abstractor 1.0.8

data/db/migrate/20131227205320_create_abstractor_relation_types.rb

@@ -0,0 +1,10 @@
+class CreateAbstractorRelationTypes < ActiveRecord::Migration
+  def change
+    create_table :abstractor_relation_types do |t|
+      t.string :name
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227205354_create_abstractor_rule_types.rb

@@ -0,0 +1,11 @@
+class CreateAbstractorRuleTypes < ActiveRecord::Migration
+  def change
+    create_table :abstractor_rule_types do |t|
+      t.string :name
+      t.text :description
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227205432_create_abstractor_abstraction_schemas.rb

@@ -0,0 +1,13 @@
+class CreateAbstractorAbstractionSchemas < ActiveRecord::Migration
+  def change
+    create_table :abstractor_abstraction_schemas do |t|
+      t.string :predicate
+      t.string :display_name
+      t.integer :abstractor_object_type_id
+      t.string :preferred_name
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227205456_create_abstractor_abstraction_schema_object_values.rb

@@ -0,0 +1,10 @@
+class CreateAbstractorAbstractionSchemaObjectValues < ActiveRecord::Migration
+  def change
+    create_table :abstractor_abstraction_schema_object_values do |t|
+      t.integer :abstractor_abstraction_schema_id
+      t.integer :abstractor_object_value_id
+      t.datetime :deleted_at
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227205529_create_abstractor_abstraction_schema_predicate_variants.rb

@@ -0,0 +1,11 @@
+class CreateAbstractorAbstractionSchemaPredicateVariants < ActiveRecord::Migration
+  def change
+    create_table :abstractor_abstraction_schema_predicate_variants do |t|
+      t.integer :abstractor_abstraction_schema_id
+      t.string :value
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227205610_create_abstractor_abstraction_schema_relations.rb

@@ -0,0 +1,11 @@
+class CreateAbstractorAbstractionSchemaRelations < ActiveRecord::Migration
+  def change
+    create_table :abstractor_abstraction_schema_relations do |t|
+      t.integer :subject_id
+      t.integer :object_id
+      t.integer :abstractor_relation_type_id
+      t.datetime :deleted_at
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227205652_create_abstractor_subjects.rb

@@ -0,0 +1,12 @@
+class CreateAbstractorSubjects < ActiveRecord::Migration
+  def change
+    create_table :abstractor_subjects do |t|
+      t.integer :abstractor_abstraction_schema_id
+      t.integer :abstractor_rule_type_id
+      t.string :subject_type
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227205732_create_abstractor_subject_relations.rb

@@ -0,0 +1,11 @@
+class CreateAbstractorSubjectRelations < ActiveRecord::Migration
+  def change
+    create_table :abstractor_subject_relations do |t|
+      t.integer :subject_id
+      t.integer :object_id
+      t.integer :abstractor_relation_type_id
+      t.datetime :deleted_at
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227205831_create_abstractor_abstraction_sources.rb

@@ -0,0 +1,11 @@
+class CreateAbstractorAbstractionSources < ActiveRecord::Migration
+  def change
+    create_table :abstractor_abstraction_sources do |t|
+      t.integer :abstractor_subject_id
+      t.string :from_method
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227210211_create_abstractor_subject_groups.rb

@@ -0,0 +1,10 @@
+class CreateAbstractorSubjectGroups < ActiveRecord::Migration
+  def change
+    create_table :abstractor_subject_groups do |t|
+      t.string :name
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227210244_create_abstractor_subject_group_members.rb

@@ -0,0 +1,11 @@
+class CreateAbstractorSubjectGroupMembers < ActiveRecord::Migration
+  def change
+    create_table :abstractor_subject_group_members do |t|
+      t.integer :abstractor_subject_id
+      t.integer :abstractor_subject_group_id
+      t.integer :display_order
+      t.datetime :deleted_at
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227210350_create_abstractor_abstraction_groups.rb

@@ -0,0 +1,12 @@
+class CreateAbstractorAbstractionGroups < ActiveRecord::Migration
+  def change
+    create_table :abstractor_abstraction_groups do |t|
+      t.integer :abstractor_subject_group_id
+      t.string :about_type
+      t.integer :about_id
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227210353_create_abstractor_abstraction_group_members.rb

@@ -0,0 +1,11 @@
+class CreateAbstractorAbstractionGroupMembers < ActiveRecord::Migration
+  def change
+    create_table :abstractor_abstraction_group_members do |t|
+      t.integer :abstractor_abstraction_group_id
+      t.integer :abstractor_abstraction_id
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227211050_create_abstractor_suggestion_statuses.rb

@@ -0,0 +1,10 @@
+class CreateAbstractorSuggestionStatuses < ActiveRecord::Migration
+  def change
+    create_table :abstractor_suggestion_statuses do |t|
+      t.string :name
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227211303_create_abstractor_abstractions.rb

@@ -0,0 +1,15 @@
+class CreateAbstractorAbstractions < ActiveRecord::Migration
+  def change
+    create_table :abstractor_abstractions do |t|
+      t.integer :abstractor_subject_id
+      t.string :value
+      t.string :about_type
+      t.integer :about_id
+      t.string :value
+      t.boolean :unknown
+      t.boolean :not_applicable
+      t.datetime :deleted_at
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131227213427_create_abstractor_suggestions.rb

@@ -0,0 +1,14 @@
+class CreateAbstractorSuggestions < ActiveRecord::Migration
+  def change
+    create_table :abstractor_suggestions do |t|
+      t.integer :abstractor_abstraction_id
+      t.integer :abstractor_suggestion_status_id
+      t.string :suggested_value
+      t.boolean :unknown
+      t.boolean :not_applicable
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131228041944_create_abstractor_suggestion_object_values.rb

@@ -0,0 +1,11 @@
+class CreateAbstractorSuggestionObjectValues < ActiveRecord::Migration
+  def change
+    create_table :abstractor_suggestion_object_values do |t|
+      t.integer :abstractor_suggestion_id
+      t.integer :abstractor_object_value_id
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/db/migrate/20131228041945_create_abstractor_suggestion_sources.rb

@@ -0,0 +1,16 @@
+class CreateAbstractorSuggestionSources < ActiveRecord::Migration
+  def change
+    create_table :abstractor_suggestion_sources do |t|
+      t.integer :abstractor_abstraction_source_id
+      t.integer :abstractor_suggestion_id
+      t.text :match_value
+      t.text :sentence_match_value
+      t.integer :source_id
+      t.string :source_method
+      t.string :source_type
+      t.datetime :deleted_at
+
+      t.timestamps
+    end
+  end
+end

data/lib/abstractor.rb

@@ -0,0 +1,8 @@
+require "abstractor/engine"
+require 'abstractor/core_ext/string'
+ENV['CLASSPATH'] = "$CLASSPATH:#{File.expand_path('../..', __FILE__)}/lib/lingscope/dist/lingscope.jar:#{File.expand_path('../..', __FILE__)}/lib/lingscope/dist/lib/abner.jar"
+module Abstractor
+  def self.table_name_prefix
+    ''
+  end
+end

data/lib/abstractor/abstractable.rb

@@ -0,0 +1,190 @@
+module Abstractor
+  module Abstractable
+    def self.included(base)
+      base.send(:include, InstanceMethods)
+      base.extend(ClassMethods)
+      base.class_eval do
+        has_many :abstractor_abstractions, class_name: Abstractor::AbstractorAbstraction, as: :about
+
+        has_many :abstractor_abstraction_groups, class_name: Abstractor::AbstractorAbstractionGroup, as: :about
+
+        accepts_nested_attributes_for :abstractor_abstractions, allow_destroy: false
+      end
+    end
+
+    module InstanceMethods
+      def abstract
+        self.class.abstractor_subjects.each do |abstractor_subject|
+          abstractor_subject.abstract(self)
+        end
+      end
+
+      def detect_abstractor_abstraction(abstractor_subject)
+        abstractor_abstractions(true).not_deleted.detect { |abstractor_abstraction| abstractor_abstraction.abstractor_subject == abstractor_subject }
+      end
+
+      def find_or_create_abstractor_abstraction(abstractor_abstraction_schema, abstractor_subject)
+        if abstractor_abstraction = detect_abstractor_abstraction(abstractor_subject)
+        else
+          abstractor_abstraction = Abstractor::AbstractorAbstraction.create!(abstractor_subject: abstractor_subject, about: self)
+          if abstractor_subject.groupable?
+            abstractor_abstraction_group = find_or_create_abstractor_abstraction_group(abstractor_subject.abstractor_subject_group)
+            abstractor_abstraction_group.abstractor_abstractions << abstractor_abstraction
+          end
+        end
+        abstractor_abstraction
+      end
+
+      def detect_abstractor_abstraction_group(abstractor_subject_group)
+        abstractor_abstraction_groups(true).detect { |abstractor_abstraction_group| abstractor_abstraction_group.abstractor_subject_group ==  abstractor_subject_group }
+      end
+
+      def find_or_create_abstractor_abstraction_group(abstractor_subject_group)
+        if abstractor_abstraction_group = detect_abstractor_abstraction_group(abstractor_subject_group)
+        else
+          abstractor_abstraction_group = Abstractor::AbstractorAbstractionGroup.create(abstractor_subject_group: abstractor_subject_group, about: self)
+        end
+        abstractor_abstraction_group
+      end
+
+      def abstractor_abstractions_by_abstractor_suggestion_status(abstractor_suggestion_statuses)
+        abstractor_abstractions.map(&:abstractor_suggestions).flatten.select { |as| Array.new(abstractor_suggestion_statuses).any? { |abstractor_suggestion_status| as.abstractor_suggestion_status == abstractor_suggestion_status } }
+      end
+
+      def remove_abstractions
+        abstractor_abstractions.each do |abstractor_abstraction|
+          abstractor_abstraction.abstractor_suggestions.each do |abstractor_suggestion|
+            abstractor_suggestion.abstractor_suggestion_sources.destroy_all
+            abstractor_suggestion.abstractor_suggestion_object_value.destroy
+            abstractor_suggestion.destroy
+          end
+          abstractor_abstraction.destroy
+        end
+      end
+    end
+
+    module ClassMethods
+      def by_abstractor_suggestion_status(abstractor_suggestion_status)
+        abstractor_suggestion_status_needs_review = Abstractor::AbstractorSuggestionStatus.where(:name => 'Needs review').first
+        abstractor_suggestion_status_accepted= Abstractor::AbstractorSuggestionStatus.where(:name => 'Accepted').first
+        abstractor_suggestion_status_rejected = Abstractor::AbstractorSuggestionStatus.where(:name => 'Rejected').first
+
+        case abstractor_suggestion_status
+        when 'needs_review'
+          where(["EXISTS (SELECT 1 FROM abstractor_subjects asb JOIN abstractor_abstractions aa ON asb.id = aa.abstractor_subject_id AND asb.subject_type = '#{self.to_s}' JOIN abstractor_suggestions aas ON aa.id = aas.abstractor_abstraction_id AND aas.abstractor_suggestion_status_id = ? WHERE #{self.table_name}.id = aa.about_id)", abstractor_suggestion_status_needs_review])
+        when 'reviewed'
+          where(["EXISTS (SELECT 1 FROM abstractor_subjects asb JOIN abstractor_abstractions aa ON asb.id = aa.abstractor_subject_id AND asb.subject_type = '#{self.to_s}' JOIN abstractor_suggestions aas ON aa.id = aas.abstractor_abstraction_id WHERE #{self.table_name}.id = aa.about_id) AND NOT EXISTS (SELECT 1 FROM abstractor_subjects asb JOIN abstractor_abstractions aa ON asb.id = aa.abstractor_subject_id AND asb.subject_type = '#{self.to_s}' JOIN abstractor_suggestions aas ON aa.id = aas.abstractor_abstraction_id  AND aas.abstractor_suggestion_status_id = ? WHERE #{self.table_name}.id = aa.about_id)", abstractor_suggestion_status_needs_review])
+        else
+          where(nil)
+        end
+      end
+
+      def abstractor_subjects
+        Abstractor::AbstractorSubject.where(subject_type: self.to_s)
+      end
+
+      def abstractor_abstraction_schemas
+        abstractor_subjects.map(&:abstractor_abstraction_schema)
+      end
+
+      def abstractor_subject_groups
+        abstractor_subjects.map(&:abstractor_subject_group).uniq
+      end
+
+      def prepare_pivot_select
+        select =[]
+        abstractor_abstraction_schemas.map(&:predicate).each do |predicate|
+          select << "MAX(CASE WHEN data.predicate = '#{predicate}' THEN data.value ELSE NULL END) AS #{predicate}"
+        end
+        select = select.join(',')
+      end
+
+      ##
+      # Pivot abstractions to simulate regular columns on an abstractable entity.
+      #
+      # Example: an ActiveRecod model PathologyCaseReport with the columns
+      # * 'collection_date'
+      # * 'report_text'
+      # And the abstraction 'has_cancer_diagnosis'.
+      #
+      # This method allows for the querying of the pathology_cases table as if
+      # it was strucutred like so:
+      # 'select id, collection_date, report_text, has_cancer_diagnosis from pathology_cases'
+      #
+      # @return ActiveRecord::Relation
+      def pivot_abstractions
+        select = prepare_pivot_select
+        joins = "JOIN
+        (
+        SELECT #{self.table_name}.id AS subject_id,
+        #{select}
+        FROM
+        (SELECT   aas.predicate
+                , aas.id AS abstractor_abstraction_schema_id
+                , asb.subject_type
+                , aa.about_id
+                , aa.value
+        FROM abstractor_abstractions aa JOIN abstractor_subjects asb            ON aa.abstractor_subject_id = asb.id
+                                        JOIN abstractor_abstraction_schemas aas ON asb.abstractor_abstraction_schema_id = aas.id
+        WHERE asb.subject_type = '#{self.to_s}'
+        AND NOT EXISTS (
+          SELECT 1
+          FROM abstractor_abstraction_group_members aagm
+          WHERE aa.id = aagm.abstractor_abstraction_id
+        )
+        ) data join #{self.table_name} ON  data.about_id = #{self.table_name}.id
+        GROUP BY #{self.table_name}.id
+        ) pivoted_abstractions ON pivoted_abstractions.subject_id = #{self.table_name}.id
+        "
+        joins(joins).select("#{self.table_name}.*, pivoted_abstractions.*")
+      end
+
+      ##
+      # Pivot grouped abstractions to simulate regular columns on an abstractable entity.
+      #
+      # Example: an ActiveRecod model RadationTreatment with the columns
+      # * 'treatment_date'
+      # * 'total_dose'
+      # And the abstractions grouped together with the name 'has_treatment_target':
+      # * 'has_anatomical_location'.
+      # * 'has_laterality'
+      #
+      # This method allows for the querying of the radiation_treatments table as if
+      # it was strucutred like so:
+      # 'select id, treatment_date, toatl_dose, has_anatomical_location, has_laterality from radiation_treatments'
+      #
+      # If an abstractable entity has multiple instances of grouped abstractions the entity will be returned mutlple times.
+      #
+      # @param [String] abstractor_subject_groups_name name of {Abstractor::Methods::Models:AbtractorSubjectGroup}
+      # @return ActiveRecord::Relation
+      # @see Abstractor::Methods::Models:AbtractorSubjectGroup
+
+      def pivot_grouped_abstractions(abstractor_subject_groups_name)
+        abstractor_subject_group = abstractor_subject_groups.detect { |abstractor_subject_group| abstractor_subject_group.name ==  abstractor_subject_groups_name }
+        select = prepare_pivot_select
+        joins = "JOIN
+        (
+        SELECT #{self.table_name}.id AS subject_id,
+        #{select}
+        FROM
+        (SELECT   aas.predicate
+                , aas.id AS abstraction_schema_id
+                , asb.subject_type
+                , aa.about_id
+                , aa.value
+                , aag.id AS abstractor_abstraction_group_id
+        FROM abstractor_abstractions aa JOIN abstractor_subjects asb                    ON aa.abstractor_subject_id = asb.id
+                                        JOIN abstractor_abstraction_schemas aas         ON asb.abstractor_abstraction_schema_id = aas.id
+                                        JOIN abstractor_abstraction_group_members aagm  ON aa.id = aagm.abstractor_abstraction_id
+                                        JOIN abstractor_abstraction_groups aag          ON aagm.abstractor_abstraction_group_id= aag.id
+        WHERE asb.subject_type = '#{self.to_s}'
+        AND aag.abstractor_subject_group_id = #{abstractor_subject_group.id}
+        ) data join #{self.table_name} ON  data.about_id = #{self.table_name}.id
+        GROUP BY #{self.table_name}.id, abstractor_abstraction_group_id
+        ) pivoted_abstractions ON pivoted_abstractions.subject_id = #{self.table_name}.id
+        "
+        joins(joins).select("#{self.table_name}.*, pivoted_abstractions.*")
+      end
+    end
+  end
+end