conceptql 0.4.1 → 0.5.0

data/lib/conceptql/operators/snf.rb

@@ -5,8 +5,7 @@ require_relative "operator"
 module ConceptQL
   module Operators
     class Snf < Operator
-      # GDM only: omopv4_plus has no provenance vocabularies (conceptql-myp).
-      register __FILE__, :gdm, :gdm_wide
+      register __FILE__
       include ConceptQL::Behaviors::Utilizable
 
       desc "Selects admission records of type 'SNF'"

data/lib/conceptql/operators/vocabulary.rb

@@ -38,10 +38,23 @@ module ConceptQL
         args -= bad_arguments
 
         missing_args = args - dm.known_codes(db, vocabulary_id, args)
+        add_warning("unknown code(s)", *missing_args) unless missing_args.empty?
 
-        return if missing_args.empty?
+        warn_about_reused_codes(db, args - missing_args)
+      end
 
-        add_warning("unknown code(s)", *missing_args)
+      # A code that the vocabulary reused for a new meaning selects records of
+      # both meanings: DRG 410 selects chemotherapy stays before 2007-10-01 and
+      # biliary tract procedures after it (conceptql-ttk). Each item names the
+      # code and all of its names, so the user sees the problem without a
+      # vocabulary lookup.
+      def warn_about_reused_codes(db, codes)
+        meanings = dm.code_meanings(db, vocabulary_id, codes)
+        reused = codes.filter_map do |code|
+          names = meanings[code.downcase]
+          "#{code}: #{names.join(' | ')}" if names
+        end
+        add_warning("code(s) with more than one meaning", *reused) unless reused.empty?
       end
 
       def describe_codes(db, codes)

data/lib/conceptql/paths.rb

@@ -37,5 +37,11 @@ module ConceptQL
     def race_file
       ConceptQL.config_dir / "race.yml"
     end
+
+    # The ConceptQL specification, shipped in the gem for applications that
+    # serve it to readers (the Jigsaw diagram editor serves it over MCP).
+    def spec_path
+      root / "doc" / "spec.md"
+    end
   end
 end

data/lib/conceptql/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module ConceptQL
-  VERSION = "0.4.1"
+  VERSION = "0.5.0"
 end

data/lib/conceptql/vocabularies/entry.rb

@@ -9,7 +9,6 @@ module ConceptQL
 
       METHODS = %i[
         id
-        omopv4_vocabulary_id
         omopv5_vocabulary_id
         domain
         vocabulary_short_name
@@ -28,11 +27,6 @@ module ConceptQL
         predominant_domains
       ]
 
-      COST_RELATED_VOCABS = [
-        "Revenue Code",
-        "DRG"
-      ].freeze
-
       def initialize(hash)
         @hash = hash
         @hash[:omopv5_vocabulary_id] ||= @hash[:id]
@@ -54,12 +48,6 @@ module ConceptQL
         self.class.new(hash.merge(other_entry.hash))
       end
 
-      def belongs_in_omopv4_plus?
-        @belongs_in_omopv4_plus ||= (!from_lexicon? || from_csv?) \
-          && has_domain? \
-          && visible?
-      end
-
       def to_hash
         METADATA_METHODS.to_h do |meth|
           [ meth, send(meth) ]
@@ -114,10 +102,6 @@ module ConceptQL
         hash[:domain] =~ /drug_exposure/i
       end
 
-      def is_costish?
-        belongs_in_omopv4_plus? && COST_RELATED_VOCABS.include?(omopv5_vocabulary_id)
-      end
-
       def visible?
         !hidden?
       end
@@ -126,10 +110,6 @@ module ConceptQL
         omopv5_vocabulary_id || id
       end
 
-      def omopv4_id
-        omopv4_vocabulary_id
-      end
-
       def get_klasses
         VocabularyClassFactory.new(self).get_klasses
       end

data/lib/conceptql/vocabularies/vocabulary_class_factory.rb

@@ -3,8 +3,6 @@
 require_relative "../behaviors/drugish"
 require_relative "../behaviors/labish"
 require_relative "behaviors/gdmish"
-require_relative "behaviors/omopish"
-require_relative "behaviors/costish"
 require_relative "../operators/vocabulary"
 
 module ConceptQL
@@ -19,9 +17,8 @@ module ConceptQL
       def get_klasses
         {
           gdm: get_gdm_klass,
-          gdm_wide: get_gdm_klass,
-          omopv4_plus: get_omopv4_plus_klass
-        }.compact
+          gdm_wide: get_gdm_klass
+        }
       end
 
       def get_gdm_klass
@@ -30,16 +27,6 @@ module ConceptQL
         end
       end
 
-      def get_omopv4_plus_klass
-        return nil unless entry.belongs_in_omopv4_plus?
-
-        get_klass do
-          include Behaviors::Omopish
-
-          include Behaviors::Costish if entry.is_costish?
-        end
-      end
-
       def get_klass(&block)
         ventry = entry
         Class.new(ConceptQL::Operators::Vocabulary) do |klass|

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: conceptql
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.5.0
 platform: ruby
 authors:
 - Ryan Duryea
@@ -328,6 +328,7 @@ files:
 - config/provenance.yml
 - config/race.yml
 - config/vocabularies.csv
+- doc/spec.md
 - lib/conceptql.rb
 - lib/conceptql/behaviors/code_lister.rb
 - lib/conceptql/behaviors/drugish.rb
@@ -344,7 +345,6 @@ files:
 - lib/conceptql/data_model/base.rb
 - lib/conceptql/data_model/gdm.rb
 - lib/conceptql/data_model/gdm_wide.rb
-- lib/conceptql/data_model/omopv4_plus.rb
 - lib/conceptql/database.rb
 - lib/conceptql/date_adjuster.rb
 - lib/conceptql/diagram.rb
@@ -418,11 +418,6 @@ files:
 - lib/conceptql/query_modifiers/gdm_wide/lab_query_modifier.rb
 - lib/conceptql/query_modifiers/gdm_wide/pos_query_modifier.rb
 - lib/conceptql/query_modifiers/gdm_wide/provenance_query_modifier.rb
-- lib/conceptql/query_modifiers/omopv4_plus/admission_date_query_modifier.rb
-- lib/conceptql/query_modifiers/omopv4_plus/drug_query_modifier.rb
-- lib/conceptql/query_modifiers/omopv4_plus/pos_query_modifier.rb
-- lib/conceptql/query_modifiers/omopv4_plus/provenance_query_modifier.rb
-- lib/conceptql/query_modifiers/omopv4_plus/provider_query_modifier.rb
 - lib/conceptql/query_modifiers/query_modifier.rb
 - lib/conceptql/rdbms.rb
 - lib/conceptql/rdbms/duckdb.rb
@@ -434,9 +429,7 @@ files:
 - lib/conceptql/utils_cli.rb
 - lib/conceptql/version.rb
 - lib/conceptql/visitors/metadata_extractor.rb
-- lib/conceptql/vocabularies/behaviors/costish.rb
 - lib/conceptql/vocabularies/behaviors/gdmish.rb
-- lib/conceptql/vocabularies/behaviors/omopish.rb
 - lib/conceptql/vocabularies/dynamic_vocabularies.rb
 - lib/conceptql/vocabularies/entry.rb
 - lib/conceptql/vocabularies/vocabulary_class_factory.rb
@@ -449,8 +442,6 @@ files:
 - schemas/gdm.yml
 - schemas/gdm_wide.yml
 - schemas/ohdsi_vocabs.yml
-- schemas/omopv4_plus.yml
-- schemas/omopv4_plus_more_ignorables.tsv
 homepage: https://github.com/outcomesinsights/conceptql
 licenses:
 - MIT

data/lib/conceptql/data_model/omopv4_plus.rb

@@ -1,12 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "base"
-module ConceptQL
-  module DataModel
-    class Omopv4Plus < Base
-      def base
-        :omop
-      end
-    end
-  end
-end

data/lib/conceptql/query_modifiers/omopv4_plus/admission_date_query_modifier.rb

@@ -1,45 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "../query_modifier"
-
-module ConceptQL
-  module QueryModifiers
-    module Omopv4Plus
-      class AdmissionDateQueryModifier < QueryModifier
-        def self.provided_columns
-          %i[
-            admission_date
-            discharge_date
-          ]
-        end
-
-        def self.has_required_columns?(cols)
-          cols.map(&:to_s).any? { |col| col =~ /start_date/i }
-        end
-
-        def modified_query
-          cols = dm.table_cols(source_table).map(&:to_s)
-          return query unless cols.any? { |col| col =~ /start_date/i }
-
-          start_col = cols.find { |col| col =~ /start_date/i }.to_sym
-          end_col = cols.find { |col| col =~ /end_date/i }.to_sym
-
-          query.from_self(alias: :t)
-               .select_all(:t)
-               .select_append(Sequel[:t][start_col].as(:admission_date))
-               .select_append(Sequel.function(:coalesce, Sequel[:t][end_col],
-                                              Sequel[:t][start_col]).as(:discharge_date))
-               .from_self
-        end
-
-        private
-
-        def domain
-          op.domain
-        rescue StandardError
-          nil
-        end
-      end
-    end
-  end
-end

data/lib/conceptql/query_modifiers/omopv4_plus/drug_query_modifier.rb

@@ -1,80 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "../query_modifier"
-
-module ConceptQL
-  module QueryModifiers
-    module Omopv4Plus
-      class DrugQueryModifier < QueryModifier
-        attr_reader :db
-
-        def self.provided_columns
-          %i[
-            drug_name
-            drug_amount
-            drug_amount_units
-            drug_quantity
-            drug_days_supply
-          ]
-        end
-
-        def self.has_required_columns?(cols)
-          needed = [ :drug_concept_id ]
-          found = needed & cols
-          needed == found
-        end
-
-        def initialize(*args)
-          super
-          @db = query.db
-        end
-
-        def modified_query
-          return query unless dm.table_cols(source_table).include?(:drug_concept_id)
-
-          query.db
-          drug_concept_ids = query.select(:drug_concept_id).distinct
-          query.from_self(alias: :de)
-               .left_join(micro_table(drug_concept_ids).as(:mt), drug_concept_id: :drug_concept_id)
-               .select_all(:de)
-               .select_append(Sequel[:de][:quantity].as(:drug_quantity))
-               .select_append(Sequel[:de][:days_supply].as(:drug_days_supply))
-               .select_append(Sequel[:mt][:amount_value].as(:drug_amount))
-               .select_append(Sequel[:mt][:amount_unit].as(:drug_amount_units))
-               .select_append(Sequel[:mt][:drug_name].as(:drug_name))
-               .from_self
-        end
-
-        private
-
-        def micro_table(drug_concept_ids)
-          # TODO: Does drug_strength only have RXNORM concept_ids?
-          # TODO: What is vocabulary for units?  Can we shrink concept table to just that vocab before joining?
-          collapsed_strengths = db[:drug_strength]
-                                .where(drug_concept_id: drug_concept_ids)
-                                .select_group(:drug_concept_id)
-                                .select_append(
-                                  Sequel.function(:min, :amount_value).as(:amount_value),
-                                  Sequel.function(:min, :amount_unit).as(:amount_unit),
-                                  Sequel.function(:count, 1).as(:dcount)
-                                )
-
-          value_case = Sequel.case({ 1 => :amount_value }, nil, :dcount).as(:amount_value)
-          unit_case = Sequel.case({ 1 => :amount_unit }, nil, :dcount).as(:amount_unit)
-
-          collapsed_strengths = collapsed_strengths.from_self.select(:drug_concept_id, value_case, unit_case)
-
-          db.from(Sequel[:concept].as(:dc))
-            .left_join(collapsed_strengths, { drug_concept_id: :concept_id }, { table_alias: :ds })
-            .where(Sequel[:dc][:concept_id] => drug_concept_ids)
-            .select(
-              Sequel[:dc][:concept_id].as(:drug_concept_id),
-              Sequel[:dc][:concept_name].as(:drug_name),
-              Sequel[:ds][:amount_value].as(:amount_value),
-              Sequel[:ds][:amount_unit].as(:amount_unit)
-            )
-        end
-      end
-    end
-  end
-end

data/lib/conceptql/query_modifiers/omopv4_plus/pos_query_modifier.rb

@@ -1,47 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "../query_modifier"
-
-module ConceptQL
-  module QueryModifiers
-    module Omopv4Plus
-      class PoSQueryModifier < QueryModifier
-        attr_reader :join_id, :table, :source_column, :column
-
-        def self.provided_columns
-          [ :visit_source_concept_id ]
-        end
-
-        def self.has_required_columns?(cols)
-          needed = [ :visit_occurrence_id ]
-          found = needed & cols
-          needed == found
-        end
-
-        def initialize(*args)
-          super
-          @column = :visit_source_concept_id
-          @join_id = :visit_occurrence_id
-          @table = :visit_occurrence
-          @source_column = :visit_source_concept_id
-        end
-
-        def modified_query
-          return query unless dm.table_cols(source_table).include?(join_id)
-          return query if dm.table_cols(source_table).include?(column)
-
-          left_alias = "tab1".to_sym
-          right_alias = "tab2".to_sym
-
-          extra_table = query.db.from(table).select(Sequel.as(source_column, column), join_id)
-          ds = query.from_self(alias: left_alias)
-          ds.left_join(extra_table.as(right_alias),
-                       Sequel.qualify(left_alias, join_id) => Sequel.qualify(right_alias, join_id))
-            .select_all(left_alias)
-            .select_append(Sequel.qualify(right_alias, column).as(column))
-            .from_self
-        end
-      end
-    end
-  end
-end

data/lib/conceptql/query_modifiers/omopv4_plus/provenance_query_modifier.rb

@@ -1,45 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "../query_modifier"
-
-module ConceptQL
-  module QueryModifiers
-    module Omopv4Plus
-      class ProvenanceQueryModifier < QueryModifier
-        RELATED_COLUMNS = %w[
-          condition_type_concept_id
-          procedure_type_concept_id
-          death_type_concept_id
-          observation_type_concept_id
-          drug_type_concept_id
-        ].sort.map(&:to_sym)
-
-        attr_reader :db
-
-        def self.provided_columns
-          %i[
-            file_provenance_type
-            code_provenance_type
-          ]
-        end
-
-        def self.has_required_columns?(cols)
-          !(RELATED_COLUMNS & cols).empty?
-        end
-
-        def initialize(*args)
-          super
-          @db = query.db
-        end
-
-        def modified_query
-          return query unless self.class.has_required_columns?(dm.table_cols(source_table))
-
-          query.select_append(Sequel[dm.file_provenance_type_column(query, source_table)].as(:file_provenance_type),
-                              Sequel[dm.code_provenance_type_column(query,
-                                                                    source_table)].as(:code_provenance_type)).from_self
-        end
-      end
-    end
-  end
-end

data/lib/conceptql/query_modifiers/omopv4_plus/provider_query_modifier.rb

@@ -1,26 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "../query_modifier"
-
-module ConceptQL
-  module QueryModifiers
-    module Omopv4Plus
-      class ProviderQueryModifier < QueryModifier
-        def self.provided_columns
-          [ :provider_id ]
-        end
-
-        def self.has_required_columns?(cols)
-          cols.find { |col| col.to_s =~ /provider_id/ }
-        end
-
-        def modified_query
-          col = self.class.has_required_columns?(dm.table_cols(source_table))
-          return query if col.nil? || col.to_sym == :provider_id
-
-          query.select_append(Sequel[col].as(:provider_id)).from_self
-        end
-      end
-    end
-  end
-end

data/lib/conceptql/vocabularies/behaviors/costish.rb

@@ -1,24 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "../../operators/vocabulary"
-
-module ConceptQL
-  module Vocabularies
-    module Behaviors
-      module Costish
-        def query(db)
-          costs = db[:procedure_cost].where(column_to_search => values).select(:procedure_occurrence_id)
-          db[:procedure_occurrence].where(procedure_occurrence_id: costs)
-        end
-
-        def table
-          :procedure_occurrence
-        end
-
-        def column_to_search
-          vocab_entry.id == "revenue_code" ? :revenue_code_source_value : :disease_class_source_value
-        end
-      end
-    end
-  end
-end

data/lib/conceptql/vocabularies/behaviors/omopish.rb

@@ -1,32 +0,0 @@
-# frozen_string_literal: true
-
-module ConceptQL
-  module Vocabularies
-    module Behaviors
-      module Omopish
-        # Overrides Operator#tables
-        def tables
-          domains
-        end
-
-        def vocabulary_condition
-          { dm.source_vocabulary_id(domain) => vocabulary_id.to_i }
-        end
-
-        def where_clause(_db)
-          conds = vocabulary_condition
-          conds[dm.source_value_column(domain)] = arguments unless select_all?
-          conds
-        end
-
-        def query_cols
-          dm.table_columns(domain)
-        end
-
-        def translated_vocabulary_id
-          vocab_entry.omopv4_id
-        end
-      end
-    end
-  end
-end