rbbt-util 5.44.1 → 6.0.4

data/lib/rbbt/tsv/change_id.rb

@@ -1,245 +1,244 @@
-require 'rbbt/tsv'
-require 'rbbt/persist'
-
-
-module TSV
-  def self.change_key(tsv, format, options = {}, &block)
-    options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers
-
-    identifiers, persist_input = Misc.process_options options, :identifiers, :persist_input
-
-    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? && tsv.namespace && 
-      defined?(Organism) && Organism.identifiers(tsv.namespace).exists?
-
-    if ! tsv.fields.include?(format)
-      new = {}
-      tsv.each do |k,v|
-        if v === String or v === Array
-          new[k] = v.dup 
-        else
-          new[k] = v
-        end
-      end
-      orig_fields = tsv.fields
-      tsv = tsv.annotate new
-      new.fields = new.fields.collect{|f| "TMP-" << f }
-
-      orig_type = tsv.type 
-      tsv = tsv.to_double if orig_type != :double
-
-      if Array === identifiers
-        tsv = tsv.attach identifiers.first, :fields => [format], :persist_input => true, :identifiers => identifiers.last
-      else
-        tsv = tsv.attach identifiers, :fields => [format], :persist_input => true
-      end
-
-
-      tsv = tsv.reorder(format, tsv.fields[0..-2])
-
-      tsv = tsv.to_flat  if orig_type == :flat
-
-      tsv = tsv.to_list(&block)  if orig_type == :list
-
-      tsv.fields = orig_fields
-
-      tsv
-    else
-      tsv.reorder(format)
-    end
-  end
-
-  def change_key(format, options = {}, &block)
-    options = Misc.add_defaults options, :identifiers => self.identifiers
-    TSV.change_key(self, format, options, &block)
-  end
-
-  def self.swap_id(tsv, field, format, options = {}, &block)
-    options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers, :compact => true
-
-    identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
-    identifiers = tsv.identifier_files.first if identifiers.nil?
-
-    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? && tsv.namespace && 
-      defined?(Organism) && Organism.identifiers(tsv.namespace).exists?
-
-    identifiers.namespace ||= tsv.namespace
-
-    fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil 
-    #index = identifiers.index :target => format, :fields => fields, :persist => persist_input, :order => true
-
-    grep = Organism.blacklist_genes(tsv.namespace).list  if defined?(Organism) && identifiers.namespace && Organism.blacklist_genes(tsv.namespace).exists?
-    if fields.nil?
-      index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :persist => true, :order => true, :unnamed => true, :data_persist => true)
-    else
-      index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :fields => fields, :order => true, :unnamed => true, :persist => true, :data_persist => true)
-    end
-
-    orig_type = tsv.type 
-    tsv = tsv.to_double if orig_type != :double
-
-    pos = tsv.fields.index field
-    tsv.with_unnamed do
-      if tsv.type == :list or tsv.type == :single
-        tsv.through do |k,v|
-          v[pos] = index[v[pos]]
-          tsv[k] = v
-        end
-      else
-        tsv.through do |k,v|
-          _values = index.values_at(*v[pos])
-          _values.compact! if compact
-          v[pos] = _values
-          tsv[k] = v
-        end
-      end
-
-      tsv.fields = tsv.fields.collect{|f| f == field ? format : f}
-    end
-
-    tsv = tsv.to_flat  if orig_type == :flat
-
-    tsv = tsv.to_list(&block)  if orig_type == :list
-
-    tsv
-  end
-
-  def swap_id(*args)
-    TSV.swap_id(self, *args)
-  end
-
-  def self.translation_index(files, target = nil, source = nil, options = {})
-    return nil if source == target
-    options = Misc.add_defaults options.dup, :persist => true
-
-    target = Entity.formats.find(target) if Entity.formats.find(target)
-    source = Entity.formats.find(source) if Entity.formats.find(source)
-    fields = (source and not source.empty?) ? [source] : nil
-
-    files.each do |file|
-      if TSV === file
-        all_fields = file.all_fields
-        target = file.fields.first if target.nil?
-        if (source.nil? or all_fields.include? source) and all_fields.include? target
-          return file.index(options.merge(:target => target, :fields => fields, :order => true)) 
-        end
-      else
-        next unless file.exists?
-        begin
-          all_fields = TSV.parse_header(file).all_fields
-          target = all_fields[1] if target.nil?
-          if (source.nil? or all_fields.include? source) and all_fields.include? target
-            index = TSV.index(file, options.merge(:target => target, :fields => fields, :order => true)) 
-            return index
-          end
-        rescue Exception
-          Log.exception $!
-          Log.error "Exception reading identifier file: #{file.find}"
-        end
-      end
-    end
-
-    files.each do |file|
-      all_fields = TSV === file ? file.all_fields : TSV.parse_header(file).all_fields 
-
-      files.each do |other_file|
-        next if file == other_file
-
-        other_all_fields = TSV === other_file ? other_file.all_fields : TSV.parse_header(other_file).all_fields 
-
-        common_field = (all_fields & other_all_fields).first
-
-        if common_field and (source.nil? or source.empty? or all_fields.include? source) and other_all_fields.include? target 
-
-          index = Persist.persist_tsv(nil, Misc.fingerprint(files), {:files => files, :source => source, :target => target}, :prefix => "Translation index", :persist => options[:persist]) do |data|
-
-            index = TSV === file ? 
-              file.index(options.merge(:target => common_field, :fields => fields)) :
-              TSV.index(file, options.merge(:target => common_field, :fields => fields))
-
-            other_index = TSV === other_file ? 
-              other_file.index(options.merge(:target => target, :fields => [common_field])) :
-              TSV.index(other_file, options.merge(:target => target, :fields => [common_field]))
-
-            data.serializer = :clean
-            
-            # ToDo: remove the need to to the `to_list` transformation
-            data.merge! index.to_list.attach(other_index.to_list).slice([target]).to_single
-          end
-          return index
-        end
-      end
-    end
-    return nil
-  end
-
-  def self.translate(tsv, field, format, options = {})
-    persist_options = Misc.pull_keys options, :persist
-    new = TSV.open translate_stream(tsv, field, format, options), :persist => persist_options[:persist], :persist_data => persist_options[:data], :persist_file => persist_options[:file]
-    new.identifiers = tsv.identifiers
-    new
-  end
-
-  def self.translate_stream(tsv, field, format, options = {}, &block)
-    options = Misc.add_defaults options, :persist => false, :identifier_files => tsv.identifier_files, :compact => true
-
-    identifier_files, identifiers, persist_input, compact = Misc.process_options options, :identifier_files, :identifiers, :persist, :compact
-    identifier_files = [tsv, identifiers].compact if identifier_files.nil? or identifier_files.empty?
-
-    identifier_files.uniq!
-
-    index = translation_index identifier_files, format, field, options.dup
-    raise "No index: #{Misc.fingerprint([identifier_files, field, format])}" if index.nil?
-
-    orig_type = tsv.type 
-    tsv = tsv.to_double if orig_type != :double
-
-    pos = tsv.identify_field field
-
-    new_options = tsv.options
-    new_options[:identifiers] = tsv.identifiers.find if tsv.identifiers
-
-    case pos
-    when :key
-      new_options[:key_field] = format if tsv.key_field == field
-      dumper = TSV::Dumper.new new_options
-      dumper.init
-      TSV.traverse tsv, :into => dumper do |key,values|
-        new_key = index[key]
-        [new_key, values]
-      end
-    else
-      new_options[:fields] = tsv.fields.collect{|f| f == field ? format : f }
-      dumper = TSV::Dumper.new new_options
-      dumper.init
-
-      case tsv.type
-      when :double
-        TSV.traverse tsv, :into => dumper do |key,values|
-          original = values[pos]
-          new = index.values_at *original
-          values[pos] = new
-          [key, values]
-        end
-      when :list
-        TSV.traverse tsv, :into => dumper do |key,values|
-          original = values[pos]
-          new = index[original]
-          values[pos] = new
-          [key, values]
-        end
-      when :flat
-        TSV.traverse tsv, :into => dumper do |key,values|
-          new = index.values_at *values
-          [key, new]
-        end
-      when :single
-        TSV.traverse tsv, :into => dumper do |key,original|
-          new = index[original]
-          [key, new]
-        end
-      end
-    end
-
-    dumper.stream
-  end
-end
+require_relative '../refactor'
+Rbbt.require_instead 'scout/tsv'
+#require 'rbbt/tsv'
+#require 'rbbt/persist'
+#
+#
+#module TSV
+#  def self.change_key(tsv, format, options = {}, &block)
+#    options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers
+#
+#    identifiers, persist_input = Misc.process_options options, :identifiers, :persist_input
+#
+#    identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace
+#
+#
+#    if ! tsv.fields.include?(format)
+#      new = {}
+#      tsv.each do |k,v|
+#        if v === String or v === Array
+#          new[k] = v.dup 
+#        else
+#          new[k] = v
+#        end
+#      end
+#      orig_fields = tsv.fields
+#      tsv = tsv.annotate new
+#      new.fields = new.fields.collect{|f| "TMP-" << f }
+#
+#      orig_type = tsv.type 
+#      tsv = tsv.to_double if orig_type != :double
+#
+#      if Array === identifiers
+#        tsv = tsv.attach identifiers.first, :fields => [format], :persist_input => true, :identifiers => identifiers.last
+#      else
+#        tsv = tsv.attach identifiers, :fields => [format], :persist_input => true
+#      end
+#
+#
+#      tsv = tsv.reorder(format, tsv.fields[0..-2])
+#
+#      tsv = tsv.to_flat  if orig_type == :flat
+#
+#      tsv = tsv.to_list(&block)  if orig_type == :list
+#
+#      tsv.fields = orig_fields
+#
+#      tsv
+#    else
+#      tsv.reorder(format)
+#    end
+#  end
+#
+#  def change_key(format, options = {}, &block)
+#    options = Misc.add_defaults options, :identifiers => self.identifiers
+#    TSV.change_key(self, format, options, &block)
+#  end
+#
+#  def self.swap_id(tsv, field, format, options = {}, &block)
+#    options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers, :compact => true
+#
+#    identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
+#    identifiers = tsv.identifier_files.first if identifiers.nil?
+#    identifiers = Organism.identifiers(tsv.namespace) if defined?(Organism) && identifiers.nil? && tsv.namespace && Organism.identifiers(tsv.namespace).exists?
+#    identifiers.namespace ||= tsv.namespace
+#
+#    fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil 
+#    #index = identifiers.index :target => format, :fields => fields, :persist => persist_input, :order => true
+#
+#    grep = Organism.blacklist_genes(tsv.namespace).list  if defined?(Organism) && identifiers.namespace && Organism.blacklist_genes(tsv.namespace).exists?
+#    if fields.nil?
+#      index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :persist => true, :order => true, :unnamed => true, :data_persist => true)
+#    else
+#      index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :fields => fields, :order => true, :unnamed => true, :persist => true, :data_persist => true)
+#    end
+#
+#    orig_type = tsv.type 
+#    tsv = tsv.to_double if orig_type != :double
+#
+#    pos = tsv.fields.index field
+#    tsv.with_unnamed do
+#      if tsv.type == :list or tsv.type == :single
+#        tsv.through do |k,v|
+#          v[pos] = index[v[pos]]
+#          tsv[k] = v
+#        end
+#      else
+#        tsv.through do |k,v|
+#          _values = index.values_at(*v[pos])
+#          _values.compact! if compact
+#          v[pos] = _values
+#          tsv[k] = v
+#        end
+#      end
+#
+#      tsv.fields = tsv.fields.collect{|f| f == field ? format : f}
+#    end
+#
+#    tsv = tsv.to_flat  if orig_type == :flat
+#
+#    tsv = tsv.to_list(&block)  if orig_type == :list
+#
+#    tsv
+#  end
+#
+#  def swap_id(*args)
+#    TSV.swap_id(self, *args)
+#  end
+#
+#  def self.translation_index(files, target = nil, source = nil, options = {})
+#    return nil if source == target
+#    options = Misc.add_defaults options.dup, :persist => true
+#
+#    target = Entity.formats.find(target) if Entity.formats.find(target)
+#    source = Entity.formats.find(source) if Entity.formats.find(source)
+#    fields = (source and not source.empty?) ? [source] : nil
+#
+#    files.each do |file|
+#      if TSV === file
+#        all_fields = file.all_fields
+#        target = file.fields.first if target.nil?
+#        if (source.nil? or all_fields.include? source) and all_fields.include? target
+#          return file.index(options.merge(:target => target, :fields => fields, :order => true)) 
+#        end
+#      else
+#        next unless file.exists?
+#        begin
+#          all_fields = TSV.parse_header(file).all_fields
+#          target = all_fields[1] if target.nil?
+#          if (source.nil? or all_fields.include? source) and all_fields.include? target
+#            index = TSV.index(file, options.merge(:target => target, :fields => fields, :order => true)) 
+#            return index
+#          end
+#        rescue Exception
+#          Log.exception $!
+#          Log.error "Exception reading identifier file: #{file.find}"
+#        end
+#      end
+#    end
+#
+#    files.each do |file|
+#      all_fields = TSV === file ? file.all_fields : TSV.parse_header(file).all_fields 
+#
+#      files.each do |other_file|
+#        next if file == other_file
+#
+#        other_all_fields = TSV === other_file ? other_file.all_fields : TSV.parse_header(other_file).all_fields 
+#
+#        common_field = (all_fields & other_all_fields).first
+#
+#        if common_field and (source.nil? or source.empty? or all_fields.include? source) and other_all_fields.include? target 
+#
+#          index = Persist.persist_tsv(nil, Misc.fingerprint(files), {:files => files, :source => source, :target => target}, :prefix => "Translation index", :persist => options[:persist]) do |data|
+#
+#            index = TSV === file ? 
+#              file.index(options.merge(:target => common_field, :fields => fields)) :
+#              TSV.index(file, options.merge(:target => common_field, :fields => fields))
+#
+#            other_index = TSV === other_file ? 
+#              other_file.index(options.merge(:target => target, :fields => [common_field])) :
+#              TSV.index(other_file, options.merge(:target => target, :fields => [common_field]))
+#
+#            data.serializer = :clean
+#            
+#            # ToDo: remove the need to to the `to_list` transformation
+#            data.merge! index.to_list.attach(other_index.to_list).slice([target]).to_single
+#          end
+#          return index
+#        end
+#      end
+#    end
+#    return nil
+#  end
+#
+#  def self.translate(tsv, field, format, options = {})
+#    persist_options = Misc.pull_keys options, :persist
+#    new = TSV.open translate_stream(tsv, field, format, options), :persist => persist_options[:persist], :persist_data => persist_options[:data], :persist_file => persist_options[:file]
+#    new.identifiers = tsv.identifiers
+#    new
+#  end
+#
+#  def self.translate_stream(tsv, field, format, options = {}, &block)
+#    options = Misc.add_defaults options, :persist => false, :identifier_files => tsv.identifier_files, :compact => true
+#
+#    identifier_files, identifiers, persist_input, compact = Misc.process_options options, :identifier_files, :identifiers, :persist, :compact
+#    identifier_files = [tsv, identifiers].compact if identifier_files.nil? or identifier_files.empty?
+#
+#    identifier_files.uniq!
+#
+#    index = translation_index identifier_files, format, field, options.dup
+#    raise "No index: #{Misc.fingerprint([identifier_files, field, format])}" if index.nil?
+#
+#    orig_type = tsv.type 
+#    tsv = tsv.to_double if orig_type != :double
+#
+#    pos = tsv.identify_field field
+#
+#    new_options = tsv.options
+#    new_options[:identifiers] = tsv.identifiers.find if tsv.identifiers
+#
+#    case pos
+#    when :key
+#      new_options[:key_field] = format if tsv.key_field == field
+#      dumper = TSV::Dumper.new new_options
+#      dumper.init
+#      TSV.traverse tsv, :into => dumper do |key,values|
+#        new_key = index[key]
+#        [new_key, values]
+#      end
+#    else
+#      new_options[:fields] = tsv.fields.collect{|f| f == field ? format : f }
+#      dumper = TSV::Dumper.new new_options
+#      dumper.init
+#
+#      case tsv.type
+#      when :double
+#        TSV.traverse tsv, :into => dumper do |key,values|
+#          original = values[pos]
+#          new = index.values_at *original
+#          values[pos] = new
+#          [key, values]
+#        end
+#      when :list
+#        TSV.traverse tsv, :into => dumper do |key,values|
+#          original = values[pos]
+#          new = index[original]
+#          values[pos] = new
+#          [key, values]
+#        end
+#      when :flat
+#        TSV.traverse tsv, :into => dumper do |key,values|
+#          new = index.values_at *values
+#          [key, new]
+#        end
+#      when :single
+#        TSV.traverse tsv, :into => dumper do |key,original|
+#          new = index[original]
+#          [key, new]
+#        end
+#      end
+#    end
+#
+#    dumper.stream
+#  end
+#end