miga-base 0.2.0.6 → 0.2.0.7

data/actions/create_project

@@ -1,10 +1,7 @@
 #!/usr/bin/env ruby
-#
+
 # @package MiGA
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Oct-01-2015
-#
+# @license Artistic-2.0
 
 o = {q:true, update:false}
 OptionParser.new do |opt|

data/actions/daemon

@@ -1,10 +1,7 @@
 #!/usr/bin/env ruby
-#
+
 # @package MiGA
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Oct-01-2015
-#
+# @license Artistic-2.0
 
 require "miga/daemon"
 

data/actions/download_dataset

@@ -1,77 +1,107 @@
 #!/usr/bin/env ruby
-#
+
 # @package MiGA
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Oct-01-2015
-#
+# @license Artistic-2.0
 
 require "miga/remote_dataset"
 
-o = {q:true, ref:true, universe: :ebi, db: :embl}
+o = {q:true, query:false, universe: :ebi, db: :embl}
 OptionParser.new do |opt|
-   opt.banner = <<BAN
+  opt.banner = <<BAN
 Creates an empty dataset in a pre-existing MiGA project.
 
 Usage: #{$0} #{File.basename(__FILE__)} [options]
 BAN
-   opt.separator ""
-   opt.on("-P", "--project PATH",
-      "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
-   opt.on("-D", "--dataset STRING",
-      "(Mandatory) ID of the dataset to create."){ |v| o[:dataset]=v }
-   opt.on("-I", "--ids ID1,ID2,...",
-      "(Mandatory) IDs in the remote database separated by commas."
-      ){ |v| o[:ids]=v }
-   opt.on("-U", "--universe STRING",
-      "Universe where the remote database lives. By default: #{o[:universe]}."
-      ){ |v| o[:universe]=v.to_sym }
-   opt.on("--db STRING",
-      "Name of the remote database. By default: #{o[:db]}."
-      ){ |v| o[:db]=v.to_sym }
-   opt.on("-t", "--type STRING",
-      "Type of dataset. Recognized types include:",
-      *MiGA::Dataset.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
-      ){ |v| o[:type]=v.to_sym }
-   opt.on("-q", "--query",
-      "If set, the dataset is registered as a query, not a reference dataset."
-      ){ |v| o[:ref]=!v }
-   opt.on("-d", "--description STRING",
-      "Description of the dataset."){ |v| o[:description]=v }
-   opt.on("-u", "--user STRING",
-      "Owner of the dataset."){ |v| o[:user]=v }
-   opt.on("-c", "--comments STRING",
-      "Comments on the dataset."){ |v| o[:comments]=v }
-   opt.on("-v", "--verbose",
-      "Print additional information to STDERR."){ o[:q]=false }
-   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
-      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
-   end
-   opt.on("-h", "--help", "Display this screen.") do
-      puts opt
-      exit
-   end
-   opt.separator ""
+  opt.separator ""
+  opt.on("-P", "--project PATH",
+    "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
+  opt.on("-D", "--dataset STRING",
+    "(Mandatory unless -F) ID of the dataset to create."){ |v| o[:dataset]=v }
+  opt.on("-I", "--ids ID1,ID2,...",
+    "(Mandatory unless -F) IDs in the remote database separated by commas."
+    ){ |v| o[:ids]=v }
+  opt.on("-U", "--universe STRING",
+    "Universe where the remote database lives. By default: #{o[:universe]}."
+    ){ |v| o[:universe]=v.to_sym }
+  opt.on("--db STRING",
+    "Name of the remote database. By default: #{o[:db]}."
+    ){ |v| o[:db]=v.to_sym }
+  opt.on("-F", "--file PATH",
+    "Tab-delimited file (with header) listing the datasets to download.",
+    "The long form of all the options are supported as header (without the --)",
+    "including dataset, ids, universe, and db. For query use true/false values."
+    ){ |v| o[:file] = v }
+  opt.on("-t", "--type STRING",
+    "Type of dataset. Recognized types include:",
+    *MiGA::Dataset.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}" }
+    ){ |v| o[:type]=v.to_sym }
+  opt.on("-q", "--query",
+    "If set, the dataset is registered as a query, not a reference dataset."
+    ){ |v| o[:query]=v }
+  opt.on("--ignore-dup",
+    "If set, ignores datasets that already exist."){ |v| o[:ignore_dup]=v }
+  opt.on("-d", "--description STRING",
+    "Description of the dataset."){ |v| o[:description]=v }
+  opt.on("-u", "--user STRING",
+    "Owner of the dataset."){ |v| o[:user]=v }
+  opt.on("-c", "--comments STRING",
+    "Comments on the dataset."){ |v| o[:comments]=v }
+  opt.on("-v", "--verbose",
+    "Print additional information to STDERR."){ o[:q]=false }
+  opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+    v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+  end
+  opt.on("-h", "--help", "Display this screen.") do
+    puts opt
+    exit
+  end
+  opt.separator ""
 end.parse!
 
 
 ### MAIN
-raise "-P is mandatory." if o[:project].nil?
-raise "-D is mandatory." if o[:dataset].nil?
-raise "-I is mandatory." if o[:ids].nil?
+glob = [o]
+unless o[:file].nil?
+  glob = []
+  fh = File.open(o[:file], "r")
+  h = nil
+  fh.each do |ln|
+    r = ln.chomp.split(/\t/)
+    if h.nil?
+       h = r
+    else
+       glob << o.dup
+       h.each_index do |i|
+	 glob[glob.size-1][h[i].to_sym] = h[i]=="query" ? r[i]=="true" :
+	   %w[type universe db].include?(h[i]) ? r[i].to_sym : r[i]
+       end
+    end
+  end
+  fh.close
+end
 
-$stderr.puts "Locating remote dataset." unless o[:q]
-rd = MiGA::RemoteDataset.new(o[:ids], o[:db], o[:universe])
+glob.each do |o_i|
+  raise "-P is mandatory." if o_i[:project].nil?
+  raise "-D is mandatory." if o_i[:dataset].nil?
+  raise "-I is mandatory." if o_i[:ids].nil?
 
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
+  $stderr.puts "Dataset: #{o_i[:dataset]}" unless o_i[:q]
+  $stderr.puts "Loading project." unless o_i[:q]
+  p = MiGA::Project.load(o_i[:project])
+  raise "Impossible to load project: #{o_i[:project]}" if p.nil?
 
-$stderr.puts "Creating dataset." unless o[:q]
-md = {}
-[:type, :description, :user, :comments].each{ |k| md[k]=o[k] unless o[k].nil? }
-d = rd.save_to(p, o[:dataset], o[:ref], md)
-p.add_dataset(o[:dataset])
+  next if o_i[:ignore_dup] and not p.dataset(o_i[:dataset]).nil?
+  
+  $stderr.puts "Locating remote dataset." unless o_i[:q]
+  rd = MiGA::RemoteDataset.new(o_i[:ids], o_i[:db], o_i[:universe])
 
-$stderr.puts "Done." unless o[:q]
+  $stderr.puts "Creating dataset." unless o_i[:q]
+  md = {}
+  [:type, :description, :user, :comments].each do |k|
+    md[k]=o_i[k] unless o_i[k].nil?
+  end
+  rd.save_to(p, o_i[:dataset], !o_i[:query], md)
+  p.add_dataset(o_i[:dataset])
 
+  $stderr.puts "Done." unless o_i[:q]
+end

data/actions/find_datasets

@@ -1,42 +1,39 @@
 #!/usr/bin/env ruby
-#
+
 # @package MiGA
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Oct-01-2015
-#
+# @license Artistic-2.0
 
 o = {q:true, add:false, ref:false}
 OptionParser.new do |opt|
-   opt.banner = <<BAN
+  opt.banner = <<BAN
 Finds unregistered datasets based on result files.
 
 Usage: #{$0} #{File.basename(__FILE__)} [options]
 BAN
-   opt.separator ""
-   opt.on("-P", "--project PATH",
-      "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
-   opt.on("-a", "--add",
-      "Register the datasets found. By default, only lists them (dry run)."
-      ){ |v| o[:add]=v }
-   opt.on("-t", "--type STRING",
-      "Type of datasets. Recognized types include:",
-      *MiGA::Dataset.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
-      ){ |v| o[:type]=v.to_sym }
-   opt.on("-r", "--ref",
-      "If set, all datasets are registered as reference datasets."
-      ){ |v| o[:ref]=v }
-   opt.on("-u", "--user STRING", "Owner of the dataset."){ |v| o[:user]=v }
-   opt.on("-v", "--verbose",
-      "Print additional information to STDERR."){ o[:q]=false }
-   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
-      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
-   end
-   opt.on("-h", "--help", "Display this screen.") do
-      puts opt
-      exit
-   end
-   opt.separator ""
+  opt.separator ""
+  opt.on("-P", "--project PATH",
+    "(Mandatory) Path to the project to use."){ |v| o[:project]=v }
+  opt.on("-a", "--add",
+    "Register the datasets found. By default, only lists them (dry run)."
+    ){ |v| o[:add]=v }
+  opt.on("-t", "--type STRING",
+    "Type of datasets. Recognized types include:",
+    *MiGA::Dataset.KNOWN_TYPES.map{ |k,v| "~ #{k}: #{v[:description]}"}
+    ){ |v| o[:type]=v.to_sym }
+  opt.on("-r", "--ref",
+    "If set, all datasets are registered as reference datasets."
+    ){ |v| o[:ref]=v }
+  opt.on("-u", "--user STRING", "Owner of the dataset."){ |v| o[:user]=v }
+  opt.on("-v", "--verbose",
+    "Print additional information to STDERR."){ o[:q]=false }
+  opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+    v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+  end
+  opt.on("-h", "--help", "Display this screen.") do
+    puts opt
+    exit
+  end
+  opt.separator ""
 end.parse!
 
 
@@ -50,14 +47,15 @@ raise "Impossible to load project: #{o[:project]}" if p.nil?
 $stderr.puts "Finding datasets." unless o[:q]
 ud = p.unregistered_datasets
 ud.each do |dn|
-   puts dn
-   if o[:add]
-      md = {}
-      [:type, :user].each{ |k| md[k]=o[k] unless o[k].nil? }
-      d = MiGA::Dataset.new(p, dn, o[:ref], md)
-      p.add_dataset(dn)
-   end
+  puts dn
+  if o[:add]
+    md = {}
+    [:type, :user].each{ |k| md[k]=o[k] unless o[k].nil? }
+    d = MiGA::Dataset.new(p, dn, o[:ref], md)
+    p.add_dataset(dn)
+    res = d.first_preprocessing
+    puts "- #{res}" unless o[:q]
+  end
 end
 
 $stderr.puts "Done." unless o[:q]
-

data/actions/import_datasets

@@ -1,10 +1,7 @@
 #!/usr/bin/env ruby
-#
+
 # @package MiGA
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Oct-01-2015
-#
+# @license Artistic-2.0
 
 o = {q:true, info:false, force:false, method: :hardlink }
 OptionParser.new do |opt|

data/actions/index_taxonomy

@@ -1,10 +1,7 @@
 #!/usr/bin/env ruby
-#
+
 # @package MiGA
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Oct-01-2015
-#
+# @license Artistic-2.0
 
 require "miga/tax_index"
 

data/actions/list_datasets

@@ -1,46 +1,45 @@
 #!/usr/bin/env ruby
-#
+
 # @package MiGA
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Oct-01-2015
-#
+# @license Artistic-2.0
 
-o = {q:true, info:false}
+o = {q:true, info:false, processing:false}
 OptionParser.new do |opt|
-   opt.banner = <<BAN
+  opt.banner = <<BAN
 Lists all registered datasets in an MiGA project.
 
 Usage: #{$0} #{File.basename(__FILE__)} [options]
 BAN
-   opt.separator ""
-   opt.on("-P", "--project PATH",
-      "(Mandatory) Path to the project to read."){ |v| o[:project]=v }
-   opt.on("-D", "--dataset STRING",
-      "ID of the dataset to read."){ |v| o[:dataset]=v.miga_name }
-   opt.on("--[no-]ref",
-      "If set, lists only reference (or only non-reference) datasets."
-      ){ |v| o[:ref]=v }
-   opt.on("--[no-]multi",
-      "If set, lists only multi-species (or only single-species) datasets."
-      ){ |v| o[:multi]=v }
-   opt.on("-i", "--info",
-      "Print additional information on each dataset."){ o[:info]=true }
-   opt.on("-t", "--taxonomy RANK:TAXON",
-      "Filter by taxonomy."){ |v| o[:taxonomy]=MiGA::Taxonomy.new v }
-   opt.on("-m", "--metadata STRING",
-      "Print name and metadata field only. If set, ignores -i."
-      ){ |v| o[:datum]=v }
-   opt.on("-v", "--verbose",
-      "Print additional information to STDERR."){ o[:q]=false }
-   opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
-      v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
-   end
-   opt.on("-h", "--help", "Display this screen.") do
-      puts opt
-      exit
-   end
-   opt.separator ""
+  opt.separator ""
+  opt.on("-P", "--project PATH",
+    "(Mandatory) Path to the project to read."){ |v| o[:project]=v }
+  opt.on("-D", "--dataset STRING",
+    "ID of the dataset to read."){ |v| o[:dataset]=v.miga_name }
+  opt.on("--[no-]ref",
+    "If set, lists only reference (or only non-reference) datasets."
+    ){ |v| o[:ref]=v }
+  opt.on("--[no-]multi",
+    "If set, lists only multi-species (or only single-species) datasets."
+    ){ |v| o[:multi]=v }
+  opt.on("-i", "--info",
+    "Print additional information on each dataset."){ |v| o[:info]=v }
+  opt.on("-p", "--processing",
+    "Print information on processing advance."){ |v| o[:processing]=v }
+  opt.on("-t", "--taxonomy RANK:TAXON",
+    "Filter by taxonomy."){ |v| o[:taxonomy]=MiGA::Taxonomy.new v }
+  opt.on("-m", "--metadata STRING",
+    "Print name and metadata field only. If set, ignores -i."
+    ){ |v| o[:datum]=v }
+  opt.on("-v", "--verbose",
+    "Print additional information to STDERR."){ o[:q]=false }
+  opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
+    v.to_i>1 ? MiGA::MiGA.DEBUG_TRACE_ON : MiGA::MiGA.DEBUG_ON
+  end
+  opt.on("-h", "--help", "Display this screen.") do
+    puts opt
+    exit
+  end
+  opt.separator ""
 end.parse!
 
 
@@ -53,31 +52,30 @@ raise "Impossible to load project: #{o[:project]}" if p.nil?
 
 $stderr.puts "Listing datasets." unless o[:q]
 if o[:dataset].nil?
-   ds = p.datasets
+  ds = p.datasets
 elsif MiGA::Dataset.exist? p, o[:dataset]
-   ds = [p.dataset(o[:dataset])]
+  ds = [p.dataset(o[:dataset])]
 else
-   ds = []
+  ds = []
 end
 ds.select!{|d| d.is_ref? == o[:ref] } unless o[:ref].nil?
 ds.select! do |d|
-   (not d.metadata[:type].nil?) and
-      (MiGA::Dataset.KNOWN_TYPES[d.metadata[:type]][:multi] == o[:multi])
+  (not d.metadata[:type].nil?) and
+    (MiGA::Dataset.KNOWN_TYPES[d.metadata[:type]][:multi] == o[:multi])
 end unless o[:multi].nil?
 ds.select! do |d|
-   (not d.metadata[:tax].nil?) and d.metadata[:tax].is_in?(o[:taxonomy])
+  (not d.metadata[:tax].nil?) and d.metadata[:tax].is_in?(o[:taxonomy])
 end unless o[:taxonomy].nil?
 if not o[:datum].nil?
-   ds.each{|d| puts "#{d.name}\t#{(d.metadata[ o[:datum] ] || "?").to_s}"}
+  ds.each{|d| puts "#{d.name}\t#{d.metadata[ o[:datum] ] || "?"}"}
 elsif o[:info]
-   header = MiGA::Dataset.INFO_FIELDS.map{|i| i.ljust(25)}.join("  ")
-   puts header, header.gsub(/\S/,"-")
-   ds.each do |d|
-      puts d.info.map{|i| i.nil? ? "?" : i.to_s}.map{|i| i.ljust(25)}.join("  ")
-   end
+  puts MiGA::MiGA.tabulate(MiGA::Dataset.INFO_FIELDS, ds.map{ |d| d.info })
+elsif o[:processing]
+  comp = ["undef","done","queued"]
+  puts MiGA::MiGA.tabulate([:name] + MiGA::Dataset.PREPROCESSING_TASKS,
+    ds.map{ |d| [d.name] + d.profile_advance.map{ |i| comp[i] } })
 else
-   ds.each{|d| puts d.name}
+  ds.each{|d| puts d.name}
 end
 
 $stderr.puts "Done." unless o[:q]
-

data/actions/list_files

@@ -1,10 +1,7 @@
 #!/usr/bin/env ruby
-#
+
 # @package MiGA
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Oct-01-2015
-#
+# @license Artistic-2.0
 
 o = {q:true, details:false, json:true}
 OptionParser.new do |opt|
@@ -22,9 +19,9 @@ BAN
    opt.on("-i", "--info",
       "If set, it prints additional details for each file."
       ){ |v| o[:details]=v }
-   opt.on("--exclude-json",
-      "If set, excludes json files containing results metadata."
-      ){ |v| o[:json]=!v }
+   opt.on("--[no-]json",
+      "If set to no, excludes json files containing results metadata."
+      ){ |v| o[:json]=v }
    opt.on("-v", "--verbose",
       "Print additional information to STDERR."){ o[:q]=false }
    opt.on("-d", "--debug INT", "Print debugging information to STDERR.") do |v|
@@ -56,10 +53,9 @@ end
 
 $stderr.puts "Listing files." unless o[:q]
 results.each do |result|
-   puts (o[:details] ? result.path + "\t" + "\t" : "") + result.path if o[:json]
+   puts "#{ "#{result.path}\t\t" if o[:details] }#{result.path}" if o[:json]
    result.each_file do |k,f|
-      puts (o[:details] ? result.path + "\t" + k.to_s + "\t" : "") +
-	 File.dirname(result.path) + "/" + f.to_s
+      puts "#{ "#{result.path}\t#{k}\t" if o[:details] }#{result.dir}/#{f}"
    end
 end
 

data/actions/unlink_dataset

@@ -1,10 +1,7 @@
 #!/usr/bin/env ruby
-#
+
 # @package MiGA
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-# @update  Oct-01-2015
-#
+# @license Artistic-2.0
 
 o = {q:true, remove:false}
 OptionParser.new do |opt|

data/bin/miga

@@ -31,7 +31,7 @@ elsif execs.include? ARGV[0]
       err
    end
 else
-   print <<HELP.gsub /^   /,""
+   print <<HELP.gsub(/^   /,"")
    Microbial Genomes Atlas.
 
    Usage: #{$0} {action} [options]

data/lib/miga/common.rb

@@ -0,0 +1,132 @@
+# @package MiGA
+# @license Artistic-2.0
+
+require "miga/version"
+require "json"
+
+##
+# Generic class used to handle system-wide information and methods, and parent
+# of all other MiGA::* classes.
+class MiGA::MiGA
+  
+  ENV["MIGA_HOME"] ||= ENV["HOME"]
+
+  ##
+  # Root path to MiGA (as estimated from the location of the current file).
+  def self.root_path ; File.expand_path("../../..", __FILE__) ; end
+
+  ##
+  # Should debugging information be reported?
+  @@DEBUG = false
+
+  ##
+  # Should the trace of debugging information be reported?
+  @@DEBUG_TRACE = false
+
+  ##
+  # Turn on debugging.
+  def self.DEBUG_ON() @@DEBUG=true end
+
+  ##
+  # Turn off debugging.
+  def self.DEBUG_OFF() @@DEBUG=false end
+
+  ##
+  # Turn on debug tracing (and debugging).
+  def self.DEBUG_TRACE_ON
+    @@DEBUG_TRACE=true
+    self.DEBUG_ON
+  end
+
+  ##
+  # Turn off debug tracing (but not debugging).
+  def self.DEBUG_TRACE_OFF
+    @@DEBUG_TRACE=false
+  end
+
+  ##
+  # Send debug message.
+  def self.DEBUG *args
+    $stderr.puts(*args) if @@DEBUG
+    $stderr.puts caller.map{|v| v.gsub(/^/,"    ")}.join("\n") if
+      @@DEBUG_TRACE
+  end
+
+  ##
+  # Has MiGA been initialized?
+  def self.initialized?
+    File.exist?(File.expand_path(".miga_rc", ENV["MIGA_HOME"])) and
+      File.exist?(File.expand_path(".miga_daemon.json", ENV["MIGA_HOME"]))
+  end
+
+  ##
+  # Tabulates an +values+, and Array of Arrays, all with the same number of
+  # entries as +header+. Returns an Array of String, one per line.
+  def self.tabulate(header, values)
+    fields = [header.map{ |h| h.to_s }]
+    fields << fields.first.map{ |h| h.gsub(/\S/, "-") }
+    fields += values.map{ |row| row.map{ |cell| cell.nil? ? "?" : cell.to_s } }
+    clen = fields.map{ |row|
+      row.map{ |cell| cell.length } }.transpose.map{ |col| col.max }
+    fields.map do |row|
+      (0 .. clen.size-1).map do |col_n|
+        col_n==0 ? row[col_n].rjust(clen[col_n]) : row[col_n].ljust(clen[col_n])
+      end.join("  ")
+    end
+  end
+
+  ##
+  # Check if the result files exist with +base+ name (String) followed by the
+  # +ext+ values (Array of String).
+  def result_files_exist?(base, ext)
+    ext = [ext] unless ext.kind_of? Array
+    ext.all? do |f|
+      File.exist?(base + f) or File.exist?(base + f + ".gz")
+    end
+  end
+
+end
+
+##
+# MiGA extensions to the File class.
+class File
+
+  ##
+  # Method to transfer a file from +old_name+ to +new_name+, using a +method+
+  # that can be one of :symlink for File#symlink, :hardlink for File#link, or
+  # :copy for FileUtils#cp_r.
+  def self.generic_transfer(old_name, new_name, method)
+    return nil if exist? new_name
+    case method
+    when :symlink
+      File.symlink(old_name, new_name)
+    when :hardlink
+      File.link(old_name, new_name)
+    when :copy
+      FileUtils.cp_r(old_name, new_name)
+    else
+      raise "Unknown transfer method: #{method}."
+    end
+  end
+  
+end
+
+##
+# MiGA extensions to the String class.
+class String
+  
+  ##
+  # Replace any character not allowed in a MiGA name for underscore (_). This
+  # results in a MiGA-compliant name EXCEPT for empty strings, that results in
+  # empty strings.
+  def miga_name ; gsub(/[^A-Za-z0-9_]/, "_") ; end
+
+  ##
+  # Is the string a MiGA-compliant name?
+  def miga_name? ; not(self !~ /^[A-Za-z0-9_]+$/) ; end
+
+  ##
+  # Replace underscores by spaces.
+  def unmiga_name ; tr("_", " ") ; end
+  
+end