miga-base 0.3.1.3 → 0.3.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6d05cad62382523776174b6300e3a3cc8cbf87b6
-  data.tar.gz: 71db2e7e0d361c770f978ab265d862e52cd30727
+  metadata.gz: 2edb583f3cefe6b6f36a52b50b595e0f0d8be81c
+  data.tar.gz: 11a9c0c45f7144e88c01d5c7d4fc1c1bcda6b8e6
 SHA512:
-  metadata.gz: 761cf711acb535bacc7e789e16545904b2147f498caf9edcb190f7d2a3a6417bf567d86175bb255ff3d1c353bf7b9eaffdc50f9fb998458f2db81d91286a5217
-  data.tar.gz: 91bdc8ddbb06407ea78b120a96823dd46efb5521f85423a5840b0f2e72771f9d67c6ccf8291fd6e7033ebd711a0d1c32c5c48ad2f4e98179ec4d36d108b91347
+  metadata.gz: 75748d35171225261a4fc962ea80aa3ffc64ccf76206203866eb9fc60a3ae6b69c9b362f8e8248b5e7740aff2b63b8021c912f2b0a76950d5a7da04e95ef94b7
+  data.tar.gz: eece83478cfe635f9828eae45807a6bc072c5960a3320d05d154cf2ad8cd117fc0a1d801ec6b2ac18f527b62053bc698ee5f85f0ac4a0b8f5890516383130817

data/actions/stats.rb

@@ -111,10 +111,12 @@ if o[:compute]
         end
       end
       stats[:quality] = stats[:completeness][0] - stats[:contamination][0]*5
-      q_range = stats[:quality] > 80.0 ? :excellent :
-        stats[:quality] > 50.0 ? :high :
-        stats[:quality] > 20.0 ? :intermediate : :low
-      d.metadata[:quality] = q_range
+      d.metadata[:quality] = case stats[:quality]
+        when 80..100 ; :excellent
+        when 50..80  ; :high
+        when 20..50  ; :intermediate
+        else         ; :low
+      end
       d.save
     end
   when :distances

data/bin/miga

@@ -139,6 +139,8 @@ def opt_filter_datasets(opt, o, what=[:ref, :multi, :taxonomy])
     ){ |v| o[:multi]=v } if what.include? :multi
   opt.on("-t", "--taxonomy RANK:TAXON", "Filter by taxonomy."
     ){ |v| o[:taxonomy]=MiGA::Taxonomy.new v } if what.include? :taxonomy
+  opt.on("-k", "--key INTEGER",
+    "Returns only the k-th dataset in the list."){ |v| o[:key]=v.to_i }
 end
 
 def opt_require(o, req={project:"-P", dataset:"-D"})
@@ -161,7 +163,7 @@ def filter_datasets!(ds, o)
   ds.select! do |d|
     (not d.metadata[:tax].nil?) and d.metadata[:tax].is_in?(o[:taxonomy])
   end unless o[:taxonomy].nil?
-  ds
+  o[:key].nil? ? ds : ds.values_at(o[:key]-1)
 end
 
 def add_metadata(o, obj)

data/lib/miga/common.rb

@@ -80,28 +80,36 @@ class MiGA::MiGA
   ##
   # Cleans a FastA file in place.
   def self.clean_fasta_file(file)
-    tmp = Tempfile.new("MiGA")
+    tmp_fh = nil
     begin
-      File.open(file, "r") do |fh|
-        buffer = ""
-        fh.each_line do |ln|
-          ln.chomp!
-          if ln =~ /^>\s*(\S+)(.*)/
-            (id, df) = [$1, $2]
-            tmp.print buffer.wrap_width(80)
-            buffer = ""
-            tmp.puts ">#{id.gsub(/[^A-Za-z0-9_\|\.]/, "_")}#{df}"
-          else
-            buffer << ln.gsub(/[^A-Za-z\.\-]/, "")
-          end
+      if (file =~ /\.gz/)
+        tmp_path = Tempfile.new("MiGA.gz").tap{ |i| i.close }.path
+        tmp_fh = Zlib::GzipWriter.open(tmp_path)
+        fh = Zlib::GzipReader.open(file)
+      else
+        tmp_fh = Tempfile.new("MiGA")
+        tmp_path = tmp_fh.path
+        fh = File.open(file, "r")
+      end
+      buffer = ""
+      fh.each_line do |ln|
+        ln.chomp!
+        if ln =~ /^>\s*(\S+)(.*)/
+          (id, df) = [$1, $2]
+          tmp_fh.print buffer.wrap_width(80)
+          buffer = ""
+          tmp_fh.puts ">#{id.gsub(/[^A-Za-z0-9_\|\.]/, "_")}#{df}"
+        else
+          buffer << ln.gsub(/[^A-Za-z\.\-]/, "")
         end
-        tmp.print buffer.wrap_width(80)
       end
-      tmp.close
-      FileUtils.cp(tmp.path, file)
+      tmp_fh.print buffer.wrap_width(80)
+      tmp_fh.close
+      fh.close
+      FileUtils.cp(tmp_path, file)
     ensure
-      tmp.close
-      tmp.unlink
+      tmp_fh.close unless tmp_fh.nil?
+      File.unlink(tmp_path) unless tmp_path.nil?
     end
   end
 

data/lib/miga/daemon.rb

@@ -1,27 +1,27 @@
 # @package MiGA
 # @license Artistic-2.0
 
-require "miga/project"
-require "daemons"
-require "date"
+require 'miga/project'
+require 'daemons'
+require 'date'
 
 ##
 # MiGA Daemons handling job submissions.
 class MiGA::Daemon < MiGA::MiGA
-  
+
   ##
   # When was the last time a daemon for the MiGA::Project +project+ was seen
   # active? Returns DateTime.
   def self.last_alive(project)
-    f = File.expand_path("daemon/alive", project.path)
+    f = File.expand_path('daemon/alive', project.path)
     return nil unless File.exist? f
     DateTime.parse(File.read(f))
   end
 
   # Shutdown all spawned daemons before exit.
   $_MIGA_DAEMON_LAIR = []
-  END { $_MIGA_DAEMON_LAIR.each{ |d| d.terminate } }
-  
+  END { $_MIGA_DAEMON_LAIR.each(&:terminate) }
+
   # MiGA::Project in which the daemon is running.
   attr_reader :project
   # Options used to setup the daemon.
@@ -40,8 +40,8 @@ class MiGA::Daemon < MiGA::MiGA
     $_MIGA_DAEMON_LAIR << self
     @project = project
     @runopts = JSON.parse(
-      File.read(File.expand_path("daemon/daemon.json", project.path)),
-        {:symbolize_names=>true})
+          File.read(File.expand_path('daemon/daemon.json', project.path)),
+          symbolize_names: true)
     @jobs_to_run = []
     @jobs_running = []
     @loop_i = -1
@@ -57,7 +57,7 @@ class MiGA::Daemon < MiGA::MiGA
   ##
   # Returns Hash containing the default options for the daemon.
   def default_options
-    { dir_mode: :normal, dir: File.expand_path("daemon", project.path),
+    { dir_mode: :normal, dir: File.expand_path('daemon', project.path),
       multiple: false, log_output: true }
   end
 
@@ -68,16 +68,19 @@ class MiGA::Daemon < MiGA::MiGA
   def runopts(k, v=nil, force=false)
     k = k.to_sym
     unless v.nil?
-      v = [:latency, :maxjobs, :ppn].include?(k) ? v.to_i :
-          [:shutdown_when_done].include?(k) ? !!v : v
+      if [:latency, :maxjobs, :ppn].include?(k)
+        v = v.to_i
+      elsif [:shutdown_when_done].include?(k)
+        v = !!v
+      end
       raise "Daemon's #{k} cannot be set to zero." if !force and v==0
       @runopts[k] = v
     end
     if k==:kill and v.nil?
       case @runopts[:type].to_s
-        when "bash" ; return "kill -9 '%s'"
-        when "qsub" ; return "qdel '%s'"
-        else        ; return "canceljob '%s'"
+      when 'bash' then return "kill -9 '%s'"
+      when 'qsub' then return "qdel '%s'"
+      else             return "canceljob '%s'"
       end
     end
     @runopts[k]
@@ -85,36 +88,36 @@ class MiGA::Daemon < MiGA::MiGA
 
   ##
   # Returns Integer indicating the number of seconds to sleep between checks.
-  def latency() runopts(:latency) ; end
+  def latency() runopts(:latency); end
 
   ##
   # Returns Integer indicating the maximum number of concurrent jobs to run.
-  def maxjobs() runopts(:maxjobs) ; end
+  def maxjobs() runopts(:maxjobs); end
 
   ##
   # Returns Integer indicating the number of CPUs per job.
-  def ppn() runopts(:ppn) ; end
+  def ppn() runopts(:ppn); end
 
   ##
   # Returns Boolean indicating if the daemon should shutdown when processing is
   # complete.
-  def shutdown_when_done?() !!runopts(:shutdown_when_done) ; end
+  def shutdown_when_done?() !!runopts(:shutdown_when_done); end
 
   ##
   # Initializes the daemon with +opts+.
-  def start(opts=[]) daemon("start", opts) ; end
+  def start(opts=[]) daemon('start', opts); end
 
   ##
   # Stops the daemon with +opts+.
-  def stop(opts=[]) daemon("stop", opts) ; end
+  def stop(opts=[]) daemon('stop', opts); end
 
   ##
   # Restarts the daemon with +opts+.
-  def restart(opts=[]) daemon("restart", opts) ; end
+  def restart(opts=[]) daemon('restart', opts); end
 
   ##
   # Returns the status of the daemon with +opts+.
-  def status(opts=[]) daemon("status", opts) ; end
+  def status(opts=[]) daemon('status', opts); end
 
   ##
   # Launches the +task+ with options +opts+ (as command-line arguments).
@@ -131,7 +134,7 @@ class MiGA::Daemon < MiGA::MiGA
   ##
   # Tell the world that you're alive.
   def declare_alive
-    f = File.open(File.expand_path("daemon/alive", project.path), "w")
+    f = File.open(File.expand_path('daemon/alive', project.path), 'w')
     f.print Time.now.to_s
     f.close
   end
@@ -139,12 +142,12 @@ class MiGA::Daemon < MiGA::MiGA
   ##
   # Report status in a JSON file.
   def report_status
-    f = File.open(File.expand_path("daemon/status.json", project.path), "w")
+    f = File.open(File.expand_path('daemon/status.json', project.path), 'w')
     f.print JSON.pretty_generate(
       jobs_running:@jobs_running, jobs_to_run:@jobs_to_run)
     f.close
   end
-  
+
   ##
   # Traverse datasets
   def check_datasets
@@ -164,34 +167,37 @@ class MiGA::Daemon < MiGA::MiGA
   # project-level tasks
   def check_project
     return if project.dataset_names.empty?
-    if project.done_preprocessing?(false)
-      to_run = project.next_distances(true)
-      to_run = project.next_inclade(true) if to_run.nil?
-      queue_job(to_run) unless to_run.nil?
-    end
+    return unless project.done_preprocessing?(false)
+    to_run = project.next_distances(true)
+    to_run = project.next_inclade(true) if to_run.nil?
+    queue_job(to_run) unless to_run.nil?
   end
-  
+
   ##
   # Add the task to the internal queue with symbol key +job+. If the task is
   # dataset-specific, +ds+ specifies the dataset. To submit jobs to the
   # scheduler (or to bash) see #flush!.
   def queue_job(job, ds=nil)
     return nil unless get_job(job, ds).nil?
-    ds_name = (ds.nil? ? "miga-project" : ds.name)
-    say "Queueing ", ds_name, ":#{job}"
-    vars = { "PROJECT"=>project.path, "RUNTYPE"=>runopts(:type),
-      "CORES"=>ppn, "MIGA"=>MiGA::MiGA.root_path }
-    vars["DATASET"] = ds.name unless ds.nil?
+    ds_name = (ds.nil? ? 'miga-project' : ds.name)
+    say 'Queueing %s:%s' % [ds_name, job]
+    vars = {
+      'PROJECT' => project.path,
+      'RUNTYPE' => runopts(:type),
+      'CORES'   => ppn,
+      'MIGA'    => MiGA::MiGA.root_path
+    }
+    vars['DATASET'] = ds.name unless ds.nil?
     log_dir = File.expand_path("daemon/#{job}", project.path)
     Dir.mkdir(log_dir) unless Dir.exist? log_dir
     task_name = "#{project.metadata[:name][0..9]}:#{job}:#{ds_name}"
     to_run = {ds: ds, job: job, task_name: task_name,
       cmd: sprintf(runopts(:cmd),
         # 1: script
-        MiGA::MiGA.script_path(job, miga:vars["MIGA"], project:project),
+        MiGA::MiGA.script_path(job, miga:vars['MIGA'], project:project),
         # 2: vars
-        vars.keys.map { |k|
-	  sprintf(runopts(:var), k, vars[k]) }.join(runopts(:varsep)),
+        vars.keys.map { |k| sprintf(runopts(:var), k, vars[k]) }.
+          join(runopts(:varsep)),
         # 3: CPUs
         ppn,
         # 4: log file
@@ -213,7 +219,7 @@ class MiGA::Daemon < MiGA::MiGA
       end
     end
   end
-  
+
   ##
   # Remove finished jobs from the internal queue and launch as many as
   # possible respecting #maxjobs.
@@ -245,9 +251,9 @@ class MiGA::Daemon < MiGA::MiGA
   # Run one loop step. Returns a Boolean indicating if the loop should continue.
   def in_loop
     if loop_i == -1
-      say "-----------------------------------"
-      say "MiGA:#{project.name} launched."
-      say "-----------------------------------"
+      say '-----------------------------------'
+      say 'MiGA:%s launched.' % project.name
+      say '-----------------------------------'
       @loop_i = 0
     end
     @loop_i += 1
@@ -257,14 +263,14 @@ class MiGA::Daemon < MiGA::MiGA
     check_project
     flush!
     if loop_i==4
-      say "Housekeeping for sanity"
+      say 'Housekeeping for sanity'
       @loop_i = 0
       purge!
     end
     report_status
     sleep(latency)
     if shutdown_when_done? and jobs_running.size+jobs_to_run.size == 0
-      say "Nothing else to do, shutting down."
+      say 'Nothing else to do, shutting down.'
       return false
     end
     true
@@ -279,32 +285,32 @@ class MiGA::Daemon < MiGA::MiGA
   ##
   # Terminates a daemon.
   def terminate
-    say "Terminating daemon..."
+    say 'Terminating daemon...'
     report_status
     k = runopts(:kill)
     @jobs_running.each do |i|
       `#{k % i[:pid]}`
       puts "Terminating pid:#{i[:pid]} for #{i[:task_name]}"
     end
-    f = File.expand_path("daemon/alive", project.path)
+    f = File.expand_path('daemon/alive', project.path)
     File.unlink(f) if File.exist? f
   end
 
   private
-    
+
     def launch_job(job)
       # Execute job
-      if runopts(:type) == "bash"
+      if runopts(:type) == 'bash'
         # Local job
         job[:pid] = spawn job[:cmd]
-        Process.detach job[:pid] unless [nil, "", 0].include?(job[:pid])
+        Process.detach job[:pid] unless [nil, '', 0].include?(job[:pid])
       else
         # Schedule cluster job
         job[:pid] = `#{job[:cmd]}`.chomp
       end
-      
+
       # Check if registered
-      if [nil, "", 0].include?(job[:pid])
+      if [nil, '', 0].include? job[:pid]
         job[:pid] = nil
         @jobs_to_run << job
         say "Unsuccessful #{job[:task_name]}, rescheduling."
@@ -313,5 +319,4 @@ class MiGA::Daemon < MiGA::MiGA
         say "Spawned pid:#{job[:pid]} for #{job[:task_name]}."
       end
     end
-
 end

data/lib/miga/dataset.rb

@@ -2,85 +2,30 @@
 # @license Artistic-2.0
 
 require "miga/metadata"
-require "miga/result"
-require "miga/dataset_result"
+require "miga/dataset/result"
 require "sqlite3"
 
 ##
 # Dataset representation in MiGA.
 class MiGA::Dataset < MiGA::MiGA
   
-  include MiGA::DatasetResult
+  include MiGA::Dataset::Result
   
   # Class-level
+  class << self
 
-  ##
-  # Directories containing the results from dataset-specific tasks.
-  def self.RESULT_DIRS ; @@RESULT_DIRS end
-  @@RESULT_DIRS = {
-    # Preprocessing
-    raw_reads: "01.raw_reads", trimmed_reads: "02.trimmed_reads",
-    read_quality: "03.read_quality", trimmed_fasta: "04.trimmed_fasta",
-    assembly: "05.assembly", cds: "06.cds",
-    # Annotation
-    essential_genes: "07.annotation/01.function/01.essential",
-    ssu: "07.annotation/01.function/02.ssu",
-    mytaxa: "07.annotation/02.taxonomy/01.mytaxa",
-    mytaxa_scan: "07.annotation/03.qa/02.mytaxa_scan",
-    # Distances (for single-species datasets)
-    distances: "09.distances", taxonomy: "09.distances/05.taxonomy",
-    # General statistics
-    stats: "90.stats"
-  }
-
-  ##
-  # Supported dataset types.
-  def self.KNOWN_TYPES ; @@KNOWN_TYPES end
-  @@KNOWN_TYPES = {
-    genome: {description: "The genome from an isolate.", multi: false},
-    scgenome: {description: "A Single-cell Genome Amplification (SGA).",
-      multi: false},
-    popgenome: {description: "A population genome (including " +
-      "metagenomic bins).", :multi=>false},
-    metagenome: {description: "A metagenome (excluding viromes).",
-      multi: true},
-    virome: {description: "A viral metagenome.", multi: true}
-  }
+    ##
+    # Does the +project+ already have a dataset with that +name+?
+    def exist?(project, name)
+      project.dataset_names.include? name
+    end
 
-  ##
-  # Returns an Array of tasks to be executed before project-wide tasks.
-  def self.PREPROCESSING_TASKS ; @@PREPROCESSING_TASKS ; end
-  @@PREPROCESSING_TASKS = [:raw_reads, :trimmed_reads, :read_quality,
-    :trimmed_fasta, :assembly, :cds, :essential_genes, :ssu, :mytaxa,
-    :mytaxa_scan, :distances, :taxonomy, :stats]
-  
-  ##
-  # Tasks to be excluded from query datasets.
-  @@EXCLUDE_NOREF_TASKS = [:mytaxa_scan, :taxonomy]
-  @@_EXCLUDE_NOREF_TASKS_H = Hash[@@EXCLUDE_NOREF_TASKS.map{ |i| [i,true] }]
+    ##
+    # Standard fields of metadata for datasets.
+    def INFO_FIELDS
+      %w(name created updated type ref user description comments)
+    end
   
-  ##
-  # Tasks to be executed only in datasets that are not multi-organism. These
-  # tasks are ignored for multi-organism datasets or for unknown types.
-  @@ONLY_NONMULTI_TASKS = [:mytaxa_scan, :distances, :taxonomy]
-  @@_ONLY_NONMULTI_TASKS_H = Hash[@@ONLY_NONMULTI_TASKS.map{ |i| [i,true] }]
-
-  ##
-  # Tasks to be executed only in datasets that are multi-organism. These
-  # tasks are ignored for single-organism datasets or for unknwon types.
-  @@ONLY_MULTI_TASKS = [:mytaxa]
-  @@_ONLY_MULTI_TASKS_H = Hash[@@ONLY_MULTI_TASKS.map{ |i| [i,true] }]
-
-  ##
-  # Does the +project+ already have a dataset with that +name+?
-  def self.exist?(project, name)
-    File.exist? "#{project.path}/metadata/#{name}.json"
-  end
-
-  ##
-  # Standard fields of metadata for datasets.
-  def self.INFO_FIELDS
-    %w(name created updated type ref user description comments)
   end
 
   # Instance-level
@@ -164,79 +109,6 @@ class MiGA::Dataset < MiGA::MiGA
     !@@KNOWN_TYPES[type][:multi]
   end
   
-  ##
-  # Get the result MiGA::Result in this dataset identified by the symbol +k+.
-  def result(k)
-    return nil if @@RESULT_DIRS[k.to_sym].nil?
-    MiGA::Result.load(
-      "#{project.path}/data/#{@@RESULT_DIRS[k.to_sym]}/#{name}.json" )
-  end
-  
-  ##
-  # Get all the results (Array of MiGA::Result) in this dataset.
-  def results ; @@RESULT_DIRS.keys.map{ |k| result k }.compact ; end
-  
-  ##
-  # For each result executes the 2-ary +blk+ block: key symbol and MiGA::Result.
-  def each_result(&blk)
-    @@RESULT_DIRS.keys.each do |k|
-      blk.call(k, result(k)) unless result(k).nil?
-    end
-  end
-  
-  ##
-  # Look for the result with symbol key +result_type+ and register it in the
-  # dataset. If +save+ is false, it doesn't register the result, but it still
-  # returns a result if the expected files are complete. The +opts+ hash
-  # controls result creation (if necessary). Supported values include:
-  # - +is_clean+: A Boolean indicating if the input files are clean.
-  # - +force+: A Boolean indicating if the result must be re-indexed. If true, it
-  #   implies save=true.
-  # Returns MiGA::Result or nil.
-  def add_result(result_type, save=true, opts={})
-    dir = @@RESULT_DIRS[result_type]
-    return nil if dir.nil?
-    base = File.expand_path("data/#{dir}/#{name}", project.path)
-    unless opts[:force]
-      r_pre = MiGA::Result.load("#{base}.json")
-      return r_pre if (r_pre.nil? and not save) or not r_pre.nil?
-    end
-    r = File.exist?("#{base}.done") ?
-        self.send("add_result_#{result_type}", base, opts) : nil
-    r.save unless r.nil?
-    r
-  end
-
-  ##
-  # Gets a result as MiGA::Result for the datasets with +result_type+. This is
-  # equivalent to +add_result(result_type, false)+.
-  def get_result(result_type) ; add_result(result_type, false) ; end
-
-  ##
-  # Returns the key symbol of the first registered result (sorted by the
-  # execution order). This typically corresponds to the result used as the
-  # initial input. Passes +save+ to #add_result.
-  def first_preprocessing(save=false)
-    @@PREPROCESSING_TASKS.find do |t|
-      not ignore_task?(t) and not add_result(t, save).nil?
-    end
-  end
-  
-  ##
-  # Returns the key symbol of the next task that needs to be executed. Passes
-  # +save+ to #add_result.
-  def next_preprocessing(save=false)
-    after_first = false
-    first = first_preprocessing(save)
-    return nil if first.nil?
-    @@PREPROCESSING_TASKS.each do |t|
-      next if ignore_task? t
-      return t if after_first and add_result(t, save).nil?
-      after_first = (after_first or (t==first))
-    end
-    nil
-  end
-
   ##
   # Should I ignore +task+ for this dataset?
   def ignore_task?(task)
@@ -248,40 +120,13 @@ class MiGA::Dataset < MiGA::MiGA
       [@@_ONLY_NONMULTI_TASKS_H[task], is_nonmulti?]==pattern )
   end
 
-  ##
-  # Are all the dataset-specific tasks done? Passes +save+ to #add_result.
-  def done_preprocessing?(save=false)
-    !first_preprocessing(save).nil? and next_preprocessing(save).nil?
-  end
-  
-  ##
-  # Returns an array indicating the stage of each task (sorted by execution
-  # order). The values are integers:
-  # - 0 for an undefined result (a task before the initial input).
-  # - 1 for a registered result (a completed task).
-  # - 2 for a queued result (a task yet to be executed).
-  # It passes +save+ to #add_result
-  def profile_advance(save=false)
-    first_task = first_preprocessing(save)
-    return Array.new(@@PREPROCESSING_TASKS.size, 0) if first_task.nil?
-    adv = []
-    state = 0
-    next_task = next_preprocessing(save)
-    @@PREPROCESSING_TASKS.each do |task|
-      state = 1 if first_task==task
-      state = 2 if !next_task.nil? and next_task==task
-      adv << state
-    end
-    adv
-  end
-  
   ##
   # Returns an Array of +how_many+ duples (Arrays) sorted by AAI:
   # - +0+: A String with the name(s) of the reference dataset.
   # - +1+: A Float with the AAI.
-  # This function is currently only supported for query datasets when +ref_project+ is false
-  # (default), and only for reference dataset when +ref_project+ is true. It returns
-  # +nil+ if this analysis is not supported.
+  # This function is currently only supported for query datasets when
+  # +ref_project+ is false (default), and only for reference dataset when
+  # +ref_project+ is true. It returns +nil+ if this analysis is not supported.
   def closest_relatives(how_many=1, ref_project=false)
     return nil if (is_ref? != ref_project) or is_multi?
     r = result(ref_project ? :taxonomy : :distances)
@@ -292,3 +137,4 @@ class MiGA::Dataset < MiGA::MiGA
   end
 
 end # class MiGA::Dataset
+