conceptql 0.7.0 → 0.8.0

data/lib/conceptql/lexicon/lexicon_gdm.rb

@@ -1,50 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "lexicon_strategy"
-
-module ConceptQL
-  class LexiconGDM < LexiconStrategy
-    # The GDM vocabulary tables. A db that has all four can be the lexicon.
-    VOCABULARY_TABLES = %i[ancestors concepts mappings vocabularies].freeze
-
-    class << self
-      def db_has_all_vocabulary_tables?(db)
-        VOCABULARY_TABLES.all? { |t| db.table_exists?(t) }
-      end
-    end
-
-    def vocabularies_query
-      db[:vocabularies]
-        .select(Sequel[:id].as(:id),
-                Sequel[:id].as(:omopv5_vocabulary_id),
-                Sequel[:vocabulary_name].as(:vocabulary_short_name),
-                Sequel[:vocabulary_name].as(:vocabulary_full_name),
-                Sequel[:domain],
-                Sequel.expr(1).as(:from_lexicon))
-    end
-
-    def vocabularies
-      vocabularies_query.all
-    end
-
-    def is_a_relationships(_data_db)
-      db[:mappings].where { Sequel.function(:lower, :relationship_id) =~ "is_a" }
-    end
-
-    def ancestors_table(_data_db)
-      db[:ancestors]
-    end
-
-    def concepts_table(_data_db, _some_schema = nil)
-      db[:concepts]
-    end
-
-    def table_is_missing?(_data_db)
-      !db.table_exists?(:concepts)
-    end
-
-    def strategy
-      :gdm
-    end
-  end
-end

data/lib/conceptql/operators/read.rb

@@ -1,79 +0,0 @@
-# frozen_string_literal: true
-
-require "sequel"
-require "sequel/adapters/mock"
-require_relative "../behaviors/labish"
-require_relative "vocabulary"
-
-module ConceptQL
-  module Operators
-    class Read < Operator
-      include ConceptQL::Behaviors::CodeLister
-      extend Vocabulary::SharedDocumentation
-      register __FILE__
-
-      preferred_name "READ"
-      # The vocabulary_name of Read in the OHDSI vocabulary table
-      long_name "NHS UK Read Codes Version 2 (HSCIC)"
-      # Metadata only: the records come from ReadGDM, which selects condition_occurrence
-      predominant_domains :condition_occurrence
-      desc "Selects records based on the Read vocabulary."
-      argument :read_codes, type: :codelist, vocab: "Read",
-                            meaning: "One or more Read codes. Write each code as the Read vocabulary writes it. " \
-                                     "A code matches exactly, including case, and it does not select its child codes. " \
-                                     "A code alone of * selects every Read record."
-      basic_type :selection
-      validate_no_upstreams
-      category "Select by Clinical Codes"
-      conceptql_spec_id "vocabulary"
-
-      def query(db)
-        ops(db).first.evaluate(db)
-      end
-
-      def domains(db)
-        ops.first.domains(db)
-      end
-
-      def query_cols
-        ops.first.query_cols
-      end
-
-      def required_columns
-        ops.flat_map(&:required_columns).uniq
-      end
-
-      private
-
-      def ops(_db = nil)
-        [ ReadGDM.new(nodifier, "read_condition_occurrence", *arguments) ]
-      end
-
-      def describe_codes(db, codes)
-        ops.flat_map { |op| op.describe_codes(db, codes) }
-      end
-
-      class ReadBase < ConceptQL::Operators::Vocabulary
-        preferred_name "READ"
-        argument :read_codes, type: :codelist, vocab: "Read"
-      end
-
-      class ReadGDM < ReadBase
-        include ConceptQL::Vocabularies::Behaviors::Gdmish
-        include ConceptQL::Behaviors::Labish
-
-        def vocabulary_id
-          "Read"
-        end
-
-        def domain_map(_v_id)
-          :condition_occurrence
-        end
-
-        def domains(_db)
-          [ :condition_occurrence ]
-        end
-      end
-    end
-  end
-end