Class: KnowledgeBase

Inherits:
Object
  • Object
show all
Defined in:
lib/rbbt/knowledge_base.rb,
lib/rbbt/knowledge_base/query.rb,
lib/rbbt/knowledge_base/entity.rb,
lib/rbbt/knowledge_base/registry.rb,
lib/rbbt/knowledge_base/traverse.rb,
lib/rbbt/knowledge_base/syndicate.rb,
lib/rbbt/knowledge_base/enrichment.rb

Defined Under Namespace

Classes: Traverser

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(dir, namespace = nil) ⇒ KnowledgeBase

Returns a new instance of KnowledgeBase.



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# File 'lib/rbbt/knowledge_base.rb', line 11

def initialize(dir, namespace = nil)
  @dir = Path.setup(dir.dup)

  @namespace = namespace
  @format = IndiferentHash.setup({})

  @registry ||= IndiferentHash.setup({})
  @entity_options = IndiferentHash.setup({})

  @indices = IndiferentHash.setup({})
  @databases = IndiferentHash.setup({})
  @identifiers = IndiferentHash.setup({})
  @fields = {}
  @descriptions = {}
  @databases = {}
end

Instance Attribute Details

#databases ⇒ Object

Returns the value of attribute databases.



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# File 'lib/rbbt/knowledge_base.rb', line 10

def databases
  @databases
end

#dir ⇒ Object

Returns the value of attribute dir.



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# File 'lib/rbbt/knowledge_base.rb', line 10

def dir
  @dir
end

#entity_options ⇒ Object

Returns the value of attribute entity_options.



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# File 'lib/rbbt/knowledge_base.rb', line 10

def entity_options
  @entity_options
end

#format ⇒ Object

Returns the value of attribute format.



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# File 'lib/rbbt/knowledge_base.rb', line 10

def format
  @format
end

#indices ⇒ Object

Returns the value of attribute indices.



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# File 'lib/rbbt/knowledge_base.rb', line 10

def indices
  @indices
end

#namespace ⇒ Object

Returns the value of attribute namespace.



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# File 'lib/rbbt/knowledge_base.rb', line 10

def namespace
  @namespace
end

#registry ⇒ Object

Returns the value of attribute registry.



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# File 'lib/rbbt/knowledge_base.rb', line 10

def registry
  @registry
end

Class Method Details

.load(dir) ⇒ Object 



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# File 'lib/rbbt/knowledge_base.rb', line 28

def self.load(dir)
  KnowledgeBase.new dir
end

Instance Method Details

#_children(name, entity) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/query.rb', line 55

def _children(name, entity)
  repo = get_index name
  repo.match(entity)
end

#_neighbours(name, entity) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/query.rb', line 77

def _neighbours(name, entity)
  if undirected(name) and source(name) == target(name)
    {:children => _children(name, entity)}
  else
    {:parents => _parents(name, entity), :children => _children(name, entity)}
  end
end

#_parents(name, entity) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/query.rb', line 65

def _parents(name, entity)
  repo = get_index name
  repo.reverse.match(entity)
end

#_subset(name, source = :all, target = :all, options = {}) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/query.rb', line 5

def _subset(name, source = :all, target = :all, options = {})
  repo = get_index name, options

  repo.subset(source, target)
end

#all(name, options = {}) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/query.rb', line 50

def all(name, options={})
  repo = get_index name, options
  setup name, repo.keys
end

#all_databases ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 17

def all_databases
  @registry.keys 
end

#annotate(entities, type, database = nil) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 39

def annotate(entities, type, database = nil)
  format = @format[type] || type
  entity_options = entity_options_for(type, database)
  Misc.prepare_entity(entities, format, entity_options)
end

#children(name, entity) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/query.rb', line 60

def children(name, entity)
  entity = identify_source(name, entity)
  setup(name, _children(name, entity))
end

#db_namespace(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 73

def db_namespace(name)
  get_database(name).namespace
end

#description(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 25

def description(name)
  @descriptions[name] ||= get_index(name).key_field.split("~")
end

#enrichment(name, entities, options = {}) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/enrichment.rb', line 3

def enrichment(name, entities, options = {})
  require 'rbbt/statistics/hypergeometric'
  database = get_database(name, options)
  entities = identify_source name, entities
  database.enrichment entities, database.fields.first, :persist => false
end

#entities ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 61

def entities
  all_databases.inject([]){|acc,name| acc << source(name); acc << target(name)}.uniq
end

#entity_options_for(type, database_name = nil) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 22

def entity_options_for(type, database_name = nil)
  entity_options = self.entity_options
  IndiferentHash.setup entity_options if entity_options and not IndiferentHash === entity_options
  options = entity_options[type.to_s] || entity_options[Entity.formats[type.to_s].to_s] || {}
  options[:format] = @format[type] if Hash === @format && @format.include?(type)
  namespace = self.namespace
  namespace = db_namespace(database_name) if namespace.nil? and database_name
  options = {:organism => namespace}.merge(options)
  if database_name  
    database = get_database(database_name)
    if database.entity_options and (database.entity_options[type] or database.entity_options[Entity.formats[type.to_s].to_s])
      options = options.merge(database.entity_options[type] || database.entity_options[Entity.formats[type.to_s].to_s])
    end
  end
  options
end

#entity_types ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 65

def entity_types
  entities.collect{|entity| Entity.formats[entity] }.uniq
end

#fields(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 21

def fields(name)
  @fields[name] ||= get_index(name).fields
end

#get_database(name, options = {}) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 93

def get_database(name, options = {})
  name = name.to_s

  options = options.dup
  if self.namespace == options[:namespace]
    options.delete(:namespace) 
  end
  if self.namespace == options[:organism]
    options.delete(:organism) 
  end
  @databases[[name, options]] ||= 
    begin 
      fp = Misc.fingerprint([name,options])

      if options.empty?
        key = name.to_s
      else
        fp = Misc.hash2md5(options)
        key = name.to_s + "_" + fp
      end

      options[:organism] ||= options[:namespace] ||= self.namespace unless self.namespace.nil?

      key += '.database'
      Persist.memory("Database:" << [key, dir] * "@") do
        options = options.dup

        persist_dir = dir
        persist_file = persist_dir[key].find
        file, registered_options = registry[name]

        options = Misc.add_defaults options, registered_options if registered_options and registered_options.any?
        options = Misc.add_defaults options, :persist_file => persist_file, :format => format, :persist => true

        if entity_options
          options[:entity_options] ||= {}
          entity_options.each do |type, info|
            options[:entity_options][type] ||= {}
            options[:entity_options][type] = Misc.add_defaults options[:entity_options][type], info
          end
        end

        persist_options = Misc.pull_keys options, :persist

        database = if persist_file.exists? and persist_options[:persist] and not persist_options[:update]
                     Log.low "Re-opening database #{ name } from #{ Misc.fingerprint persist_file }. #{options}"
                     Association.open(file, options, persist_options)
                   else
                     options = Misc.add_defaults options, registered_options if registered_options
                     raise "Repo #{ name } not found and not registered" if file.nil?
                     Log.medium "Opening database #{ name } from #{ Misc.fingerprint file }. #{options}"
                     Association.open(file, options, persist_options)
                   end

        database.namespace = self.namespace if self.namespace

        database
      end
    end
end

#get_index(name, options = {}) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 41

def get_index(name, options = {})
  name = name.to_s
  options[:organism] ||= options[:namespace] ||= self.namespace unless self.namespace.nil?
  @indices[[name, options]] ||= 
    begin 
      if options.empty?
        key = name.to_s
      elsif options[:key]
        key = options[:key]
        key = name if key == :name
      else
        fp = Misc.hash2md5(options)
        key = name.to_s + "_" + fp
      end

      Persist.memory("Index:" << [key, dir] * "@") do
        options = options.dup

        persist_dir = dir
        persist_file = persist_dir[key].find
        file, registered_options = registry[name]

        options = Misc.add_defaults options, registered_options if registered_options and registered_options.any?
        options = Misc.add_defaults options, :persist_file => persist_file, :persist_dir => persist_dir, :format => format, :persist => true

        if entity_options
          options[:entity_options] ||= {}
          entity_options.each do |type, info|
            options[:entity_options][type] ||= {}
            options[:entity_options][type] = Misc.add_defaults options[:entity_options][type], info
          end
        end

        persist_options = Misc.pull_keys options, :persist

        index = if persist_file.exists? and persist_options[:persist] and not persist_options[:update]
                  Log.low "Re-opening index #{ name } from #{ Misc.fingerprint persist_file }. #{options}"
                  Association.index(file, options, persist_options.dup)
                else
                  options = Misc.add_defaults options, registered_options if registered_options
                  raise "Repo #{ name } not found and not registered" if file.nil?
                  Log.medium "Opening index #{ name } from #{ Misc.fingerprint file }. #{options}"
                  Association.index(file, options, persist_options.dup)
                end

        index.namespace = self.namespace unless self.namespace

        index
      end
    end
end

#identifier_files(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 69

def identifier_files(name)
  get_database(name).identifier_files.dup
end

#identify(name, entity) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 116

def identify(name, entity)
  identify_source(name, entity) || identify_target(name, entity)
end

#identify_source(name, entity) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 101

def identify_source(name, entity)
  return :all if entity == :all
  index = source_index(name)
  return entity if index.nil?
  Array === entity ? index.values_at(*entity) : index[entity]
end

#identify_target(name, entity) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 109

def identify_target(name, entity)
  return :all if entity == :all
  index = target_index(name)
  return entity if index.nil?
  Array === entity ? index.values_at(*entity) : index[entity]
end

#index_fields(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 154

def index_fields(name)
  get_index(name).fields
end

#info(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 163

def info(name)

  source = self.source(name)
  target = self.target(name)
  source_type = self.source_type(name)
  target_type = self.target_type(name)
  fields = self.fields(name)
  source_entity_options = self.entity_options_for source_type, name
  target_entity_options = self.entity_options_for target_type, name
  undirected = self.undirected(name) == 'undirected'

  info = {
    :source => source,
    :target => target,
    :source_type => source_type,
    :target_type => target_type,
    :source_entity_options => source_entity_options,
    :target_entity_options => target_entity_options,
    :fields => fields,
    :undirected => undirected,
  }

  info
end

#neighbours(name, entity) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/query.rb', line 85

def neighbours(name, entity)
  hash = _neighbours(name, entity)
  IndiferentHash.setup(hash)
  setup(name, hash[:children]) if hash[:children] 
  setup(name, hash[:parents], true) if hash[:parents]
  hash
end

#parents(name, entity) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/query.rb', line 70

def parents(name, entity)
  entity = identify_target(name, entity)
  matches = _parents(name, entity)
  #matches.each{|m| m.replace(m.partition("~").reverse*"") } unless undirected(name)
  setup(name, matches, true)
end

#produce(name, *rest, &block) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 158

def produce(name, *rest,&block)
  register(name, *rest, &block)
  get_index(name)
end

#register(name, file = nil, options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 6

def register(name, file = nil, options = {}, &block)
  if block_given?
    block.define_singleton_method(:filename) do name.to_s end
    Log.debug("Registering #{ name } from code block")
    @registry[name] = [block, options]
  else
    Log.debug("Registering #{ name }: #{ Misc.fingerprint file } #{Misc.fingerprint options}")
    @registry[name] = [file, options]
  end
end

#select_entities(name, entities, options = {}) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 6

def select_entities(name, entities, options = {})
  index = get_index(name, options)

  source_field = index.source_field
  target_field = index.target_field

  source_type = Entity.formats[source_field] 
  target_type = Entity.formats[target_field]

  source_entities = entities[:source] || entities[source_field] || entities[Entity.formats[source_field].to_s] || entities[:both]
  target_entities = entities[:target] || entities[target_field] || entities[Entity.formats[target_field].to_s] || entities[:both]

  [source_entities, target_entities]
end

#setup(name, matches, reverse = false) ⇒ Object 



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# File 'lib/rbbt/knowledge_base.rb', line 32

def setup(name, matches, reverse = false)
  AssociationItem.setup matches, self, name, reverse
end

#source(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 29

def source(name)
  description(name)[0]
end

#source_index(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 77

def source_index(name)
  Persist.memory("Source index #{name}: KB directory #{dir}") do
    identifier_files = identifier_files(name)
    identifier_files.concat Entity.identifier_files(source(name)) if defined? Entity
    identifier_files.uniq!
    identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, namespace))} if namespace
    identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, db_namespace(name)))} if not namespace and db_namespace(name)
    identifier_files.reject!{|f| f.match(/\bNAMESPACE\b/)}
    TSV.translation_index identifier_files, source(name), nil, :persist => true
  end
end

#source_type(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 53

def source_type(name)
  Entity.formats[source(name)]
end

#subset(name, entities, options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/query.rb', line 11

def subset(name, entities, options = {}, &block)
  entities, options = options, entities if entities.nil? and Hash === options

  entities = case entities
             when :all
               {:target => :all, :source => :all}
             when AnnotatedArray
               format = entities.format if entities.respond_to? :format 
               format ||= entities.base_entity.to_s
               {format => entities.clean_annotations}
             when Hash
               entities
             else
               raise "Entities are not a Hash or an AnnotatedArray: #{Misc.fingerprint entities}"
             end

  identify, identify_source, identify_target = entities.merge(options || {}).values_at :identify, :identify_source, :identify_target

  source, target = select_entities(name, entities, options)
  
  source = identify_source(name, source) if identify_source
  target = identify_target(name, target) if identify_target

  source = identify(name, source) if identify && !identify_source
  target = identify(name, target) if identify && !identify_target

  return [] if source.nil? or target.nil?
  return [] if Array === target and target.empty?
  return [] if Array === source and source.empty?

  matches = _subset name, source, target, options

  setup(name, matches)

  matches = matches.select(&block) if block_given? 

  matches
end

#syndicate(name, kb) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/syndicate.rb', line 2

def syndicate(name, kb)
  kb.all_databases.each do |database|
    if name.nil?
      db_name = database
    else
      db_name = [database, name] * "@"
    end
    file, kb_options = kb.registry[database]
    options = {}
    options[:entity_options] = kb_options[:entity_options]
    options[:undirected] = kb_options[:undirected] if kb_options 
    if kb.entity_options
      options[:entity_options] = kb.entity_options.merge(options[:entity_options] || {})
    end

    register(db_name, nil, options) do
      kb.get_database(database)
    end
  end
end

#target(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 33

def target(name)
  description(name)[1]
end

#target_index(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 89

def target_index(name)
  Persist.memory("Target index #{name}: KB directory #{dir}") do
    identifier_files = identifier_files(name)
    identifier_files.concat Entity.identifier_files(target(name)) if defined? Entity
    identifier_files.uniq!
    identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, namespace))} if self.namespace
    identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, db_namespace(name)))} if namespace.nil? and db_namespace(name)
    identifier_files.reject!{|f| f.match(/\bNAMESPACE\b/)}
    TSV.translation_index identifier_files, target(name), nil, :persist => true
  end
end

#target_type(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 57

def target_type(name)
  Entity.formats[target(name)]
end

#translate(entities, type) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/entity.rb', line 45

def translate(entities, type)
  if format = @format[type] and (entities.respond_to? :format and format != entities.format)
    entities.to format
  else
    entities
  end
end

#traverse(rules) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/traverse.rb', line 310

def traverse(rules)
  traverser = KnowledgeBase::Traverser.new self, rules
  traverser.traverse
end

#undirected(name) ⇒ Object 



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# File 'lib/rbbt/knowledge_base/registry.rb', line 37

def undirected(name)
  description(name)[2]
end