rbbt-util 5.44.1 → 6.0.3

data/lib/rbbt/association/item.rb

@@ -1,227 +1,227 @@
-require 'rbbt/entity'
-
-module AssociationItem
-  extend Object::Entity
-
-  annotation :knowledge_base
-  annotation :database
-  annotation :reverse
-
-  property :name => :single do
-    [source_entity, target_entity].collect{|e| e.respond_to?(:name)? e.name || e : e } * "~"
-  end 
-
-  property :full_name => :single do
-    database ? [database, name] * ":" : name
-  end 
-
-  property :invert => :both do
-    if Array === self
-      inverted = self.collect do |item|
-        s,_sep,t= item.partition "~"
-        new = [t,s] * _sep
-      end
-      self.annotate inverted
-      inverted.reverse = ! reverse
-      inverted
-    else
-      s,_sep,t= self.partition "~"
-      inverted = self.annotate([t,s] * _sep)
-      inverted.reverse = ! reverse
-      inverted
-    end
-  end
-
-  property :namespace => :both do
-    knowledge_base.namespace
-  end
-
-  property :part => :array2single do
-    self.clean_annotations.collect{|p| p.partition("~") }
-  end
-
-  property :target => :array2single do
-    self.part.collect{|p| p[2]}
-  end
-
-  property :source => :array2single do
-    self.clean_annotations.collect{|p| p[/[^~]+/] }
-  end
-
-  property :target_entity_type => :both do
-    Entity.formats[target_type].to_s
-  end
-
-  property :source_entity_type => :both do
-    Entity.formats[source_type].to_s
-  end
-
-  property :target_type => :both do
-    if reverse
-      knowledge_base.source(database)
-    else
-      knowledge_base.target(database)
-    end
-  end
-
-  property :source_type => :both do
-    if reverse
-      knowledge_base.target(database)
-    else
-      knowledge_base.source(database)
-    end
-  end
-
-  property :undirected => :both do
-    knowledge_base.undirected(database)
-  end
-
-  property :target_entity => :array2single do
-    type = target_type
-    knowledge_base.annotate self.target, type, database #if self.target.any?
-  end
-
-  property :source_entity => :array2single do
-    type = source_type
-    knowledge_base.annotate self.source, type, database #if self.source.any?
-  end
-
-  property :index => :both do |database|
-    @index ||= knowledge_base.get_index(database)
-  end
-  property :value => :array2single do
-    index = index(database)
-    value = self.reverse ? index.chunked_values_at(self.invert) : index.chunked_values_at(self)
-    value.collect{|v| NamedArray.setup(v, index.fields)}
-  end
-
-  property :info_fields => :both do
-    knowledge_base.index_fields(database)
-  end
-
-  property :info => :array2single do
-    fields = self.info_fields
-
-    return [{}] * self.length if fields.nil? or fields.empty?
-
-    value = self.value
-    value.collect{|v|
-      raise "No info for pair; not registered in index" if v.nil?
-      Hash[*fields.zip(v).flatten]
-    }
-  end
-
-  property :tsv => :array do
-    info_fields = self.info_fields
-    fields = [self.source_type, self.target_type].concat info_fields
-    type = [self.source_type, self.target_type] * "~"
-    tsv = TSV.setup({}, :key_field => type, :fields => fields, :type => :list, :namespace => self.namespace)
-    index = index(database)
-    index.with_unnamed do
-      index.chunked_values_at(self).each_with_index do |v,i|
-        p = self[i]
-        source, _sep, target = p.partition("~")
-        if info_fields.empty?
-          tsv[p] = [source, target]
-        else
-          tsv[p] = [source, target].concat v 
-        end
-      end
-    end
-    tsv.entity_options = {:organism => namespace}
-    knowledge_base.entity_options.each do |type,options|
-      tsv.entity_options.merge! options
-    end
-    tsv
-  end
-
-  property :filter => :array do |*args,&block|
-    block = args.pop if Proc === args.last
-    keys = tsv.with_unnamed do tsv.select(*args, &block).keys end
-    keys = self.annotate keys
-    keys
-  end
-
-  def self.incidence(pairs, key_field = nil, &block)
-    matrix = {}
-    targets = []
-    sources = []
-    matches = {}
-
-    pairs.inject([]){|acc,m| acc << m; acc << m.invert if m.respond_to?(:undirected) and m.undirected; acc  }.each do |p|
-      s, sep, t = p.partition "~"
-
-      sources << s
-      targets << t
-      if block_given?
-        matches[s] ||= Hash.new{nil}
-        value = block.call p
-        matches[s][t] = value unless value.nil? or (mv = matches[s][t] and value > mv)
-      else
-        matches[s] ||= Hash.new{false}
-        matches[s][t] ||= true 
-      end
-    end
-
-    sources.uniq!
-    targets = targets.uniq.sort
-
-    matches.each do |s,hash|
-      matrix[s] = hash.values_at(*targets)
-    end
-
-    defined?(TSV)? TSV.setup(matrix, :key_field => (key_field || "Source") , :fields => targets, :type => :list) : matrix
-  end
-
-  def self.adjacency(pairs, key_field = nil, &block)
-    incidence = incidence(pairs, key_field, &block)
-
-    targets = incidence.fields
-    adjacency = TSV.setup({}, :key_field => incidence.key_field, :fields => ["Target"], :type => :double)
-    TSV.traverse incidence, :into => adjacency, :unnamed => true do |k,values|
-      target_values = targets.zip(values).reject{|t,v| v.nil? }.collect{|t,v| [t,v]}
-      next if target_values.empty?
-      [k, Misc.zip_fields(target_values)]
-    end
-  end
-
-  def self._select_match(orig, elem)
-    if Array === orig and Array === elem
-      (orig & elem).any?
-    elsif Array === orig
-      orig.include? elem
-    elsif Array === elem
-      elem.include? orig
-    else
-      elem === orif
-    end
-    false
-  end
-
-  def self.select(list, method = nil, &block)
-    if method and method.any?
-      list.select do |item|
-        method.collect do |key,value|
-          case key
-          when :target
-            _select_match item.target, value
-          when :source
-            _select_match item.source, value
-          else
-            orig = item.info[key]
-            orig = orig.split(";;") if String orig
-            _select_match orig, value 
-          end
-        end
-      end
-    else
-      list.select(&block)
-    end
-  end
-end
-
-module TSV
-  def self.incidence(tsv)
-    AssociationItem.incidence Association.index(tsv, :persist => false).keys
-  end
-end
+#require_relative '../entity'
+#
+#module AssociationItem
+#  extend Entity
+#
+#  annotation :knowledge_base
+#  annotation :database
+#  annotation :reverse
+#
+#  property :name => :single do
+#    [source_entity, target_entity].collect{|e| e.respond_to?(:name)? e.name || e : e } * "~"
+#  end 
+#
+#  property :full_name => :single do
+#    database ? [database, name] * ":" : name
+#  end 
+#
+#  property :invert => :both do
+#    if Array === self
+#      inverted = self.collect do |item|
+#        s,_sep,t= item.partition "~"
+#        new = [t,s] * _sep
+#      end
+#      self.annotate inverted
+#      inverted.reverse = ! reverse
+#      inverted
+#    else
+#      s,_sep,t= self.partition "~"
+#      inverted = self.annotate([t,s] * _sep)
+#      inverted.reverse = ! reverse
+#      inverted
+#    end
+#  end
+#
+#  property :namespace => :both do
+#    knowledge_base.namespace
+#  end
+#
+#  property :part => :array2single do
+#    self.clean_annotations.collect{|p| p.partition("~") }
+#  end
+#
+#  property :target => :array2single do
+#    self.part.collect{|p| p[2]}
+#  end
+#
+#  property :source => :array2single do
+#    self.clean_annotations.collect{|p| p[/[^~]+/] }
+#  end
+#
+#  property :target_entity_type => :both do
+#    Entity.formats[target_type].to_s
+#  end
+#
+#  property :source_entity_type => :both do
+#    Entity.formats[source_type].to_s
+#  end
+#
+#  property :target_type => :both do
+#    if reverse
+#      knowledge_base.source(database)
+#    else
+#      knowledge_base.target(database)
+#    end
+#  end
+#
+#  property :source_type => :both do
+#    if reverse
+#      knowledge_base.target(database)
+#    else
+#      knowledge_base.source(database)
+#    end
+#  end
+#
+#  property :undirected => :both do
+#    knowledge_base.undirected(database)
+#  end
+#
+#  property :target_entity => :array2single do
+#    type = target_type
+#    knowledge_base.annotate self.target, type, database #if self.target.any?
+#  end
+#
+#  property :source_entity => :array2single do
+#    type = source_type
+#    knowledge_base.annotate self.source, type, database #if self.source.any?
+#  end
+#
+#  property :index => :both do |database|
+#    @index ||= knowledge_base.get_index(database)
+#  end
+#  property :value => :array2single do
+#    index = index(database)
+#    value = self.reverse ? index.chunked_values_at(self.invert) : index.chunked_values_at(self)
+#    value.collect{|v| NamedArray.setup(v, index.fields)}
+#  end
+#
+#  property :info_fields => :both do
+#    knowledge_base.index_fields(database)
+#  end
+#
+#  property :info => :array2single do
+#    fields = self.info_fields
+#
+#    return [{}] * self.length if fields.nil? or fields.empty?
+#
+#    value = self.value
+#    value.collect{|v|
+#      raise "No info for pair; not registered in index" if v.nil?
+#      Hash[*fields.zip(v).flatten]
+#    }
+#  end
+#
+#  property :tsv => :array do
+#    info_fields = self.info_fields
+#    fields = [self.source_type, self.target_type].concat info_fields
+#    type = [self.source_type, self.target_type] * "~"
+#    tsv = TSV.setup({}, :key_field => type, :fields => fields, :type => :list, :namespace => self.namespace)
+#    index = index(database)
+#    index.with_unnamed do
+#      index.chunked_values_at(self).each_with_index do |v,i|
+#        p = self[i]
+#        source, _sep, target = p.partition("~")
+#        if info_fields.empty?
+#          tsv[p] = [source, target]
+#        else
+#          tsv[p] = [source, target].concat v 
+#        end
+#      end
+#    end
+#    tsv.entity_options = {:namespace => namespace}
+#    knowledge_base.entity_options.each do |type,options|
+#      tsv.entity_options.merge! options
+#    end
+#    tsv
+#  end
+#
+#  property :filter => :array do |*args,&block|
+#    block = args.pop if Proc === args.last
+#    keys = tsv.with_unnamed do tsv.select(*args, &block).keys end
+#    keys = self.annotate keys
+#    keys
+#  end
+#
+#  def self.incidence(pairs, key_field = nil, &block)
+#    matrix = {}
+#    targets = []
+#    sources = []
+#    matches = {}
+#
+#    pairs.inject([]){|acc,m| acc << m; acc << m.invert if m.respond_to?(:undirected) and m.undirected; acc  }.each do |p|
+#      s, sep, t = p.partition "~"
+#
+#      sources << s
+#      targets << t
+#      if block_given?
+#        matches[s] ||= Hash.new{nil}
+#        value = block.call p
+#        matches[s][t] = value unless value.nil? or (mv = matches[s][t] and value > mv)
+#      else
+#        matches[s] ||= Hash.new{false}
+#        matches[s][t] ||= true 
+#      end
+#    end
+#
+#    sources.uniq!
+#    targets = targets.uniq.sort
+#
+#    matches.each do |s,hash|
+#      matrix[s] = hash.values_at(*targets)
+#    end
+#
+#    defined?(TSV)? TSV.setup(matrix, :key_field => (key_field || "Source") , :fields => targets, :type => :list) : matrix
+#  end
+#
+#  def self.adjacency(pairs, key_field = nil, &block)
+#    incidence = incidence(pairs, key_field, &block)
+#
+#    targets = incidence.fields
+#    adjacency = TSV.setup({}, :key_field => incidence.key_field, :fields => ["Target"], :type => :double)
+#    TSV.traverse incidence, :into => adjacency, :unnamed => true do |k,values|
+#      target_values = targets.zip(values).reject{|t,v| v.nil? }.collect{|t,v| [t,v]}
+#      next if target_values.empty?
+#      [k, Misc.zip_fields(target_values)]
+#    end
+#  end
+#
+#  def self._select_match(orig, elem)
+#    if Array === orig and Array === elem
+#      (orig & elem).any?
+#    elsif Array === orig
+#      orig.include? elem
+#    elsif Array === elem
+#      elem.include? orig
+#    else
+#      elem === orif
+#    end
+#    false
+#  end
+#
+#  def self.select(list, method = nil, &block)
+#    if method and method.any?
+#      list.select do |item|
+#        method.collect do |key,value|
+#          case key
+#          when :target
+#            _select_match item.target, value
+#          when :source
+#            _select_match item.source, value
+#          else
+#            orig = item.info[key]
+#            orig = orig.split(";;") if String orig
+#            _select_match orig, value 
+#          end
+#        end
+#      end
+#    else
+#      list.select(&block)
+#    end
+#  end
+#end
+#
+#module TSV
+#  def self.incidence(tsv)
+#    AssociationItem.incidence Association.index(tsv, :persist => false).keys
+#  end
+#end

data/lib/rbbt/association/open.rb

@@ -1,35 +1,36 @@
-require 'rbbt/association/database'
+#require 'rbbt/association/database'
 
-module Association
-  def self.version_file(file, namespace)
-    old_file, file = file, file.sub('NAMESPACE', namespace) if namespace and String === file
-    old_file.annotate file if Path === old_file
-    file
-  end
-  
-  def self.open(file, options = nil, persist_options = nil)
-    options = options.nil? ? {} : options.dup
-    persist_options = persist_options.nil? ?  Misc.pull_keys(options, :persist)  : persist_options.dup 
-
-    options = Misc.add_defaults options, :zipped => true, :merge => true, :monitor => {:desc => "Opening database #{Misc.fingerprint file}"}
-    options[:zipped] = false unless options[:merge]
-    persist_options = Misc.add_defaults persist_options.dup, :persist => true, :dir => Rbbt.var.associations
-    persist = persist_options[:persist]
-
-    file = version_file(file, options[:namespace]) if options[:namespace] and String === file
-
-    data = Persist.persist_tsv(file, nil, options, persist_options.merge(:prefix => "Association Database")) do |data|
-      file = file.call if Proc === file
-
-      options = options.dup
-      data.serializer = :double if data.respond_to? :serializer
-
-      tsv = Association.database(file, options.merge(:unnamed => true, :data => data, :type => :double))
-
-      data
-    end
-    data.entity_options = options[:entity_options] if options[:entity_options]
-    data
-  end
-  
-end
+#module Association
+#  def self.version_file(file, namespace)
+#    old_file, file = file, file.sub('NAMESPACE', namespace) if namespace and String === file
+#    old_file.annotate file if Path === old_file
+#    file
+#  end
+#  
+#  def self.open(file, options = nil, persist_options = nil)
+#    options = options.nil? ? {} : options.dup
+#    persist_options = persist_options.nil? ?  IndiferentHash.pull_keys(options, :persist)  : persist_options.dup 
+#
+#    options = IndiferentHash.add_defaults options, :zipped => true, :merge => true, :monitor => {:desc => "Opening database #{Log.fingerprint file}"}
+#    options[:zipped] = false unless options[:merge]
+#    persist_options = IndiferentHash.add_defaults persist_options.dup, :persist => true, :dir => Rbbt.var.associations
+#    persist = persist_options[:persist]
+#
+#    file = version_file(file, options[:namespace]) if options[:namespace] and String === file
+#
+#    data = Persist.persist_tsv(file, nil, options, persist_options.merge(:prefix => "Association Database")) do |data|
+#      data = {} if data.nil?
+#      file = file.call if Proc === file
+#
+#      options = options.dup
+#      data.serializer = :double if data.respond_to? :serializer
+#
+#      tsv = Association.database(file, options.merge(:unnamed => true, :data => data, :type => :double))
+#
+#      data
+#    end
+#    data.entity_options = options[:entity_options] if options[:entity_options]
+#    data
+#  end
+#  
+#end