miga-base 0.4.1.0 → 0.4.2.0

data/actions/files.rb

@@ -1,43 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true, details:false, json:true}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset_opt])
-  opt.on("-i", "--info",
-    "If set, it prints additional details for each file."
-    ){ |v| o[:details]=v }
-  opt.on("--[no-]json",
-    "If set to no, excludes json files containing results metadata."
-    ){ |v| o[:json]=v }
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-opt_require(o, project:"-P")
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-if o[:dataset].nil?
-  results = p.results
-else
-  $stderr.puts "Loading dataset." unless o[:q]
-  ds = p.dataset(o[:dataset])
-  raise "Impossible to load dataset: #{o[:dataset]}" if ds.nil?
-  results = ds.results
-end
-
-$stderr.puts "Listing files." unless o[:q]
-results.each do |result|
-  puts "#{ "#{result.path}\t\t" if o[:details] }#{result.path}" if o[:json]
-  result.each_file do |k,f|
-    puts "#{ "#{result.path}\t#{k}\t" if o[:details] }#{result.dir}/#{f}"
-  end
-end
-
-$stderr.puts "Done." unless o[:q]

data/actions/find.rb

@@ -1,41 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true, add:false, ref:true}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset_type])
-  opt.on("-a", "--add",
-    "Register the datasets found. By default, only lists them (dry run)."
-    ){ |v| o[:add]=v }
-  opt.on("-q", "--query",
-    "If set, all datasets are registered as query datasets."
-    ){ |v| o[:ref]=!v }
-  opt.on("-u", "--user STRING", "Owner of the dataset."){ |v| o[:user]=v }
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-opt_require(o, project:"-P")
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-$stderr.puts "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)
-    res = d.first_preprocessing(true)
-    puts "- #{res}" unless o[:q]
-  end
-end
-
-$stderr.puts "Done." unless o[:q]

data/actions/get.rb

@@ -1,105 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-require 'miga/remote_dataset'
-
-o = {q: true, query: false, universe: :ebi, db: :embl,
-  get_md: false, only_md: false}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset, :dataset_type])
-  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('-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('-c', '--comments STRING',
-    'Comments on the dataset.'){ |v| o[:comments]=v }
-  opt.on('-m', '--metadata STRING',
-    'Metadata as key-value pairs separated by = and delimited by comma.',
-    'Values are saved as strings except for booleans (true / false) or nil.'
-    ){ |v| o[:metadata]=v }
-  opt.on('--get-metadata',
-    'Only download and update metadata for existing datasets'
-    ){ |v| o[:get_md] = v }
-  opt.on('--only-metadata',
-    'Create datasets without input data but retrieve all metadata.'
-    ){ |v| o[:only_md] = v }
-  opt.on('--api-key STRING',
-    'API key for the given universe.'){ |v| o[:api_key] = v }
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-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
-
-glob.each do |o_i|
-  opt_require(o_i, project: '-P', dataset: '-D', ids: '-I')
-  unless o_i[:api_key].nil?
-    ENV["#{o_i[:universe].to_s.upcase}_API_KEY"] = o_i[:api_key]
-  end
-
-  $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?
-
-  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])
-
-  if o[:get_md]
-    $stderr.puts 'Updating dataset.' unless o_i[:q]
-    d = p.dataset(o_i[:dataset])
-    next if d.nil?
-    md = add_metadata(o_i, d).metadata.data
-    rd.update_metadata(d, md)
-  else
-    $stderr.puts 'Creating dataset.' unless o_i[:q]
-    dummy_d = MiGA::Dataset.new(p, o_i[:dataset])
-    md = add_metadata(o_i, dummy_d).metadata.data
-    md[:metadata_only] = true if o[:only_md]
-    dummy_d.remove!
-    rd.save_to(p, o_i[:dataset], !o_i[:query], md)
-    p.add_dataset(o_i[:dataset])
-  end
-
-  $stderr.puts 'Done.' unless o_i[:q]
-end

data/actions/init.rb

@@ -1,301 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-require 'shellwords'
-
-o = {q: true, mytaxa: nil,
-  config: File.expand_path('.miga_modules', ENV['HOME']),
-  ask: false, auto: false, dtype: 'bash'}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt.on('-c', '--config PATH',
-    'Path to the Bash configuration file.',
-    "By default: #{o[:config]}."){ |v| o[:config] = v }
-  opt.on('--[no-]mytaxa',
-    'Should I try setting up MyTaxa its dependencies?',
-    'By default: interactive (true if --auto).'
-    ){ |v| o[:mytaxa] = v }
-  opt.on('--daemon-type STRING',
-    'Type of daemon launcher, one of: bash, qsub, msub, slurm.',
-    "By default: interactive (#{o[:dtype]} if --auto)."
-    ){ |v| o[:dtype]=v }
-  opt.on('--ask-all', 'If set, asks for the location of all software.',
-    'By default, only the locations missing in PATH are requested.'
-    ){ |v| o[:ask] = v }
-  opt.on('--auto', 'If set, accepts all defaults as answers.'
-    ){ |v| o[:auto] = v }
-  opt_common(opt, o)
-end.parse!
-$auto_answer = o[:auto]
-
-def ask_user(q, d = nil, ans = nil, force = false)
-  $stderr.print "#{q}#{" (#{ans.join(" / ")})" unless ans.nil?}" +
-    "#{"  [#{d}]" unless d.nil?} > "
-  if $auto_answer and not force
-    $stderr.puts ''
-  else
-    o = gets.chomp
-  end
-  o = d if o.nil? or o.empty?
-  unless ans.nil? or ans.include? o
-    $stderr.puts 'Answer not recognized.'
-    return ask_user(q, d, ans)
-  end
-  o
-end
-
-##=> Main <=
-
-miga = MiGA::MiGA.root_path
-$stderr.puts <<BANNER
-===[ Welcome to MiGA, the Microbial Genome Atlas ]===
-
-I'm the initialization script, and I'll sniff around your computer to
-make sure you have all the requirements for MiGA data processing.
-
-BANNER
-
-if ask_user(
-      'Would you like to see all the requirements before starting?',
-      'no', %w(yes no)) == 'yes'
-  File.open(File.expand_path('utils/requirements.txt', miga), 'r') do |fh|
-    fh.each_line{ |ln| $stderr.puts ln }
-  end
-end
-
-rc_path = File.expand_path('.miga_rc', ENV['HOME'])
-if File.exist? rc_path
-  if ask_user(
-        'I found a previous configuration. Do you want to continue?',
-        'yes', %w(yes no)) == 'no'
-    $stderr.puts 'OK, see you soon!'
-    exit 0
-  end
-end
-rc_fh = File.open(rc_path, 'w')
-rc_fh.puts <<BASH
-#!/bin/bash
-# `miga init` made this on #{Time.now}
-
-BASH
-
-# Check bash configuration file
-unless File.exist? o[:config]
-  o[:config] = ask_user(
-        'Is there a script I need to load at startup?', o[:config])
-end
-if File.exist? o[:config]
-  o[:config] = File.expand_path o[:config]
-  $stderr.puts "Found bash configuration script: #{o[:config]}."
-  rc_fh.puts "MIGA_STARTUP='#{o[:config]}'"
-  rc_fh.puts '. "$MIGA_STARTUP"'
-end
-$stderr.puts ''
-
-# Check for software requirements
-$stderr.puts 'Looking for requirements:'
-if o[:mytaxa].nil?
-  o[:mytaxa] = ask_user(
-        'Should I include MyTaxa modules?', 'yes', %w(yes no)) == 'yes'
-end
-rc_fh.puts 'export MIGA_MYTAXA="no"' unless o[:mytaxa]
-paths = {}
-rc_fh.puts 'MIGA_PATH=""'
-File.open(File.expand_path('utils/requirements.txt', miga), 'r') do |fh|
-  fh.each_line do |ln|
-    next if $. < 3
-    r = ln.chomp.split(/\t+/)
-    next if r[0] =~ /\(opt\)$/ and not o[:mytaxa]
-    $stderr.print "Testing #{r[0]}#{" (#{r[3]})" if r[3]}... "
-    path = nil
-    loop do
-      if File.exist? o[:config]
-        d_path = File.dirname(`. "#{o[:config]}" && which "#{r[1]}"`)
-      else
-        d_path = File.dirname(`which "#{r[1]}"`)
-      end
-      if o[:ask] or d_path == '.'
-        path = ask_user('Where can I find it?', d_path, nil, true)
-      else
-        path = d_path
-        $stderr.puts path
-      end
-      if File.executable? File.expand_path(r[1], path)
-        if d_path != path
-          rc_fh.puts "MIGA_PATH=\"#{path}:$MIGA_PATH\" # #{r[1]}"
-        end
-        break
-      end
-      $stderr.print "I cannot find #{r[1]}. "
-    end
-    paths[r[1]] = File.expand_path(r[1], path).shellescape
-  end
-end
-rc_fh.puts 'export PATH="$MIGA_PATH$PATH"'
-$stderr.puts ''
-
-# Check for other files
-if o[:mytaxa]
-  $stderr.puts 'Looking for MyTaxa databases:'
-  mt = File.dirname paths["MyTaxa"]
-  $stderr.print 'Looking for scores... '
-  unless Dir.exist? File.expand_path('db', mt)
-    $stderr.puts "no.\nExecute 'python2 #{mt}/utils/download_db.py'."
-    exit 1
-  end
-  $stderr.puts 'yes.'
-  $stderr.print 'Looking for diamond db... '
-  unless File.exist? File.expand_path('AllGenomes.faa.dmnd', mt)
-    $stderr.puts "no.\nDownload " +
-      "'http://enve-omics.ce.gatech.edu/data/public_mytaxa/" +
-      "AllGenomes.faa.dmnd' into #{mt}."
-    exit 1
-  end
-  $stderr.puts ''
-end
-
-# Check for R packages
-$stderr.puts 'Looking for R packages:'
-%w(enveomics.R ape cluster vegan).each do |pkg|
-  $stderr.print "Testing #{pkg}... "
-  `echo "library('#{pkg}')" | #{paths["R"].shellescape} --vanilla -q 2>&1`
-  if $?.success?
-    $stderr.puts 'yes.'
-  else
-    $stderr.puts 'no, installing.'
-    $stderr.print '' +
-      `echo "install.packages('#{pkg}', repos='http://cran.rstudio.com/')" \
-            | #{paths["R"].shellescape} --vanilla -q 2>&1`
-    `echo "library('#{pkg}')" | #{paths["R"].shellescape} --vanilla -q 2>&1`
-    raise "Unable to auto-install R package #{pkg}." unless $?.success?
-  end
-end
-$stderr.puts ''
-
-# Check for Ruby gems
-$stderr.puts 'Looking for Ruby gems:'
-%w(sqlite3 daemons json).each do |pkg|
-  $stderr.print "Testing #{pkg}... "
-  `#{paths["ruby"].shellescape} -r "#{pkg}" -e "" 2>/dev/null`
-  if $?.success?
-    $stderr.puts 'yes.'
-  else
-    $stderr.puts 'no, installing.'
-    # This hackey mess is meant to ensure the test and installation are done
-    # on the configuration Ruby, not on the Ruby currently executing the init
-    # action
-    $stderr.print `#{paths['ruby'].shellescape} \
-        -r rubygems -r rubygems/gem_runner \
-        -e "Gem::GemRunner.new.run %w(install --user #{pkg})" 2>&1`
-    raise "Unable to auto-install Ruby gem #{pkg}." unless $?.success?
-  end
-end
-$stderr.puts ''
-
-# Configure daemon
-$stderr.puts 'Default daemon configuration:'
-daemon_f = File.expand_path('.miga_daemon.json', ENV['HOME'])
-unless File.exist?(daemon_f) and ask_user(
-          'A template daemon already exists, do you want to preserve it?',
-          'yes', %w(yes no)) == 'yes'
-  v = {created:Time.now.to_s, updated:Time.now.to_s}
-  v[:type] = ask_user('Please select the type of daemon you want to setup',
-            o[:dtype], %w(bash qsub msub slurm))
-  case v[:type]
-    when 'bash'
-      v[:latency] = ask_user('How long should I sleep? (in seconds)', '30').to_i
-      v[:maxjobs] = ask_user('How many jobs can I launch at once?', '6').to_i
-      v[:ppn]     = ask_user('How many CPUs can I use per job?', '2').to_i
-      $stderr.puts 'Setting up internal daemon defaults.'
-      $stderr.puts 'If you don\'t understand this just leave default values:'
-      v[:cmd] = ask_user(
-        "How should I launch tasks?\n  %1$s: script path, %2$s: variables, " +
-        "%3$d: CPUs, %4$s: log file, %5$s: task name.\n",
-        "%2$s '%1$s' > '%4$s' 2>&1")
-      v[:var] = ask_user(
-        "How should I pass variables?\n  %1$s: keys, %2$s: values.\n",
-        "%1$s=%2$s")
-      v[:varsep] = ask_user('What should I use to separate variables?', ' ')
-      v[:alive] = ask_user(
-        "How can I know that a process is still alive?\n  %1$s: PID, " +
-        "output should be 1 for running and 0 for non-running.\n",
-        "ps -p '%1$s'|tail -n+2|wc -l")
-      v[:kill]    = ask_user(
-        "How should I terminate tasks?\n  %s: process ID.", "kill -9 '%s'")
-    when 'slurm'
-      queue       = ask_user('What queue should I use?', nil, nil, true)
-      v[:latency] = ask_user(
-            'How long should I sleep? (in seconds)', '150').to_i
-      v[:maxjobs] = ask_user('How many jobs can I launch at once?', '300').to_i
-      v[:ppn]     = ask_user('How many CPUs can I use per job?', '2').to_i
-      $stderr.puts 'Setting up internal daemon defaults.'
-      $stderr.puts 'If you don\'t understand this just leave default values:'
-      v[:cmd]     = ask_user(
-        "How should I launch tasks?\n  %1$s: script path, %2$s: variables, " +
-        "%3$d: CPUs, %4$d: log file, %5$s: task name.\n",
-        "%2$s sbatch --partition='#{queue}' --export=ALL " +
-        "--nodes=1 --ntasks-per-node=%3$d --output='%4$s' --job-name='%5$s' " +
-        "--mem=9G --time=12:00:00 %1$s | perl -pe 's/.* //'")
-      v[:var]     = ask_user(
-        "How should I pass variables?\n  %1$s: keys, %2$s: values.\n",
-        "%1$s=%2$s")
-      v[:varsep]  = ask_user('What should I use to separate variables?', ' ')
-      v[:alive] = ask_user(
-        "How can I know that a process is still alive?\n  %1$s: job id, " +
-        "output should be 1 for running and 0 for non-running.\n",
-        "squeue -h -o %%t -j '%1$s' | grep '^PD\\|R\\|CF\\|CG$' " +
-        "| tail -n 1 | wc -l")
-      v[:kill]    = ask_user(
-        "How should I terminate tasks?\n  %s: process ID.", "scancel '%s'")
-    else # [qm]sub
-      queue       = ask_user('What queue should I use?', nil, nil, true)
-      v[:latency] = ask_user(
-            'How long should I sleep? (in seconds)', '150').to_i
-      v[:maxjobs] = ask_user('How many jobs can I launch at once?', '300').to_i
-      v[:ppn]     = ask_user('How many CPUs can I use per job?', '2').to_i
-      $stderr.puts 'Setting up internal daemon defaults.'
-      $stderr.puts 'If you don\'t understand this just leave default values:'
-      v[:cmd]     = ask_user(
-        "How should I launch tasks?\n  %1$s: script path, %2$s: variables, " +
-        "%3$d: CPUs, %4$d: log file, %5$s: task name.\n",
-        "#{v[:type]} -q '#{queue}' -v '%2$s' -l nodes=1:ppn=%3$d %1$s " +
-        "-j oe -o '%4$s' -N '%5$s' -l mem=9g -l walltime=12:00:00 | grep .")
-      v[:var]     = ask_user(
-        "How should I pass variables?\n  %1$s: keys, %2$s: values.\n",
-        "%1$s=%2$s")
-      v[:varsep]  = ask_user('What should I use to separate variables?', ',')
-      if v[:type] == 'qsub'
-        v[:alive] = ask_user(
-          "How can I know that a process is still alive?\n  %1$s: job id, " +
-          "output should be 1 for running and 0 for non-running.\n",
-          "qstat -f '%1$s'|grep ' job_state ='|perl -pe 's/.*= //'|grep '[^C]'"+
-          "|tail -n1|wc -l|awk '{print $1}'")
-        v[:kill]    = ask_user(
-          "How should I terminate tasks?\n  %s: process ID.", "qdel '%s'")
-      else
-        v[:alive] = ask_user(
-          "How can I know that a process is still alive?\n  %1$s: job id, " +
-          "output should be 1 for running and 0 for non-running.\n",
-          "checkjob '%1$s'|grep '^State:'|perl -pe 's/.*: //'" +
-          "|grep 'Deferred\\|Hold\\|Idle\\|Starting\\|Running\\|Blocked'"+
-          "|tail -n1|wc -l|awk '{print $1}'")
-        v[:kill]    = ask_user(
-          "How should I terminate tasks?\n  %s: process ID.", "canceljob '%s'")
-      end
-  end
-  File.open(daemon_f, 'w'){ |fh| fh.puts JSON.pretty_generate(v) }
-end
-$stderr.puts ''
-
-rc_fh.puts <<FOOT
-
-MIGA_CONFIG_VERSION='#{MiGA::MiGA.VERSION}'
-MIGA_CONFIG_LONGVERSION='#{MiGA::MiGA.LONG_VERSION}'
-MIGA_CONFIG_DATE='#{Time.now}'
-
-FOOT
-
-$stderr.puts 'Configuration complete. MiGA is ready to work!'
-$stderr.puts ''

data/actions/ln.rb

@@ -1,47 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true, info:false, force:false, method: :hardlink }
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset_opt])
-  opt.on("-Q", "--project-target PATH",
-    "(Mandatory) Path to the project where to link the dataset."
-    ){ |v| o[:project2]=v }
-  opt.on("-f", "--force",
-    "Forces linking, even if dataset's preprocessing is incomplete."
-    ){ |v| o[:force]=v }
-  opt.on("-s", "--symlink",
-    "Creates symlinks instead of the default hard links."
-    ){ o[:method] = :symlink }
-  opt.on("-c", "--copy",
-    "Creates copies instead of the default hard links."){ o[:method] = :copy }
-  opt_filter_datasets(opt, o)
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-opt_require(o, project:"-P", project2:"-Q")
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-q = MiGA::Project.load(o[:project2])
-raise "Impossible to load project: #{o[:project2]}" if q.nil?
-
-$stderr.puts "Listing dataset." unless o[:q]
-if o[:dataset].nil?
-  ds = p.datasets
-else
-  ds = [p.dataset(o[:dataset])]
-end
-ds = filter_datasets!(ds, o)
-ds.each do |d|
-  next unless o[:force] or d.done_preprocessing?
-  puts d.name
-  q.import_dataset(d, o[:method])
-end
-
-$stderr.puts "Done." unless o[:q]

data/actions/ls.rb

@@ -1,61 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true, info:false, processing:false, silent:false, tabular:false}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset_opt])
-  opt_filter_datasets(opt, o)
-  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("-m", "--metadata STRING",
-    "Print name and metadata field only. If set, ignores -i and assumes --tab."
-    ){ |v| o[:datum]=v }
-  opt.on("--tab",
-    "Returns a tab-delimited table."){ |v| o[:tabular] = v }
-  opt.on("-s", "--silent",
-    "No output and exit with non-zero status if the dataset list is empty."
-    ){ |v| o[:silent] = v }
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-opt_require(o, project:"-P")
-o[:q] = true if o[:silent]
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-$stderr.puts "Listing datasets." unless o[:q]
-if o[:dataset].nil?
-  ds = p.datasets
-elsif MiGA::Dataset.exist? p, o[:dataset]
-  ds = [p.dataset(o[:dataset])]
-else
-  ds = []
-end
-ds = filter_datasets!(ds, o)
-exit(1) if o[:silent] and ds.empty?
-
-if not o[:datum].nil?
-  ds.each do |d|
-    v = d.metadata[ o[:datum] ]
-    puts "#{d.name}\t#{v.nil? ? '?' : v}"
-  end
-elsif o[:info]
-  puts MiGA::MiGA.tabulate(
-        MiGA::Dataset.INFO_FIELDS, ds.map{ |d| d.info }, o[:tabular])
-elsif o[:processing]
-  comp = ["-","done","queued"]
-  puts MiGA::MiGA.tabulate([:name] + MiGA::Dataset.PREPROCESSING_TASKS,
-    ds.map{ |d| [d.name] + d.profile_advance.map{ |i| comp[i] } }, o[:tabular])
-else
-  ds.each{|d| puts d.name}
-end
-
-$stderr.puts "Done." unless o[:q]