miga-base 0.4.1.0 → 0.4.2.0

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.4.1.0
+  version: 0.4.2.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-08-17 00:00:00.000000000 Z
+date: 2019-09-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -16,68 +16,56 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.2.4
+        version: '1.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.2'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.2.4
+        version: '1.3'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: '1.8'
-    - - "<"
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '3'
+        version: '2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: '1.8'
-    - - "<"
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '3'
+        version: '2'
 - !ruby/object:Gem::Dependency
   name: sqlite3
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '1.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '1.4'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '11'
+        version: '12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '11'
+        version: '12'
 - !ruby/object:Gem::Dependency
   name: test-unit
   requirement: !ruby/object:Gem::Requirement
@@ -104,35 +92,40 @@ files:
 - LICENSE
 - README.md
 - Rakefile
-- actions/about.rb
-- actions/add.rb
-- actions/add_result.rb
-- actions/daemon.rb
-- actions/date.rb
-- actions/doctor.rb
-- actions/edit.rb
-- actions/files.rb
-- actions/find.rb
-- actions/get.rb
-- actions/init.rb
-- actions/ln.rb
-- actions/ls.rb
-- actions/ncbi_get.rb
-- actions/new.rb
-- actions/next_step.rb
-- actions/plugins.rb
-- actions/rm.rb
-- actions/run.rb
-- actions/stats.rb
-- actions/summary.rb
-- actions/tax_dist.rb
-- actions/tax_index.rb
-- actions/tax_set.rb
-- actions/tax_test.rb
 - bin/miga
 - lib/miga.rb
 - lib/miga/_data/aai-intax.tsv.gz
 - lib/miga/_data/aai-novel.tsv.gz
+- lib/miga/cli.rb
+- lib/miga/cli/action.rb
+- lib/miga/cli/action/about.rb
+- lib/miga/cli/action/add.rb
+- lib/miga/cli/action/add_result.rb
+- lib/miga/cli/action/console.rb
+- lib/miga/cli/action/daemon.rb
+- lib/miga/cli/action/date.rb
+- lib/miga/cli/action/doctor.rb
+- lib/miga/cli/action/edit.rb
+- lib/miga/cli/action/files.rb
+- lib/miga/cli/action/find.rb
+- lib/miga/cli/action/generic.rb
+- lib/miga/cli/action/get.rb
+- lib/miga/cli/action/init.rb
+- lib/miga/cli/action/ln.rb
+- lib/miga/cli/action/ls.rb
+- lib/miga/cli/action/ncbi_get.rb
+- lib/miga/cli/action/new.rb
+- lib/miga/cli/action/next_step.rb
+- lib/miga/cli/action/plugins.rb
+- lib/miga/cli/action/rm.rb
+- lib/miga/cli/action/run.rb
+- lib/miga/cli/action/stats.rb
+- lib/miga/cli/action/summary.rb
+- lib/miga/cli/action/tax_dist.rb
+- lib/miga/cli/action/tax_index.rb
+- lib/miga/cli/action/tax_set.rb
+- lib/miga/cli/action/tax_test.rb
+- lib/miga/cli/base.rb
 - lib/miga/common.rb
 - lib/miga/common/base.rb
 - lib/miga/common/format.rb
@@ -158,6 +151,7 @@ files:
 - lib/miga/tax_dist.rb
 - lib/miga/tax_index.rb
 - lib/miga/taxonomy.rb
+- lib/miga/taxonomy/base.rb
 - lib/miga/version.rb
 - scripts/aai_distances.bash
 - scripts/ani_distances.bash

data/actions/about.rb

@@ -1,43 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true, info:false, processing:false, tabular:false}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project])
-  opt.on("-p", "--processing",
-    "Print information on processing advance."){ |v| o[:processing]=v }
-  opt.on("-m", "--metadata STRING",
-    "Print name and metadata field only."
-    ){ |v| o[:datum]=v }
-  opt.on("--tab",
-    "Returns a tab-delimited table."){ |v| o[:tabular] = v }
-  opt_common(opt, o)
-end.parse!
-
-
-##=> Main <=
-opt_require(o, project:"-P")
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-if not o[:datum].nil?
-  v = p.metadata[ o[:datum] ]
-  puts v.nil? ? '?' : v
-elsif o[:processing]
-  keys = MiGA::Project.DISTANCE_TASKS + MiGA::Project.INCLADE_TASKS
-  puts MiGA::MiGA.tabulate([:task, :status], keys.map do |k|
-    [k, p.add_result(k, false).nil? ? "queued" : "done"]
-  end, o[:tabular])
-else
-  puts MiGA::MiGA.tabulate([:key, :value], p.metadata.data.keys.map do |k|
-    v = p.metadata[k]
-    [k, k==:datasets ? v.size : v]
-  end, o[:tabular])
-end
-
-$stderr.puts "Done." unless o[:q]

data/actions/add.rb

@@ -1,129 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-input_types = {
-  raw_reads_single: 
-    ['Single raw reads in a single FastQ file',
-      :raw_reads, %w[.1.fastq]],
-  raw_reads_paired: 
-    ['Paired raw reads in two FastQ files',
-      :raw_reads, %w[.1.fastq .2.fastq]],
-  trimmed_reads_single: 
-    ['Single trimmed reads in a single FastA file',
-      :trimmed_fasta, %w[.SingleReads.fa]],
-  trimmed_reads_paired: 
-    ['Paired trimmed reads in two FastA files',
-      :trimmed_fasta, %w[.1.fasta .2.fasta]],
-  trimmed_reads_interleaved: 
-    ['Paired trimmed reads in a single FastA file',
-      :trimmed_fasta, %w[.CoupledReads.fa]],
-  assembly: 
-    ['Assembled contigs or scaffolds in FastA format',
-      :assembly, %w[.LargeContigs.fna]]
-}
-
-o = {q: true, ref: true, ignore_dups: false,
-  regexp: /^(?:.*\/)?(.+?)(?:\..*(?:[12]|Reads|Contigs))?(?i:\.f[nastq]+)?$/}
-OptionParser.new do |opt|
-  opt_banner(opt, true)
-  opt_object(opt, o, [:project, :dataset_opt, :dataset_type_req])
-  opt.on('-q', '--query',
-    'If set, the dataset is registered as a query, not a reference dataset.'
-    ){ |v| o[:ref] = !v }
-  opt.on('-d', '--description STRING',
-    'Description of the dataset.'){ |v| o[:description] = v }
-  opt.on('-c', '--comments STRING',
-    'Comments on the dataset.'){ |v| o[:comments] = v }
-  opt.on('-m', '--metadata STRING',
-    'Metadata as key-value pairs separated by = and delimited by comma.',
-    'Values are saved as strings except for booleans (true / false) or nil.'
-    ){ |v| o[:metadata] = v }
-  opt.on('-r', '--name-regexp REGEXP', Regexp,
-    'Regular expression indicating how to extract the name from the file path.',
-    "By default: '#{o[:regexp]}'"){ |v| o[:regexp] = v }
-  opt.on('-i', '--input-type STRING',
-    'Type of input data, one of the following:',
-    *input_types.map{ |k,v| "~ #{k}: #{v[0]}." }
-    ){ |v| o[:input_type] = v.downcase.to_sym }
-  opt.on('--ignore-dups', 'Continue with a warning if a dataset already exists.'
-    ){ |v| o[:ignore_dups] = v }
-  opt_common(opt, o)
-
-  opt.separator 'You can create multiple datasets with a single command, ' \
-    'simply pass all the files at the end (FILES...).'
-  opt.separator 'If -D is passed, only one dataset will be added. ' \
-    'Otherwise, dataset names will be determined by the file paths (-r).'
-  opt.separator ''
-end.parse!
-
-##=> Main <=
-opt_require(o, project: '-P')
-files = ARGV
-file_type = nil
-if files.empty?
-  opt_require_type(o, MiGA::Dataset)
-  files = [nil]
-else
-  raise 'Please specify input type (-i).' if o[:input_type].nil?
-  file_type = input_types[o[:input_type]]
-  raise "Unrecognized input type: #{o[:input_type]}." if file_type.nil?
-  raise 'Some files are duplicated, files must be unique.' if
-    files.size != files.uniq.size
-  if o[:input_type].to_s =~ /_paired$/
-    raise 'Odd number of files incompatible with input type.' if files.size.odd?
-    files = Hash[*files].to_a
-  else
-    files = files.map{ |i| [i] }
-  end
-  raise 'The dataset name (-D) can only be specified with one input file.' if
-    files.size > 1 and not o[:dataset].nil?
-end
-
-$stderr.puts 'Loading project.' unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-$stderr.puts 'Creating datasets:' unless o[:q]
-files.each do |file|
-  name = o[:dataset]
-  if name.nil?
-    ref_file = file.is_a?(Array) ? file.first : file
-    m = o[:regexp].match(ref_file)
-    raise "Cannot extract name from file: #{ref_file}" if m.nil? or m[1].nil?
-    name = m[1].miga_name
-  end
-
-  if MiGA::Dataset.exist?(p, name)
-    if o[:ignore_dups]
-      warn "Dataset already exists: #{name}."
-      next
-    else
-      raise "Dataset already exists: #{name}."
-    end
-  end
-
-  $stderr.puts "o #{name}" unless o[:q]
-  d = MiGA::Dataset.new(p, name, o[:ref])
-  raise "Unexpected: Couldn't create dataset: #{name}." if d.nil?
-
-  unless file.nil?
-    r_dir = MiGA::Dataset.RESULT_DIRS[ file_type[1] ]
-    r_path = File.expand_path("data/#{r_dir}/#{d.name}", p.path)
-    file_type[2].each_with_index do |ext, i|
-      gz = file[i] =~ /\.gz/ ? '.gz' : ''
-      FileUtils.cp(file[i], "#{r_path}#{ext}#{gz}")
-      $stderr.puts "  file: #{file[i]}" unless o[:q]
-    end
-    File.open("#{r_path}.done", 'w') { |f| f.print Time.now.to_s }
-  end
-  
-  d = add_metadata(o, d)
-  d.save
-  p.add_dataset(name)
-  res = d.first_preprocessing(true)
-  $stderr.puts "  result: #{res}" unless o[:q]
-end
-
-$stderr.puts 'Done.' unless o[:q]

data/actions/add_result.rb

@@ -1,30 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q:true, force:false}
-opts = OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset_opt, :result])
-  opt.on("-f", "--force",
-    "Forces re-indexing of the result even if it's already registered."
-    ){ |v| o[:force]=v }
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-opts.parse!
-opt_require(o, project:"-P", name:"-r")
-
-$stderr.puts "Loading project." unless o[:q]
-p = MiGA::Project.load(o[:project])
-raise "Impossible to load project: #{o[:project]}" if p.nil?
-
-$stderr.puts "Registering result." unless o[:q]
-obj = o[:dataset].nil? ? p : p.dataset(o[:dataset])
-r = obj.add_result(o[:name].to_sym, true, force: o[:force])
-
-raise "Cannot add result, incomplete expected files." if r.nil?
-
-$stderr.puts "Done." unless o[:q]

data/actions/daemon.rb

@@ -1,55 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-require 'miga/daemon'
-
-task = ARGV.shift unless %w[-h --help].include? ARGV.first
-ARGV << '-h' if ARGV.empty?
-o = {q: true, daemon_opts: []}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt.separator 'task:'
-  { start:   'Start an instance of the application.',
-    stop:    'Start an instance of the application.',
-    restart: 'Stop all instances and restart them afterwards.',
-    reload:  'Send a SIGHUP to all instances of the application.',
-    run:     'Start the application and stay on top.',
-    zap:     'Set the application to a stopped state.',
-    status:  'Show status (PID) of application instances.'
-  }.each{ |k,v| opt.separator sprintf '    %*s%s', -33, k, v }
-  opt.separator ''
-  opt.separator 'MiGA options:'
-  opt_object(opt, o, [:project])
-  opt.on('--shutdown-when-done',
-    'If passed, the daemon will exit when all processing is done.',
-    'Otherwise (default), it will stay idle awaiting for new data.'
-    ){ |v| o[:shutdown_when_done] = v }
-  opt.on('--latency INT',
-    'Number of seconds the daemon will be sleeping.'
-    ){ |v| o[:latency]=v.to_i }
-  opt.on('--max-jobs INT',
-    'Maximum number of jobs to use simultaneously.'){ |v| o[:maxjobs]=v.to_i }
-  opt.on('--ppn INT',
-    'Maximum number of cores to use in a single job.'){ |v| o[:ppn]=v.to_i }
-  opt_common(opt, o)
-  opt.separator 'Daemon options:'
-  opt.on('-t', '--ontop',
-    'Stay on top (does not daemonize).'){ o[:daemon_opts] << '-t' }
-  opt.on('-f', '--force', 'Force operation.'){ o[:daemon_opts] << '-f' }
-  opt.on('-n', '--no_wait',
-    'Do not wait for processes to stop.'){ o[:daemon_opts] << '-n' }
-  opt.on('--shush', 'Silence the daemon.'){ o[:daemon_opts] << '--shush' }
-end.parse!
-
-##=> Main <=
-opt_require(o, project: '-P')
-
-p = MiGA::Project.load(o[:project]) or raise 'Project doesn\'t exist, aborting.'
-d = MiGA::Daemon.new(p)
-[:latency, :maxjobs, :ppn, :shutdown_when_done].each do |k|
-  d.runopts(k, o[k]) unless o[k].nil?
-end
-d.daemon(task, o[:daemon_opts])
-

data/actions/date.rb

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {}
-opts = OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_common(opt, o)
-end.parse!
-
-##=> Main <=
-opts.parse!
-puts Time.now.to_s

data/actions/doctor.rb

@@ -1,201 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-require "sqlite3"
-
-tasks = {
-  db: ['databases', 'Check database files integrity'],
-  dist: ['distances', 'Check distance summary tables.'],
-  files: ['files', 'Check for outdated files.'],
-  ess: ['essential-genes', 'Check for unarchived essential genes'],
-  mts: ['mytaxa-scan', 'Check for unarchived MyTaxa scan'],
-  start: ['start', 'Check for lingering .start files'],
-  tax: ['taxonomy', 'Check for taxonomy consistency (not implemented)']
-}
-o = {q: true, ld: false}
-tasks.keys.each{ |i| o[i] = true }
-tasks_n = Hash[tasks.map{ |k,v| [v[0], k] }]
-
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project])
-  opt.on('-l', '--list-datasets',
-    'List all fixed datasets on advance.'){ |v| o[:ld]=v }
-  opt.on('--ignore TASK1,TASK2', Array,
-    'Do not perform the task(s) listed. Available tasks are:',
-    * tasks.values.map{ |v| "#{v[0]}: #{v[1]}" }
-    ){ |v| v.map{ |i| o[tasks_n[i]] = false } }
-  opt.on('--only TASK',
-    'Perform only the specified task (see --ignore).'
-    ){ |v| tasks.keys.each{ |i| o[i] = false }; o[v] = true }
-  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?
-
-def check_sqlite3_database(db_file, metric)
-  begin
-    SQLite3::Database.new(db_file) do |conn|
-      conn.execute("select count(*) from #{metric}").first
-    end
-  rescue SQLite3::SQLException
-    yield
-  end
-end
-
-if o[:db]
-  $stderr.puts 'o Checking databases integrity' unless o[:q]
-  p.each_dataset do |d|
-    [:distances, :taxonomy].each do |r_key|
-      r = d.result(r_key) or next
-      {haai_db: :aai, aai_db: :aai, ani_db: :ani}.each do |db_key, metric|
-        db_file = r.file_path(db_key) or next
-        check_sqlite3_database(db_file, metric) do
-          $stderr.puts(
-            "    > Removing #{db_key} #{r_key} table for #{d.name}.") if o[:ld]
-          [db_file, r.path(:done), r.path].each do |f|
-            File.unlink f if File.exist? f
-          end # each |f|
-        end # check_sqlite3_database
-      end # each |db_key, metric|
-    end # each |r_key|
-  end # each |d|
-end
-
-[:ani, :aai].each do |dist|
-  res = p.result("#{dist}_distances")
-  next if res.nil?
-  $stderr.puts "o Checking #{dist} table for consistent datasets" unless o[:q]
-  notok = {}
-  fix = {}
-  Zlib::GzipReader.open(res.file_path(:matrix)) do |fh|
-    lineno = 0
-    fh.each_line do |ln|
-      next if (lineno+=1)==1
-      r = ln.split("\t")
-      if [1,2].map{ |i| p.dataset(r[i]).nil? }.any?
-        [1,2].each do |i|
-          if p.dataset(r[i]).nil?
-            notok[r[i]] = true
-          else
-            fix[r[i]] = true
-          end
-        end
-      end
-    end
-  end
-  
-  $stderr.puts "  - Fixing #{fix.size} datasets" unless fix.empty? or o[:q]
-  fix.keys.each do |d_n|
-    $stderr.puts "    > Fixing #{d_n}." if o[:ld]
-    p.dataset(d_n).cleanup_distances!
-  end
-  
-  unless notok.empty?
-    unless o[:q]
-      $stderr.puts '  - Unregistered datasets detected: '
-      if notok.size < 3
-        $stderr.puts "    - #{notok.keys.join(', ')}"
-      else
-        $stderr.puts "    - #{notok.size}, including #{notok.keys.first}"
-      end
-      $stderr.puts '  - Removing tables, recompute'
-    end
-    res.remove!
-  end
-end if o[:dist]
-
-if o[:files]
-  $stderr.puts 'o Looking for outdated files in results' unless o[:q]
-  p.each_dataset do |d|
-    d.each_result do |r_k, r|
-      ok = true
-      r.each_file do |_f_sym, _f_rel, f_abs|
-        unless File.exist? f_abs
-          ok = false
-          break
-        end
-      end
-      unless ok
-        $stderr.puts "    > Registering again #{d.name}:#{r_k}" if o[:ld]
-        d.add_result(r_k, true, force: true)
-      end
-    end
-  end
-end
-
-if o[:ess]
-  $stderr.puts 'o Looking for unarchived essential genes.' unless o[:q]
-  p.each_dataset do |d|
-    res = d.result(:essential_genes)
-    next if res.nil?
-    dir = res.file_path(:collection)
-    if dir.nil?
-      $stderr.puts "    > Removing #{d.name}:essential_genes" if o[:ld]
-      res.remove!
-      next
-    end
-    unless Dir["#{dir}/*.faa"].empty?
-      $stderr.puts "    > Fixing #{d.name}." if o[:ld]
-      cmdo = `cd '#{dir}' && tar -zcf proteins.tar.gz *.faa && rm *.faa`.chomp
-      warn cmdo unless cmdo.empty?
-    end
-  end
-end
-
-if o[:mts]
-  $stderr.puts 'o Looking for unarchived MyTaxa Scan runs.' unless o[:q]
-  p.each_dataset do |d|
-    res = d.result(:mytaxa_scan)
-    next if res.nil?
-    dir = res.file_path(:regions)
-    fix = false
-    unless dir.nil?
-      if Dir.exist? dir
-        cmdo = `cd '#{dir}/..' \
-              && tar -zcf '#{d.name}.reg.tar.gz' '#{d.name}.reg' \
-              && rm -r '#{d.name}.reg'`.chomp
-        warn cmdo unless cmdo.empty?
-      end
-      fix = true
-    end
-    %w[blast mytaxain wintax gene_ids region_ids].each do |ext|
-      file = res.file_path(ext.to_sym)
-      unless file.nil?
-        FileUtils.rm(file) if File.exist? file
-        fix = true
-      end
-    end
-    if fix
-      $stderr.puts "    > Fixing #{d.name}." if o[:ld]
-      d.add_result(:mytaxa_scan, true, force: true)
-    end
-  end
-end
-
-if o[:start]
-  $stderr.puts 'o Looking for legacy .start files lingering.' unless o[:q]
-  p.each_dataset do |d|
-    d.each_result do |r_k, r|
-      if File.exist? r.path(:start)
-        $stderr.puts "    > Registering again #{d.name}:#{r_k}" if o[:ld]
-        r.save
-      end
-    end
-  end
-end
-
-if o[:tax]
-  #$stderr.puts "o Checking for taxonomy/distances consistency" unless o[:q]
-  # TODO: Find 95%ANI clusters with entries from different species
-end
-
-$stderr.puts 'Done' unless o[:q]
-

data/actions/edit.rb

@@ -1,33 +0,0 @@
-#!/usr/bin/env ruby
-
-# @package MiGA
-# @license Artistic-2.0
-
-o = {q: true}
-OptionParser.new do |opt|
-  opt_banner(opt)
-  opt_object(opt, o, [:project, :dataset_opt])
-  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_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?
-
-obj = p
-if o[:dataset]
-  $stderr.puts 'Loading dataset.' unless o[:q]
-  obj = p.dataset(o[:dataset])
-  raise 'Dataset does not exist.' if obj.nil?
-end
-obj = add_metadata(o, obj)
-obj.save
-
-$stderr.puts 'Done.' unless o[:q]