tnql 1.0.0

data/lib/tnql.rb

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+require 'active_support/time'
+
+require 'tnql/version'
+require 'tnql/parser'

data/lib/tnql/constants.rb

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+# This stores additional constants of the Tnql gem
+module Tnql
+  ALL = 'all'.freeze
+  BEGINS = 'begins'.freeze
+  EQUALS = 'equals'.freeze
+  LIMITS = 'limits'.freeze
+  MESSAGE = 'msg'.freeze
+end

data/lib/tnql/grammars.rb

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+require 'treetop'
+
+Treetop.load File.expand_path('grammars/dates', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/diagnosis', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/e_base_records', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/batch_types', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/provider', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/registration_status', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/registry', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/staging', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/treatment', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/tumour_type', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/patient', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/vital_status', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/age', File.dirname(__FILE__))
+Treetop.load File.expand_path('grammars/main', File.dirname(__FILE__))

data/lib/tnql/grammars/age.treetop

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+module Tnql
+  grammar Age
+    rule age
+      space age:(fuzzy_age / exact_age) <Nodes::AgeNode>
+    end
+
+    rule exact_age
+      [0-9] 1..3 <Nodes::ExactAgeNode>
+    end
+
+    rule fuzzy_age
+      'between' space start:exact_age space 'and' space finish:exact_age <Nodes::FuzzyAgeNode>
+    end
+
+    rule with_age_at_diagnosis
+      were_keyword aged_keyword age <Nodes::AgeAtDiagnosisNode>
+    end
+
+    rule with_death_date
+      died_keyword fuzzy_date <Nodes::DeathDateNode>
+    end
+
+    rule with_birth_date
+      were_keyword born_keyword fuzzy_date <Nodes::BirthDateNode>
+    end
+
+    rule age_group
+      space group:(ctya / paediatric / teenage / young_adult) word_break
+    end
+
+    rule ctya
+      'ctya' <Nodes::CtyaNode>
+    end
+
+    rule paediatric
+      'paediatric' <Nodes::PaediatricNode>
+    end
+
+    rule teenage
+      'teenage' <Nodes::TeenageNode>
+    end
+
+    rule young_adult
+      'young' space 'adult' <Nodes::YoungAdultNode>
+    end
+
+    rule aged_keyword
+      space 'aged' word_break
+    end
+
+    rule died_keyword
+      space 'died' word_break
+    end
+
+    rule were_keyword
+      space 'were' word_break
+    end
+
+    rule born_keyword
+      space 'born' word_break
+    end
+  end
+end

data/lib/tnql/grammars/batch_types.treetop

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+module Tnql
+  grammar BatchTypes
+    rule batch_type
+      (nogca / nbocap / lucada / uhaem / ccm /
+      cosd_mdt / cosd_xml / usom / upath / upas /
+      ucwt / ucd / uncd / uextreg) <Nodes::BatchTypeNode>
+    end
+
+    rule nogca
+      'nogca'
+    end
+
+    rule nbocap
+      'nbocap'
+    end
+
+    rule lucada
+      'lucada'
+    end
+
+    rule uhaem
+      'uhaem'
+    end
+
+    rule ccm
+      'ccm'
+    end
+
+    rule cosd_mdt
+      'cosd_mdt'
+    end
+
+    rule cosd_xml
+      'cosd_xml'
+    end
+
+    rule usom
+      ('somerset' / 'usom' / 'som' / 'scr') <Nodes::USomNode>
+    end
+
+    rule upath
+      ('upath' / 'path') <Nodes::UPathNode>
+    end
+
+    rule upas
+      ('upas' / 'pas' / 'pbr') <Nodes::UPasNode>
+    end
+
+    rule ucwt
+      (('cancer' space 'wait') / 'uwct' / 'cwt') <Nodes::UCwtNode>
+    end
+
+    rule ucd
+      (('death' space 'card') / 'death' / 'ucd') <Nodes::UCdNode>
+    end
+
+    rule uncd
+      ('uncd' / 'ncd') <Nodes::UNcdNode>
+    end
+
+    rule uextreg
+      ('extraregional' / 'uextreg') <Nodes::UExtregNode>
+    end
+  end
+end

data/lib/tnql/grammars/dates.treetop

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+module Tnql
+  grammar Dates
+    rule fuzzy_date
+      date:(between_dates / on_dates) word_break <Nodes::FuzzyDateNode>
+    end
+
+    rule on_dates
+      space ('on' / 'in') space date_fragment <Nodes::SpecificDateNode>
+    end
+
+    rule between_dates
+      space 'between' space start:date_fragment space 'and' space finish:date_fragment <Nodes::FragmentedDateRangeNode>
+    end
+
+    rule date_fragment
+     fragment:(daterange / chronic_date) word_break <Nodes::DateFragmentNode>
+    end
+
+    rule daterange
+      day_or_month? day_or_month? year <Nodes::DateRangeNode>
+    end
+
+    rule day_or_month
+      [0-9] 1..2 ('.' / '/')
+    end
+
+    rule year
+      [0-9] 4..4
+    end
+
+    rule chronic_date
+      (!(space ('and' / 'at' / 'with' / 'who')) .)+ <Nodes::ChronicDateNode>
+    end
+  end
+end

data/lib/tnql/grammars/diagnosis.treetop

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+module Tnql
+  grammar Diagnosis
+    rule diagnosis
+      diagnosed_keyword conditions:diagnosis_conditions+
+    end
+
+    rule diagnosed_keyword
+      space 'diagnosed' word_break
+    end
+
+    rule diagnosis_conditions
+      diagnosisdate_range / diagnosisdate_detail / diagnosis_provider
+    end
+
+    rule diagnosisdate_range
+      space 'between' space start:date_fragment space 'and' space finish:date_fragment <Nodes::DiagnosisDateRangeNode>
+    end
+
+    rule diagnosisdate_detail
+      space ('in' / 'on') space date_fragment <Nodes::DiagnosisDetailNode>
+    end
+  end
+end

data/lib/tnql/grammars/e_base_records.treetop

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+module Tnql
+  grammar EBaseRecords
+    rule with_clause
+      with_keyword action_or_ebr
+    end
+
+    rule action_or_ebr
+      action_and_ebr / actions / e_base_records
+    end
+
+    rule action_and_ebr
+      actions and_keyword e_base_records
+    end
+
+    rule e_base_records
+      unprocessed_keyword types:batch_types? records_keyword <Nodes::EBaseRecordsNode>
+    end
+
+    rule batch_types
+      space allowed_types word_break <Nodes::BatchTypesNode>
+    end
+
+    rule allowed_types
+      batch_type types:more_types* <Nodes::AllowedTypesNode>
+    end
+
+    rule more_types
+      ','? space? ('or' space)? batch_type <Nodes::MoreTypesNode>
+    end
+
+    rule with_keyword
+      space 'with' word_break
+    end
+
+    rule actions
+      action_type action_keyword action_provider? <Nodes::ActionsNode>
+    end
+
+    rule action_provider
+      space 'at' space provider:(action_provider_code / action_provider_name)
+    end
+
+    rule action_type
+      space accepted_action word_break
+    end
+
+    rule accepted_action
+     'pathl' / 'patho' / 'wait' / 'proforma' / 'transfer' / 'notes' / 'child' /
+      'qa' / 'staged' / 'tag' / 'qc' / 'query' / 'stage' / 'searchforstaging' /
+      'moreinfo' / 'search' / 'check' / 'gpsearch'
+    end
+
+    rule action_keyword
+      space 'action' word_break
+    end
+
+    rule at_keyword
+      space 'at' word_break
+    end
+
+    rule action_provider_code
+      provider_type space code:(!' ' .)+ <Nodes::ActionProviderCodeNode>
+    end
+
+    rule action_provider_name
+      short_desc:(!(space provider_type) .)+ space provider_type <Nodes::ActionProviderNameNode>
+    end
+
+    # TODO: support cancer network?
+    rule provider_type
+      'hospital'
+    end
+
+    rule unprocessed_keyword
+      space 'unprocessed' word_break
+    end
+
+    rule records_keyword
+      space 'records' word_break
+    end
+
+    rule and_keyword
+      space 'and' word_break
+    end
+  end
+end

data/lib/tnql/grammars/main.treetop

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+grammar Tnql
+  include Dates
+  include Diagnosis
+  include EBaseRecords
+  include BatchTypes
+  include Provider
+  include RegistrationStatus
+  include Registry
+  include Staging
+  include Treatment
+  include TumourType
+  include Patient
+  include VitalStatus
+  include Age
+
+  # The root grammar
+  rule query
+    quantity:record_count? pre:preconditions* tumours_keyword post:additional_conditions*
+  end
+
+  rule word_break
+    !(!(' '/',') .)
+  end
+
+  rule space
+    ' '+
+  end
+
+  rule number
+    [0-9]+
+  end
+
+  rule record_count
+    all_keyword
+    /
+    'first' space number <Nodes::RecordCountNode>
+  end
+
+  rule all_keyword
+     'all' word_break
+  end
+
+  rule tumours_keyword
+     space 'tumours' word_break
+  end
+
+  rule preconditions
+    registration_status / registry / behaviour / stage / tumour_type
+  end
+
+  rule additional_conditions
+    diagnosis / treatment / with_clause / for_patients_clause
+  end
+end

data/lib/tnql/grammars/patient.treetop

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+module Tnql
+  grammar Patient
+    rule for_patients_clause
+      for_keyword pre:patient_pre_classifiers* patient_keyword post:more_patient_filters?
+    end
+
+    rule patient_keyword
+      space 'patients' word_break
+    end
+
+    rule patient_pre_classifiers
+      dead_or_alive / gender / age_group
+    end
+
+    rule more_patient_filters
+      who_keyword first:patient_post_classifier rest:more_post_classifiers*
+    end
+
+    rule patient_post_classifier
+      with_age_at_diagnosis / with_death_date / with_birth_date / death_certificate
+    end
+
+    rule more_post_classifiers
+      (',' and_keyword / and_keyword / ',' )? patient_post_classifier
+    end
+
+    rule gender
+      space gender:('male' / 'female') word_break <Nodes::GenderNode>
+    end
+
+    rule who_keyword
+      space 'who' word_break
+    end
+
+    rule for_keyword
+      space 'for' word_break
+    end
+  end
+end

data/lib/tnql/grammars/provider.treetop

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+module Tnql
+  grammar Provider
+    # TODO: move diagnosis_provider logic to diagnosis.treetop and clean up the provider logic so it works for
+    # treatments (extracting diagnosis specific logic i.e. tumour.eventid from provider_name and provider_code).
+    rule diagnosis_provider
+      space 'at' space provider:(provider_code / provider_name)
+    end
+
+    rule provider_name
+      name:(!(space provider_type) .)+ space provider_type <Nodes::ProviderNameNode>
+    end
+
+    rule provider_code
+      provider_type space code:(!' ' .)+ <Nodes::ProviderCodeNode>
+    end
+
+    rule provider_type
+      'hospital' / 'cancer network'
+    end
+  end
+end

data/lib/tnql/grammars/registration_status.treetop

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+module Tnql
+  grammar RegistrationStatus
+    rule registration_status
+      space? status_keyword more_statuses:(','? space? ('and' space)?  status_keyword)* <Nodes::RegistrationStatusNode>
+    end
+
+    rule status_keyword
+      ('final' / 'provisional' / 'referenced' / 'treatment' space 'only') <Nodes::StatusKeywordNode>
+    end
+  end
+end

data/lib/tnql/grammars/registry.treetop

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+module Tnql
+  grammar Registry
+    rule registry
+      space registry:(registry_code / registry_abbr) <Nodes::RegistryNode>
+    end
+
+    rule registry_code
+      'y' [0-9] 4..4 <Nodes::RegistryCodeNode>
+    end
+
+    rule registry_abbr
+      ('nycris' / 'trent' / 'ecric' / 'thames' / 'oxford' / 'ociu' / 'swcis' / 'wmciu' / 'nwcis') <Nodes::RegistryAbbrNode>
+    end
+  end
+end