tnql 1.0.0

data/lib/tnql/grammars/staging.treetop

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+module Tnql
+  grammar Staging
+    rule stage
+      space stage_detail word_break
+    end
+
+    rule stage_detail
+      ('stage' space stages:stage_value* / 'unstaged' / 'valid stage') <Nodes::StageDetailNode>
+    end
+
+    rule stage_value
+      number / unstageable / insufficient_info
+    end
+
+    rule unstageable
+      'u'
+    end
+
+    rule insufficient_info
+      '?'
+    end
+  end
+end

data/lib/tnql/grammars/treatment.treetop

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+module Tnql
+  grammar Treatment
+    rule treatment
+      treated_keyword conditions:treatment_conditions+
+    end
+
+    rule treated_keyword
+      space 'treated' word_break
+    end
+
+    rule treatment_conditions
+      treatmentdate_range / treatmentdate_detail / treatment_provider
+    end
+
+    rule treatmentdate_range
+      space 'between' space start:date_fragment space 'and' space finish:date_fragment <Nodes::TreatmentDateRangeNode>
+    end
+
+    rule treatmentdate_detail
+      space ('in' / 'on') space date_fragment <Nodes::TreatmentPreciseDateNode>
+    end
+
+    rule treatment_provider
+      space 'at' space provider:(treatment_provider_code / treatment_provider_name)
+    end
+
+    rule treatment_provider_name
+      (!(space provider_type) .)+ space provider_type <Nodes::TreatmentProviderNameNode>
+    end
+
+    rule treatment_provider_code
+      provider_type space code:(!' ' .)+ <Nodes::TreatmentProviderCodeNode>
+    end
+  end
+end

data/lib/tnql/grammars/tumour_type.treetop

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+module Tnql
+  grammar TumourType
+    rule behaviour
+      space behaviour_detail word_break
+    end
+
+    rule behaviour_detail
+      ('behaviour' space number / 'noninvasive' / 'non-invasive' / 'invasive' / 'metastatic') <Nodes::BehaviourDetailNode>
+    end
+
+    rule tumour_type
+      space (site_group / names_type / sites) word_break
+    end
+
+    rule site_group
+      ('brain' / 'breast' / 'endocrine' / 'gynaecological'
+      / 'haematological' / 'head' space 'and' space 'neck'
+      / 'lower' space 'gi' / 'lung' / 'other' / 'sarcoma'
+      / 'skin' / 'upper' space 'gi' / 'urological') <Nodes::SiteGroupNode>
+    end
+
+    rule names_type
+      ( melanoma / non_melanoma ) word_break
+    end
+
+    rule melanoma
+      'melanoma' <Nodes::MelanomaNode>
+    end
+
+    rule non_melanoma
+      ('nmsc' / 'non-melanoma' / 'non' space 'melanoma') <Nodes::NonMelanomaNode>
+    end
+
+    rule sites
+      first:site rest:more_sites* <Nodes::SitesNode>
+    end
+
+    rule more_sites
+      ','? space? ('and' space)? site <Nodes::AdditionalSiteNode>
+    end
+
+    rule site
+      (icd_site / snomed_site) <Nodes::SingleSiteNode>
+    end
+
+    rule icd_site
+      [cd] [0-9] [0-9] '.'? [0-9]?
+    end
+
+    rule snomed_site
+      't' [0-9fxy] [0-9fxy] [0-9fxy]? [0-9fxy]? [0-9y]?
+    end
+  end
+end

data/lib/tnql/grammars/vital_status.treetop

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+module Tnql
+  grammar VitalStatus
+    rule dead_or_alive
+      space vital_status:('dead' / 'alive') word_break <Nodes::DeadOrAliveNode>
+    end
+
+    rule death_certificate
+      have_keyword space modifier:('no' / 'a') death_certificate_keywords <Nodes::DeathCertificateNode>
+    end
+
+    rule death_certificate_keywords
+      space 'death' space 'certificate' word_break
+    end
+
+    rule have_keyword
+      space 'have' word_break
+    end
+  end
+end

data/lib/tnql/nodes.rb

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+# These file contain custom mixins for treetop
+# nodes that enable them to generate meta_data_items, etc.
+
+# Treetop documentation seems to be out of date;
+# it says to create subclasses of nodes. However,
+# treetop 1.4.10 expects to extend the node with
+# the specified <MODULE> from the grammar.
+
+require 'tnql/treetop/extensions'
+require 'tnql/constants'
+
+require 'tnql/nodes/age'
+require 'tnql/nodes/batch_types'
+require 'tnql/nodes/dates'
+require 'tnql/nodes/diagnosis'
+require 'tnql/nodes/e_base_records'
+require 'tnql/nodes/main'
+require 'tnql/nodes/patient'
+require 'tnql/nodes/provider'
+require 'tnql/nodes/registration_status'
+require 'tnql/nodes/registry'
+require 'tnql/nodes/staging'
+require 'tnql/nodes/treatment'
+require 'tnql/nodes/tumour_type'
+require 'tnql/nodes/vital_status'

data/lib/tnql/nodes/age.rb

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+module Tnql #:nodoc: all
+  module Nodes
+    module AgeNode
+      def to_limits
+        age.to_limits
+      end
+    end
+
+    module ExactAgeNode
+      def to_exact
+        text_value.to_i
+      end
+
+      def to_limits
+        i = to_exact
+        [i, i]
+      end
+    end
+
+    module FuzzyAgeNode
+      def to_limits
+        [start.to_exact, finish.to_exact]
+      end
+    end
+
+    module AgeAtDiagnosisNode
+      def meta_data_item
+        { 'patient.age' => { Tnql::LIMITS => age.to_limits } }
+      end
+    end
+
+    module DeathDateNode
+      def meta_data_item
+        range = fuzzy_date.to_daterange
+        {
+          'patient.deathdate' => {
+            Tnql::LIMITS => [
+              range.date1.try(:to_date).try(:iso8601), range.date2.try(:to_date).try(:iso8601)
+            ]
+          }
+        }
+      end
+    end
+
+    module BirthDateNode
+      def meta_data_item
+        range = fuzzy_date.to_daterange
+        {
+          'patient.birthdate' => {
+            Tnql::LIMITS => [
+              range.date1.try(:to_date).try(:iso8601), range.date2.try(:to_date).try(:iso8601)
+            ]
+          }
+        }
+      end
+    end
+
+    module CtyaNode
+      def meta_data_item
+        { 'patient.age' => { Tnql::LIMITS => [0, 24] } }
+      end
+    end
+
+    module PaediatricNode
+      def meta_data_item
+        { 'patient.age' => { Tnql::LIMITS => [0, 15] } }
+      end
+    end
+
+    module TeenageNode
+      def meta_data_item
+        { 'patient.age' => { Tnql::LIMITS => [16, 18] } }
+      end
+    end
+
+    module YoungAdultNode
+      def meta_data_item
+        { 'patient.age' => { Tnql::LIMITS => [19, 24] } }
+      end
+    end
+  end
+end

data/lib/tnql/nodes/batch_types.rb

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+module Tnql #:nodoc: all
+  module Nodes
+    module BatchTypeNode
+      def to_type
+        string = respond_to?(:normalise) ? normalise : text_value
+        string.upcase
+      end
+    end
+
+    module USomNode
+      def normalise
+        'usom'
+      end
+    end
+
+    module UPathNode
+      def normalise
+        'upath'
+      end
+    end
+
+    module UPasNode
+      def normalise
+        'upas'
+      end
+    end
+
+    module UCwtNode
+      def normalise
+        'ucwt'
+      end
+    end
+
+    module UCdNode
+      def normalise
+        'ucd'
+      end
+    end
+
+    module UNcdNode
+      def normalise
+        'uncd'
+      end
+    end
+
+    module UExtregNode
+      def normalise
+        'uextreg'
+      end
+    end
+  end
+end

data/lib/tnql/nodes/dates.rb

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+require 'chronic'
+require 'ndr_support/daterange'
+
+module Tnql #:nodoc: all
+  module Nodes
+    module FuzzyDateNode
+      def to_daterange
+        date.to_daterange
+      end
+    end
+
+    module SpecificDateNode
+      def to_daterange
+        date_fragment.to_daterange
+      end
+    end
+
+    module FragmentedDateRangeNode
+      def to_daterange
+        d1 = start.to_daterange.date1
+        d2 = finish.to_daterange.date2
+
+        Daterange.new(d1, d2)
+      end
+    end
+
+    module DateFragmentNode
+      def to_daterange
+        fragment.to_daterange
+      end
+    end
+
+    module DateRangeNode
+      def to_daterange
+        Daterange.new(text_value.to_s)
+      end
+    end
+
+    module ChronicDateNode
+      def to_daterange
+        chronic = Chronic.parse(text_value.to_s, context: :past, guess: false)
+        if chronic.instance_of?(Chronic::Span)
+          Daterange.new(chronic.begin, chronic.end - 1.day)
+        else
+          Daterange.new(chronic)
+        end
+      end
+    end
+  end
+end

data/lib/tnql/nodes/diagnosis.rb

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+module Tnql #:nodoc: all
+  module Nodes
+    module DiagnosisDateRangeNode
+      def meta_data_item
+        {
+          'tumour.diagnosisdate' => {
+            Tnql::LIMITS => [
+              start.to_daterange.date1.try(:to_date).try(:iso8601),
+              finish.to_daterange.date2.try(:to_date).try(:iso8601)
+            ]
+          }
+        }
+      end
+    end
+
+    module DiagnosisDetailNode
+      def meta_data_item
+        range = date_fragment.to_daterange
+
+        {
+          'tumour.diagnosisdate' => {
+            Tnql::LIMITS => [
+              range.date1.try(:to_date).try(:iso8601),
+              range.date2.try(:to_date).try(:iso8601)
+            ]
+          }
+        }
+      end
+    end
+  end
+end

data/lib/tnql/nodes/e_base_records.rb

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+module Tnql #:nodoc: all
+  module Nodes
+    module EBaseRecordsNode
+      def meta_data_item
+        filter =
+          if types.empty?
+            { Tnql::ALL => true }
+          else
+            { Tnql::EQUALS => types.to_list }
+          end
+        { 'unprocessed_records.sources' => filter }
+      end
+    end
+
+    module BatchTypesNode
+      def to_list
+        allowed_types.to_list
+      end
+    end
+
+    module AllowedTypesNode
+      def to_list
+        list = [batch_type.to_type]
+        list.concat types.elements.map(&:extract_type)
+      end
+    end
+
+    module MoreTypesNode
+      def extract_type
+        batch_type.to_type
+      end
+    end
+
+    module ActionsNode
+      def meta_data_item
+        { 'action.actioninitiated' => { Tnql::EQUALS => action_type.text_value.upcase.strip } }
+      end
+    end
+
+    module ActionProviderCodeNode
+      def meta_data_item
+        # default to provider
+        key = provider_type.text_value == 'cancer network' ? 'cn_ukacr' : 'providercode'
+        { "action.#{key}" => { Tnql::EQUALS => code.text_value.upcase } }
+      end
+    end
+
+    module ActionProviderNameNode
+      def meta_data_item
+        # default to provider
+        key = provider_type.text_value == 'cancer network' ? 'cn_ukacrname' : 'providername'
+        {
+          "action.#{key}" => {
+            Tnql::BEGINS => short_desc.text_value.upcase,
+            :interval => interval
+          }
+        }
+      end
+    end
+  end
+end

data/lib/tnql/nodes/main.rb

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+require 'active_support/core_ext/object/blank'
+
+module Tnql #:nodoc: all
+  module Nodes
+    module RecordCountNode
+      def meta_data_item
+        { 'limit' => { Tnql::EQUALS => number.text_value.to_i } }
+      end
+    end
+  end
+end