hound.yml

@@ -0,0 +1,10 @@
+fail_on_violations: true
+
+coffeescript:
+  enabled: false
+javascript:
+  enabled: false
+ruby:
+  config_file: .rubocop.yml
+scss:
+  enabled: false

data/.rubocop.yml

@@ -0,0 +1,10 @@
+inherit_from: 'https://raw.githubusercontent.com/PublicHealthEngland/ndr_dev_support/master/.rubocop.yml'
+
+Rails:
+  Enabled: false
+
+AllCops:
+  TargetRubyVersion: 2.3
+
+Style/FrozenStringLiteralComment:
+  Enabled: true

data/.travis.yml

@@ -0,0 +1,11 @@
+language: ruby
+
+rvm:
+  - 2.2.5
+  - 2.3.1
+
+sudo: false
+
+cache: bundler
+
+before_script: "bundle update"

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,13 @@
+# Contributor Code of Conduct
+
+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.
+
+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, age, or religion.
+
+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.
+
+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.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.
+
+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

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in canql.gemspec
+gemspec

data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2015 Public Health England
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

@@ -0,0 +1,76 @@
+# CANQL [![Build Status](https://travis-ci.org/PublicHealthEngland/canql.svg?branch=master)](https://travis-ci.org/PublicHealthEngland/canql)
+
+Congenital Anomaly Natural Query Language (CANQL) is a [Treetop](http://treetop.rubyforge.org/) driven Domain Specific Language (DSL) used by the Public Health England (PHE) National Congenital Anomaly and Rare Disease Registration Service (NCARDRS) to identify cohorts of cases.
+
+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.
+
+CANQL is decoupled from the specifics of the NCARDRS systems by producing an intermediate representation, known as Disease Intermediate Representation (DIR). This allows us to:
+
+1. implement separate DIR adapters for different datastores (e.g. SQL and NoSQL datastores);
+2. utilize the same DIR adapters for different but over-lapping DSLs, including Tumour Natural Query Language ([TNQL](https://github.com/PublicHealthEngland/tnql)) ; and
+3. pass DIR queries to non-ruby backend systems using any simple format like JSON.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'canql'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install canql
+
+## Usage
+
+Here is a simple example showing a CANQL query of all male cases in south west registration region:
+
+```ruby
+require 'canql'
+require 'json'
+
+query = 'All Male South West Cases'
+parser = Canql::Parser.new(query)
+
+if parser.valid?
+  puts JSON.dump(parser.meta_data)
+end
+```
+
+would output:
+
+```json
+{"patient.sex":{"equals":"1"},"patient.registry":{"equals":"84"}}
+```
+
+The parser is case insensitive. An example of an almost fully involved CANQL query is:
+
+> First 27 Male Liveborn Thames Cases Due between 20/06/2015 and 25/06/2015 and Born on 22/06/2015 and that Died on 07/07/2015 with Prenatal Anomalies and Postnatal Tests and Missing Postcode and Date of Birth and Wait Action and Unprocessed paediatric records and Mother Born between 01/10/1990 and 10/01/1999 and who Died on 01/08/2015 with Populated Postcode and NHS Number
+
+Please see the tests for many more examples.
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `bin/console` for an interactive prompt that will allow you to experiment.
+
+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` to create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+1. Fork it ( https://github.com/PublicHealthEngland/canql/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request
+
+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.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
+

data/Rakefile

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+require 'bundler/gem_tasks'
+require 'rake/testtask'
+require 'ndr_dev_support/tasks'
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << 'test'
+  t.test_files = FileList['test/**/*_test.rb']
+  t.verbose = false
+  t.warning = false
+end
+
+task default: :test

data/bin/console

@@ -0,0 +1,11 @@
+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require 'bundler/setup'
+require 'canql'
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+require 'pry'
+Pry.start

data/bin/setup

@@ -0,0 +1,7 @@
+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/canql.gemspec

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'canql/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'canql'
+  spec.version       = Canql::VERSION
+  spec.authors       = ['PHE NDR Development Team']
+  spec.email         = []
+
+  spec.summary       = 'Congenital Anomaly Natural Query Language'
+  spec.description   = 'Domain Specific Language for querying PHE NCARDRS datastores'
+  spec.homepage      = 'https://github.com/PublicHealthEngland/canql'
+  spec.license       = 'MIT'
+
+  spec.required_ruby_version = '>= 2.2'
+
+  spec.files         = `git ls-files -z`.split("\x0").
+                       reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = 'exe'
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ['lib']
+
+  spec.add_dependency 'ndr_support', '>= 3.0', '< 6'
+  spec.add_dependency 'treetop', '>= 1.4.10'
+  spec.add_dependency 'chronic', '~> 0.3.0'
+
+  spec.add_development_dependency 'ndr_dev_support', '~> 2.0', '>= 2.0.2'
+  spec.add_development_dependency 'bundler'
+  spec.add_development_dependency 'rake'
+  spec.add_development_dependency 'minitest'
+  spec.add_development_dependency 'pry'
+  spec.add_development_dependency 'guard'
+  spec.add_development_dependency 'guard-rubocop'
+  spec.add_development_dependency 'guard-minitest'
+  spec.add_development_dependency 'terminal-notifier-guard' if RUBY_PLATFORM =~ /darwin/
+end

data/code_safety.yml

@@ -0,0 +1,201 @@
+---
+file safety:
+  ".gitignore":
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: cbb48a04cbac04a6dce845110928f69492e152a1
+  ".hound.yml":
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 0b34688f1198eace9310f47060aa8915f5b44985
+  ".rubocop.yml":
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 618d1e7fa4793df5bff0bdb763ff90dd5ea63236
+  ".travis.yml":
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 5c88b8eec43f7e7fd18fae6ac952ea6c2efddbbc
+  CODE_OF_CONDUCT.md:
+    comments: 
+    reviewed_by: drewthorp
+    safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
+  Gemfile:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  LICENSE.txt:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: ee80c4bbd5e990d38b5fc954f4fd037177672db2
+  README.md:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: cb1bd5162935d259f67a42044cbe5644fe6a76f8
+  Rakefile:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 16a9dac62316fbc2ef953457732bc7d9b2f67111
+  bin/console:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  bin/setup:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 6a666fcabe027056b1c774b2eabb3fdf686911d2
+  canql.gemspec:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: b67d28ae2648219607e40dc77d6aef846a64f647
+  lib/canql.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/constants.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/grammars.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/grammars/age.treetop:
+    comments: It is a known issue that this is potentially susceptible to certain
+      kinds of DoS attack
+    reviewed_by: timgentry
+    safe_revision: b152e94eb4e1ae6064204c95dbb56ad1200b576b
+  lib/canql/grammars/anomaly.treetop:
+    comments: It is a known issue that this is potentially susceptible to certain
+      kinds of DoS attack
+    reviewed_by: timgentry
+    safe_revision: a7b0ddabf0c3f7d8b129b4cd206b6e1d65781a10
+  lib/canql/grammars/batch_types.treetop:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 41d8f146c456e7bf252784476438574a9d283408
+  lib/canql/grammars/dates.treetop:
+    comments: It is a known issue that this is potentially susceptible to certain
+      kinds of DoS attack
+    reviewed_by: timgentry
+    safe_revision: 2346abb4435bf95cbe9b4d8c124123b9fefe60d6
+  lib/canql/grammars/e_base_records.treetop:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 41d8f146c456e7bf252784476438574a9d283408
+  lib/canql/grammars/main.treetop:
+    comments: It is a known issue that this is potentially susceptible to certain
+      kinds of DoS attack
+    reviewed_by: timgentry
+    safe_revision: 67be9ba603f1f1d1bd73c696fc1d814b4138ba5f
+  lib/canql/grammars/patient.treetop:
+    comments: It is a known issue that this is potentially susceptible to certain
+      kinds of DoS attack
+    reviewed_by: timgentry
+    safe_revision: 0bf684b681372d16145cae8c6bb831f1bb96f442
+  lib/canql/grammars/registry.treetop:
+    comments: It is a known issue that this is potentially susceptible to certain
+      kinds of DoS attack
+    reviewed_by: timgentry
+    safe_revision: c095990308c4a90316964cbe0d9bc8f4747ca8cc
+  lib/canql/grammars/test_result.treetop:
+    comments: It is a known issue that this is potentially susceptible to certain
+      kinds of DoS attack
+    reviewed_by: timgentry
+    safe_revision: a7b0ddabf0c3f7d8b129b4cd206b6e1d65781a10
+  lib/canql/nodes.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/nodes/age.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/nodes/anomaly.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/nodes/batch_types.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/nodes/dates.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 2346abb4435bf95cbe9b4d8c124123b9fefe60d6
+  lib/canql/nodes/e_base_records.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/nodes/main.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/nodes/patient.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 0bf684b681372d16145cae8c6bb831f1bb96f442
+  lib/canql/nodes/registry.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/nodes/test_result.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/parser.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: a923656606f581c220ea7af16196f2c68b5248f2
+  lib/canql/treetop/extensions.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  lib/canql/version.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: b67d28ae2648219607e40dc77d6aef846a64f647
+  test/canql_test.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  test/minitest_helper.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  test/nodes/age_test.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 2346abb4435bf95cbe9b4d8c124123b9fefe60d6
+  test/nodes/anomaly_test.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  test/nodes/e_base_rescords_test.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  test/nodes/main_test.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  test/nodes/patient_test.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: 0bf684b681372d16145cae8c6bb831f1bb96f442
+  test/nodes/registry_test.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  test/nodes/test_results_test.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a
+  test/parser_test.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: a923656606f581c220ea7af16196f2c68b5248f2
+  test/test_helper.rb:
+    comments: 
+    reviewed_by: timgentry
+    safe_revision: d6f1ccac606735190d30c962b7681ed12aec374a