tnql 1.0.0

data/lib/tnql/nodes/patient.rb

@@ -0,0 +1,9 @@
+module Tnql #:nodoc: all
+  module Nodes
+    module GenderNode
+      def meta_data_item
+        { 'patient.sex' => { Tnql::EQUALS => gender.text_value == 'male' ? '1' : '2' } }
+      end
+    end
+  end
+end

data/lib/tnql/nodes/provider.rb

@@ -0,0 +1,24 @@
+module Tnql #:nodoc: all
+  module Nodes
+    module ProviderNameNode
+      def meta_data_item
+        # default to provider
+        key = provider_type.text_value == 'cancer network' ? 'cn_ukacrname' : 'providername'
+        {
+          "diagnosis.#{key}" => {
+            Tnql::BEGINS => name.text_value.upcase,
+            :interval => interval
+          }
+        }
+      end
+    end
+
+    module ProviderCodeNode
+      def meta_data_item
+        # default to provider
+        key = provider_type.text_value == 'cancer network' ? 'cn_ukacr' : 'providercode'
+        { "diagnosis.#{key}" => { Tnql::EQUALS => code.text_value.upcase } }
+      end
+    end
+  end
+end

data/lib/tnql/nodes/registration_status.rb

@@ -0,0 +1,27 @@
+module Tnql #:nodoc: all
+  module Nodes
+    module RegistrationStatusNode
+      def meta_data_item
+        { 'tumour.statusofregistration' => { Tnql::EQUALS => statuses } }
+      end
+
+      def statuses
+        [status_keyword.statusofregistration] + remaining_statuses
+      end
+
+      def remaining_statuses
+        more_statuses.elements.map do |comma_and_status|
+          comma_and_status.status_keyword.statusofregistration
+        end
+      end
+    end
+
+    module StatusKeywordNode
+      def statusofregistration
+        # Currently every status is the upper case first letter of the description
+        # May need to replace this with a case statement at a later date, if needed
+        text_value[0, 1].upcase
+      end
+    end
+  end
+end

data/lib/tnql/nodes/registry.rb

@@ -0,0 +1,33 @@
+module Tnql #:nodoc: all
+  module Nodes
+    module RegistryNode
+      def meta_data_item
+        { 'tumour.registry' => { Tnql::EQUALS => registry.to_registrycode } }
+      end
+    end
+
+    module RegistryCodeNode
+      def to_registrycode
+        text_value.upcase
+      end
+    end
+
+    module RegistryAbbrNode
+      REGISTRY_ABBR = {
+        'nycris' => 'Y0201',
+        'trent'  => 'Y0301',
+        'ecric'  => 'Y0401',
+        'thames' => 'Y0801',
+        'oxford' => 'Y0901',
+        'ociu'   => 'Y0901',
+        'swcis'  => 'Y1001',
+        'wmciu'  => 'Y1201',
+        'nwcis'  => 'Y1701'
+      }.freeze unless defined?(REGISTRY_ABBR)
+
+      def to_registrycode
+        REGISTRY_ABBR[text_value]
+      end
+    end
+  end
+end

data/lib/tnql/nodes/staging.rb

@@ -0,0 +1,17 @@
+module Tnql #:nodoc: all
+  module Nodes
+    module StageDetailNode
+      def meta_data_item
+        case text_value
+        when 'unstaged'
+          { 'staging.stage' => { Tnql::EQUALS => nil } }
+        when 'valid stage'
+          { 'staging.stage' => { Tnql::BEGINS => %w(1 2 3 4) } }
+        else
+          stage_values = stages.elements.map(&:text_value).map(&:upcase)
+          { 'staging.stage' => { Tnql::BEGINS => stage_values } }
+        end
+      end
+    end
+  end
+end

data/lib/tnql/nodes/treatment.rb

@@ -0,0 +1,45 @@
+module Tnql #:nodoc: all
+  module Nodes
+    module TreatmentDateRangeNode
+      def meta_data_item
+        {
+          'treatment.startoradmissiondate' => {
+            Tnql::LIMITS => [
+              start.to_daterange.date1.try(:to_date).try(:iso8601),
+              finish.to_daterange.date2.try(:to_date).try(:iso8601)
+            ]
+          }
+        }
+      end
+    end
+
+    module TreatmentPreciseDateNode
+      def meta_data_item
+        date_range = date_fragment.to_daterange
+
+        {
+          'treatment.startoradmissiondate' => {
+            Tnql::LIMITS => [
+              date_range.date1.try(:to_date).try(:iso8601),
+              date_range.date2.try(:to_date).try(:iso8601)
+            ]
+          }
+        }
+      end
+    end
+
+    module TreatmentProviderNameNode
+      def meta_data_item
+        { 'treatment.providername' => { Tnql::MESSAGE => 'TODO: "' + text_value + '" ignored' } }
+      end
+    end
+
+    module TreatmentProviderCodeNode
+      def meta_data_item
+        # default to provider
+        key = provider_type.text_value == 'cancer network' ? 'cn_ukacr' : 'providercode'
+        { "treatment.#{key}" => { Tnql::EQUALS => code.text_value.upcase } }
+      end
+    end
+  end
+end

data/lib/tnql/nodes/tumour_type.rb

@@ -0,0 +1,74 @@
+module Tnql #:nodoc: all
+  module Nodes
+    module BehaviourDetailNode
+      def meta_data_item
+        case text_value
+        when 'noninvasive', 'non-invasive'
+          { 'tumour.behaviour' => { Tnql::EQUALS => %w(0 1 2) } }
+        when 'invasive'
+          { 'tumour.behaviour' => { Tnql::EQUALS => %w(3 5) } }
+        when 'metastatic'
+          { 'tumour.behaviour' => { Tnql::EQUALS => '6' } }
+        else
+          { 'tumour.behaviour' => { Tnql::EQUALS => number.text_value } }
+        end
+      end
+    end
+
+    module SiteGroupNode
+      SITE_GROUPS = {
+        'brain'          => 1,
+        'breast'         => 2,
+        'endocrine'      => 3,
+        'gynaecological' => 6,
+        'haematological' => 7,
+        'head and neck'  => 8,
+        'lower gi'       => 4,
+        'lung'           => 9,
+        'other'          => 14,
+        'sarcoma'        => 10,
+        'skin'           => 11,
+        'upper gi'       => 5,
+        'urological'     => 12
+      }.freeze unless defined?(SITE_GROUPS)
+
+      def meta_data_item
+        { 'tumour.site_group' => { Tnql::EQUALS => SITE_GROUPS[text_value] } }
+      end
+    end
+
+    module MelanomaNode
+      def meta_data_item
+        { 'tumour.icd10o2_primarycode' => { Tnql::BEGINS => 'C43' } }
+      end
+    end
+
+    module NonMelanomaNode
+      def meta_data_item
+        { 'tumour.icd10o2_primarycode' => { Tnql::BEGINS => 'C44' } }
+      end
+    end
+
+    module SitesNode
+      def meta_data_item
+        sites_array = [first.to_site]
+        rest.elements.map { |e| sites_array << e.to_site if !e.nil? && e.respond_to?(:to_site) }
+        sites_array.flatten.delete_if { |a| a.nil? || a.empty? }
+
+        { 'tumour.primarycode' => { Tnql::BEGINS => sites_array } }
+      end
+    end
+
+    module AdditionalSiteNode
+      def to_site
+        site.to_site
+      end
+    end
+
+    module SingleSiteNode
+      def to_site
+        text_value.upcase
+      end
+    end
+  end
+end

data/lib/tnql/nodes/vital_status.rb

@@ -0,0 +1,15 @@
+module Tnql #:nodoc: all
+  module Nodes
+    module DeadOrAliveNode
+      def meta_data_item
+        { 'patient.dead' => { Tnql::EQUALS => vital_status.text_value == 'dead' } }
+      end
+    end
+
+    module DeathCertificateNode
+      def meta_data_item
+        { 'patient.death_certificate' => { Tnql::EQUALS => modifier.text_value != 'no' } }
+      end
+    end
+  end
+end

data/lib/tnql/parser.rb

@@ -0,0 +1,56 @@
+require 'tnql/nodes'
+require 'tnql/grammars'
+
+module Tnql
+  # This class simplifies TNQL queries by wrapping them in a little syntactic sugar.
+  class Parser
+    attr_reader :parser
+
+    def initialize(query)
+      raise ArgumentError unless query.is_a?(String)
+
+      @parser = TnqlParser.new
+      @result = @parser.parse(query.downcase)
+
+      return if valid?
+      # FIXME: should log "Parser failed parsing \"#{query}\": #{@parser.failure_reason} " \
+      #                   "(line: #{@parser.failure_line}, column: #{@parser.failure_column})"
+    end
+
+    def valid?
+      !@result.nil?
+    end
+
+    def failure_reason
+      valid? ? nil : @parser.failure_reason
+    end
+
+    def failure_line
+      valid? ? nil : @parser.failure_line
+    end
+
+    def failure_column
+      valid? ? nil : @parser.failure_column
+    end
+
+    def diagnosis_range
+      tumour_diagnosisdate = meta_data['tumour.diagnosisdate']
+      return nil unless tumour_diagnosisdate
+
+      starts, ends = tumour_diagnosisdate[Tnql::LIMITS]
+      Daterange.new(Date.parse(starts), Date.parse(ends))
+    end
+
+    def messages # check if any query conditions been ignored or modified
+      msg = ''.html_safe
+      meta_data.each do |_canonical_name, filter|
+        msg += filter[Tnql::MESSAGE] if filter.key?(Tnql::MESSAGE)
+      end
+      msg
+    end
+
+    def meta_data
+      valid? ? @result.meta_data : {}
+    end
+  end
+end

data/lib/tnql/treetop/extensions.rb

@@ -0,0 +1,20 @@
+module Treetop
+  module Runtime
+    # We extend the SyntaxNode class to include a hash of meta data.
+    # Individual rules can define meta_data_item method that must return
+    # a hash that is merged with the hash data for the entire query.
+    class SyntaxNode
+      def meta_data(hash = {})
+        hash.merge!(meta_data_item) if respond_to?(:meta_data_item)
+
+        if nonterminal?
+          elements.each do |element|
+            element.meta_data(hash)
+          end
+        end
+
+        hash
+      end
+    end
+  end
+end

data/lib/tnql/version.rb

@@ -0,0 +1,4 @@
+# This stores the current version of the Tnql gem
+module Tnql
+  VERSION = '1.0.0'.freeze
+end

data/tnql.gemspec

@@ -0,0 +1,39 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'tnql/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'tnql'
+  spec.version       = Tnql::VERSION
+  spec.authors       = ['PHE NDR IT Development Team']
+  spec.email         = []
+
+  spec.summary       = 'Tumour Natural Query Language'
+  spec.description   = 'Domain Specific Language for querying PHE NCRAS datastores'
+  spec.homepage      = 'https://github.com/PublicHealthEngland/tnql'
+  spec.license       = 'MIT'
+
+  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.required_ruby_version = '>= 2.2.0'
+
+  spec.add_dependency 'activesupport', '>= 3.2.18', '< 5.1'
+  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', '~> 2.1'
+  spec.add_development_dependency 'bundler'
+  spec.add_development_dependency 'rake'
+  spec.add_development_dependency 'minitest', '>= 5.0.0'
+  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

metadata

@@ -0,0 +1,286 @@
+--- !ruby/object:Gem::Specification
+name: tnql
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+platform: ruby
+authors:
+- PHE NDR IT Development Team
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2017-05-25 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.2.18
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '5.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.2.18
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '5.1'
+- !ruby/object:Gem::Dependency
+  name: ndr_support
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '3.0'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '3.0'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '6'
+- !ruby/object:Gem::Dependency
+  name: treetop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.10
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.10
+- !ruby/object:Gem::Dependency
+  name: chronic
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.0
+- !ruby/object:Gem::Dependency
+  name: ndr_dev_support
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.1'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 5.0.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 5.0.0
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: guard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: guard-rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: guard-minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: terminal-notifier-guard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Domain Specific Language for querying PHE NCRAS datastores
+email: []
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".hound.yml"
+- ".rubocop.yml"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- Guardfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- code_safety.yml
+- lib/tnql.rb
+- lib/tnql/constants.rb
+- lib/tnql/grammars.rb
+- lib/tnql/grammars/age.treetop
+- lib/tnql/grammars/batch_types.treetop
+- lib/tnql/grammars/dates.treetop
+- lib/tnql/grammars/diagnosis.treetop
+- lib/tnql/grammars/e_base_records.treetop
+- lib/tnql/grammars/main.treetop
+- lib/tnql/grammars/patient.treetop
+- lib/tnql/grammars/provider.treetop
+- lib/tnql/grammars/registration_status.treetop
+- lib/tnql/grammars/registry.treetop
+- lib/tnql/grammars/staging.treetop
+- lib/tnql/grammars/treatment.treetop
+- lib/tnql/grammars/tumour_type.treetop
+- lib/tnql/grammars/vital_status.treetop
+- lib/tnql/nodes.rb
+- lib/tnql/nodes/age.rb
+- lib/tnql/nodes/batch_types.rb
+- lib/tnql/nodes/dates.rb
+- lib/tnql/nodes/diagnosis.rb
+- lib/tnql/nodes/e_base_records.rb
+- lib/tnql/nodes/main.rb
+- lib/tnql/nodes/patient.rb
+- lib/tnql/nodes/provider.rb
+- lib/tnql/nodes/registration_status.rb
+- lib/tnql/nodes/registry.rb
+- lib/tnql/nodes/staging.rb
+- lib/tnql/nodes/treatment.rb
+- lib/tnql/nodes/tumour_type.rb
+- lib/tnql/nodes/vital_status.rb
+- lib/tnql/parser.rb
+- lib/tnql/treetop/extensions.rb
+- lib/tnql/version.rb
+- tnql.gemspec
+homepage: https://github.com/PublicHealthEngland/tnql
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.2.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.5.1
+signing_key: 
+specification_version: 4
+summary: Tumour Natural Query Language
+test_files: []