Class: KnowledgeBase
- Inherits:
-
Object
- Object
- KnowledgeBase
- 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
-
#databases ⇒ Object
Returns the value of attribute databases.
-
#dir ⇒ Object
Returns the value of attribute dir.
-
#entity_options ⇒ Object
Returns the value of attribute entity_options.
-
#format ⇒ Object
Returns the value of attribute format.
-
#indices ⇒ Object
Returns the value of attribute indices.
-
#namespace ⇒ Object
Returns the value of attribute namespace.
-
#registry ⇒ Object
Returns the value of attribute registry.
Class Method Summary collapse
Instance Method Summary collapse
- #_children(name, entity) ⇒ Object
- #_neighbours(name, entity) ⇒ Object
- #_parents(name, entity) ⇒ Object
- #_subset(name, source = :all, target = :all, options = {}) ⇒ Object
- #all(name, options = {}) ⇒ Object
- #all_databases ⇒ Object
- #annotate(entities, type, database = nil) ⇒ Object
- #children(name, entity) ⇒ Object
- #db_namespace(name) ⇒ Object
- #description(name) ⇒ Object
- #enrichment(name, entities, options = {}) ⇒ Object
- #entities ⇒ Object
- #entity_options_for(type, database_name = nil) ⇒ Object
- #entity_types ⇒ Object
- #fields(name) ⇒ Object
- #get_database(name, options = {}) ⇒ Object
- #get_index(name, options = {}) ⇒ Object
- #identifier_files(name) ⇒ Object
- #identify(name, entity) ⇒ Object
- #identify_source(name, entity) ⇒ Object
- #identify_target(name, entity) ⇒ Object
- #index_fields(name) ⇒ Object
- #info(name) ⇒ Object
-
#initialize(dir, namespace = nil) ⇒ KnowledgeBase
constructor
A new instance of KnowledgeBase.
- #neighbours(name, entity) ⇒ Object
- #parents(name, entity) ⇒ Object
- #produce(name, *rest, &block) ⇒ Object
- #register(name, file = nil, options = {}, &block) ⇒ Object
- #select_entities(name, entities, options = {}) ⇒ Object
- #setup(name, matches, reverse = false) ⇒ Object
- #source(name) ⇒ Object
- #source_index(name) ⇒ Object
- #source_type(name) ⇒ Object
- #subset(name, entities, options = {}, &block) ⇒ Object
- #syndicate(name, kb) ⇒ Object
- #target(name) ⇒ Object
- #target_index(name) ⇒ Object
- #target_type(name) ⇒ Object
- #translate(entities, type) ⇒ Object
- #traverse(rules) ⇒ Object
- #undirected(name) ⇒ Object
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 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 46 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 68 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 56 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, = {}) repo = get_index name, repo.subset(source, target) end |
#all(name, options = {}) ⇒ Object
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# File 'lib/rbbt/knowledge_base/query.rb', line 41 def all(name, ={}) repo = get_index name, 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 38 def annotate(entities, type, database = nil) format = @format[type] || type = (type, database) Misc.prepare_entity(entities, format, ) end |
#children(name, entity) ⇒ Object
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# File 'lib/rbbt/knowledge_base/query.rb', line 51 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 72 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 4 def enrichment(name, entities, = {}) database = get_database(name, ) 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 60 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 21 def (type, database_name = nil) = self. IndiferentHash.setup if and not IndiferentHash === = [type.to_s] || [Entity.formats[type.to_s].to_s] || {} [:format] = @format[type] if @format.include? :type namespace = self.namespace namespace = db_namespace(database_name) if namespace.nil? and database_name = {:organism => namespace}.merge() if database_name database = get_database(database_name) if database. and (database.[type] or database.[Entity.formats[type.to_s].to_s]) = .merge(database.[type] || database.[Entity.formats[type.to_s].to_s]) end end end |
#entity_types ⇒ Object
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# File 'lib/rbbt/knowledge_base/entity.rb', line 64 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 91 def get_database(name, = {}) name = name.to_s @databases[[name, ]] ||= begin fp = Misc.fingerprint([name,]) if .empty? key = name.to_s else fp = Misc.hash2md5() key = name.to_s + "_" + fp end key += '.database' Persist.memory("Database:" << [key, dir] * "@") do = .dup [:organism] ||= [:namespace] ||= self.namespace unless self.namespace.nil? persist_dir = dir persist_file = persist_dir[key].find file, = registry[name] = Misc.add_defaults , if and .any? = Misc.add_defaults , :persist_file => persist_file, :format => format, :persist => true if [:entity_options] ||= {} .each do |type, info| [:entity_options][type] ||= {} [:entity_options][type] = Misc.add_defaults [:entity_options][type], info end end = Misc.pull_keys , :persist database = if persist_file.exists? and [:persist] and not [:update] Log.low "Re-opening database #{ name } from #{ Misc.fingerprint persist_file }. #{}" Association.open(file, , ) else = Misc.add_defaults , if raise "Repo #{ name } not found and not registered" if file.nil? Log.medium "Opening database #{ name } from #{ Misc.fingerprint file }. #{}" Association.open(file, , ) 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, = {}) name = name.to_s @indices[[name, ]] ||= begin if .empty? key = name.to_s else fp = Misc.hash2md5() key = name.to_s + "_" + fp end Persist.memory("Index:" << [key, dir] * "@") do = .dup [:organism] ||= [:namespace] ||= self.namespace unless self.namespace.nil? persist_dir = dir persist_file = persist_dir[key].find file, = registry[name] = Misc.add_defaults , if and .any? = Misc.add_defaults , :persist_file => persist_file, :persist_dir => persist_dir, :format => format, :persist => true if [:entity_options] ||= {} .each do |type, info| [:entity_options][type] ||= {} [:entity_options][type] = Misc.add_defaults [:entity_options][type], info end end = Misc.pull_keys , :persist index = if persist_file.exists? and [:persist] and not [:update] Log.low "Re-opening index #{ name } from #{ Misc.fingerprint persist_file }. #{}" Association.index(file, , .dup) else = Misc.add_defaults , if raise "Repo #{ name } not found and not registered" if file.nil? Log.medium "Opening index #{ name } from #{ Misc.fingerprint file }. #{}" Association.index(file, , .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 68 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 115 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 100 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 108 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 145 def index_fields(name) get_index(name).fields end |
#info(name) ⇒ Object
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# File 'lib/rbbt/knowledge_base/registry.rb', line 154 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) = self. source_type, name = self. target_type, name undirected = self.undirected(name) == 'undirected' info = { :source => source, :target => target, :source_type => source_type, :target_type => target_type, :source_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 76 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 61 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 149 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, = {}, &block) if block_given? block.define_singleton_method(:filename) do name.to_s end Log.debug("Registering #{ name } from code block") @registry[name] = [block, ] else Log.debug("Registering #{ name }: #{ Misc.fingerprint file } #{Misc.fingerprint }") @registry[name] = [file, ] 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, = {}) index = get_index(name, ) 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] target_entities = entities[:target] || entities[target_field] || entities[Entity.formats[target_field].to_s] [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 76 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 52 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, = {}, &block) entities, = , entities if entities.nil? and Hash === 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 source, target = select_entities(name, entities, ) 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, 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.registry[database] = {} [:entity_options] = [:entity_options] [:undirected] = [:undirected] if if kb. [:entity_options] = kb..merge([:entity_options] || {}) end register(db_name, nil, ) 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 88 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 56 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 44 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 302 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 |