miga-base 0.7.3.0 → 0.7.7.0

data/lib/miga/cli/action/init/daemon_helper.rb

@@ -8,12 +8,14 @@ module MiGA::Cli::Action::Init::DaemonHelper
     cli.puts 'Default daemon configuration:'
     daemon_f = File.expand_path('.miga_daemon.json', ENV['HOME'])
     unless File.exist?(daemon_f) and cli.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}
+      '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] = cli.ask_user(
         'Please select the type of daemon you want to setup',
-        cli[:dtype], %w(bash ssh qsub msub slurm))
+        cli[:dtype], %w(bash ssh qsub msub slurm)
+      )
       case v[:type]
       when 'bash'
         v = configure_bash_daemon(v)
@@ -36,52 +38,61 @@ module MiGA::Cli::Action::Init::DaemonHelper
     v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
     cli.puts 'Setting up internal daemon defaults.'
     cli.puts 'If you don\'t understand this just leave default values:'
-    v[:cmd]     = cli.ask_user(
+    v[:cmd] = cli.ask_user(
       "How should I launch tasks?\n" \
         "  {{variables}}: script, vars, cpus, log, task_name, miga\n ",
-      "{{vars}} {{miga}} run -r '{{script}}' -l '{{log}}' -e")
-    v[:var]     = cli.ask_user(
+      "{{vars}} {{miga}} run -r '{{script}}' -l '{{log}}' -e"
+    )
+    v[:var] = cli.ask_user(
       "How should I pass variables?\n" \
         "  {{variables}}: key, value\n ",
-      "{{key}}={{value}}")
+      "{{key}}={{value}}"
+    )
     v[:varsep]  = cli.ask_user('What should I use to separate variables?', ' ')
     v[:alive]   = cli.ask_user(
       "How can I know that a process is still alive?\n" \
         "  Output should be 1 for running and 0 for non-running\n" \
         "  {{variables}}: pid\n ",
-      "ps -p '{{pid}}' | tail -n +2 | wc -l")
-    v[:kill]    = cli.ask_user(
+      "ps -p '{{pid}}' | tail -n +2 | wc -l"
+    )
+    v[:kill] = cli.ask_user(
       "How should I terminate tasks?\n" \
         "  {{variables}}: pid\n ",
-      "kill -9 '{{pid}}'")
+      "kill -9 '{{pid}}'"
+    )
     v
   end
 
   def configure_ssh_daemon(v)
     v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '3').to_i
     v[:nodelist] = cli.ask_user(
-      'What environmental variable points to node list?', '$MIGA_NODELIST')
-    v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
+      'What environmental variable points to node list?', '$MIGA_NODELIST'
+    )
+    v[:ppn] = cli.ask_user('How many CPUs can I use per job?', '2').to_i
     cli.puts 'Setting up internal daemon defaults.'
     cli.puts 'If you don\'t understand this just leave default values:'
-    v[:cmd]     = cli.ask_user(
+    v[:cmd] = cli.ask_user(
       "How should I launch tasks?\n" \
         "  {{variables}}: script, vars, cpus, log, task_name, miga, host\n ",
-      "{{vars}} {{miga}} run -r '{{script}}' -l '{{log}}' -R {{host}} -e")
-    v[:var]     = cli.ask_user(
+      "{{vars}} {{miga}} run -r '{{script}}' -l '{{log}}' -R {{host}} -e"
+    )
+    v[:var] = cli.ask_user(
       "How should I pass variables?\n" \
         "  {{variables}}: key, value\n ",
-      "{{key}}={{value}}")
+      "{{key}}={{value}}"
+    )
     v[:varsep]  = cli.ask_user('What should I use to separate variables?', ' ')
     v[:alive]   = cli.ask_user(
       "How can I know that a process is still alive?\n" \
         "  Output should be 1 for running and 0 for non-running\n" \
         "  {{variables}}: pid\n ",
-      "ps -p '{{pid}}' | tail -n +2 | wc -l")
-    v[:kill]    = cli.ask_user(
+      "ps -p '{{pid}}' | tail -n +2 | wc -l"
+    )
+    v[:kill] = cli.ask_user(
       "How should I terminate tasks?\n" \
         "  {{variables}}: pid\n ",
-      "kill -9 '{{pid}}'")
+      "kill -9 '{{pid}}'"
+    )
     v
   end
 
@@ -92,29 +103,34 @@ module MiGA::Cli::Action::Init::DaemonHelper
     v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
     cli.puts 'Setting up internal daemon defaults'
     cli.puts 'If you don\'t understand this just leave default values:'
-    v[:cmd]     = cli.ask_user(
+    v[:cmd] = cli.ask_user(
       "How should I launch tasks?\n" \
         "  {{variables}}: script, vars, cpus, log, task_name, miga\n ",
       "{{vars}} sbatch --partition='#{queue}' --export=ALL " \
         "--nodes=1 --ntasks-per-node={{cpus}} --output='{{log}}' " \
         "--job-name='{{task_name}}' --mem=9G --time=12:00:00 {{script}} " \
-        "| perl -pe 's/.* //'")
-    v[:var]     = cli.ask_user(
+        "| perl -pe 's/.* //'"
+    )
+    v[:var] = cli.ask_user(
       "How should I pass variables?\n" \
         "  {{variables}}: key, value\n ",
-      "{{key}}={{value}}")
-    v[:varsep]  = cli.ask_user(
-      'What should I use to separate variables?', ' ')
-    v[:alive]   = cli.ask_user(
+      "{{key}}={{value}}"
+    )
+    v[:varsep] = cli.ask_user(
+      'What should I use to separate variables?', ' '
+    )
+    v[:alive] = cli.ask_user(
       "How can I know that a process is still alive?\n" \
         "  Output should be 1 for running and 0 for non-running\n" \
         "  {{variables}}: pid\n ",
       "squeue -h -o %t -j '{{pid}}' | grep '^PD\\|R\\|CF\\|CG$' " \
-        "| tail -n 1 | wc -l")
-    v[:kill]    = cli.ask_user(
+        "| tail -n 1 | wc -l"
+    )
+    v[:kill] = cli.ask_user(
       "How should I terminate tasks?\n" \
         "  {{variables}}: pid\n ",
-        "scancel '{{pid}}'")
+      "scancel '{{pid}}'"
+    )
     v
   end
 
@@ -125,29 +141,34 @@ module MiGA::Cli::Action::Init::DaemonHelper
     v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
     cli.puts 'Setting up internal daemon defaults.'
     cli.puts 'If you don\'t understand this just leave default values:'
-    v[:cmd]     = cli.ask_user(
+    v[:cmd] = cli.ask_user(
       "How should I launch tasks?\n" \
         "  {{variables}}: script, vars, cpus, log, task_name\n ",
       "#{v[:type]} -q '#{queue}' -v '{{vars}}' -l nodes=1:ppn={{cpus}} " \
         "{{script}} -j oe -o '{{log}}' -N '{{task_name}}' -l mem=9g " \
-        "-l walltime=12:00:00 | grep .")
-    v[:var]     = cli.ask_user(
+        "-l walltime=12:00:00 | grep ."
+    )
+    v[:var] = cli.ask_user(
       "How should I pass variables?\n" \
         "  {{variables}}: key, value\n ",
-      "{{key}}={{value}}")
-    v[:varsep]  = cli.ask_user(
-      'What should I use to separate variables?', ',')
+      "{{key}}={{value}}"
+    )
+    v[:varsep] = cli.ask_user(
+      'What should I use to separate variables?', ','
+    )
     if v[:type] == 'qsub'
       v[:alive] = cli.ask_user(
         "How can I know that a process is still alive?\n" \
           "  Output should be 1 for running and 0 for non-running\n" \
           "  {{variables}}: pid\n ",
         "qstat -f '{{pid}}' | grep ' job_state =' | perl -pe 's/.*= //' " \
-          "| grep '[^C]' | tail -n 1 | wc -l | awk '{print $1}'")
-      v[:kill]  = cli.ask_user(
+          "| grep '[^C]' | tail -n 1 | wc -l | awk '{print $1}'"
+      )
+      v[:kill] = cli.ask_user(
         "How should I terminate tasks?\n" \
           "  {{variables}}: pid\n ",
-        "qdel '{{pid}}'")
+        "qdel '{{pid}}'"
+      )
     else # msub
       v[:alive] = cli.ask_user(
         "How can I know that a process is still alive?\n" \
@@ -155,13 +176,14 @@ module MiGA::Cli::Action::Init::DaemonHelper
           "  {{variables}}: pid\n ",
         "checkjob '{{pid}}'|grep '^State:' | perl -pe 's/.*: //' " \
           "| grep 'Deferred\\|Hold\\|Idle\\|Starting\\|Running\\|Blocked'" \
-          "| tail -n 1 | wc -l | awk '{print $1}'")
-      v[:kill]  = cli.ask_user(
+          "| tail -n 1 | wc -l | awk '{print $1}'"
+      )
+      v[:kill] = cli.ask_user(
         "How should I terminate tasks?\n" \
           "  {{variables}}: pid\n ",
-        "canceljob '{{pid}}'")
+        "canceljob '{{pid}}'"
+      )
     end
     v
   end
-
 end

data/lib/miga/cli/action/lair.rb

@@ -5,19 +5,19 @@ require 'miga/cli/action'
 require 'miga/lair'
 
 class MiGA::Cli::Action::Lair < MiGA::Cli::Action
-
   def parse_cli
     cli.defaults = { daemon_opts: [] }
     cli.expect_operation = true
     cli.parse do |opt|
       opt.separator 'Available operations:'
-      { start:   'Start an instance of the application',
-        stop:    'Start an instance of the application',
-        run:     'Start the application and stay on top',
-        status:  'Show status (PID) of application instances',
-        list:    'List all daemons and their status',
+      {
+        start: 'Start an instance of the application',
+        stop: 'Start an instance of the application',
+        run: 'Start the application and stay on top',
+        status: 'Show status (PID) of application instances',
+        list: 'List all daemons and their status',
         terminate: 'Terminate all daemons in the lair and exit'
-      }.each { |k,v| opt.separator sprintf '    %*s%s', -33, k, v }
+      }.each { |k, v| opt.separator sprintf('    %*s%s', -33, k, v) }
       opt.separator ''
 
       opt.separator 'MiGA options:'

data/lib/miga/cli/action/ln.rb

@@ -4,27 +4,26 @@
 require 'miga/cli/action'
 
 class MiGA::Cli::Action::Ln < MiGA::Cli::Action
-
   def parse_cli
-    cli.defaults = {info: false, force: false, method: :hardlink}
+    cli.defaults = { info: false, force: false, method: :hardlink }
     cli.parse do |opt|
       cli.opt_object(opt, [:project, :dataset_opt])
       opt.on(
         '-Q', '--project-target PATH',
         '(Mandatory) Path to the project where to link the dataset'
-        ){ |v| cli[:project2] = v }
+      ) { |v| cli[:project2] = v }
       opt.on(
         '-f', '--force',
         'Force linking, even if dataset\'s preprocessing is incomplete'
-        ){ |v| cli[:force] = v }
+      ) { |v| cli[:force] = v }
       opt.on(
         '-s', '--symlink',
         'Create symlinks instead of the default hard links'
-        ){ cli[:method] = :symlink }
+      ) { cli[:method] = :symlink }
       opt.on(
         '-c', '--copy',
         'Create copies instead of the default hard links'
-        ){ cli[:method] = :copy }
+      ) { cli[:method] = :copy }
       cli.opt_filter_datasets(opt)
     end
   end
@@ -35,6 +34,7 @@ class MiGA::Cli::Action::Ln < MiGA::Cli::Action
     ds = cli.load_and_filter_datasets
     ds.each do |d|
       next unless cli[:force] or d.done_preprocessing?
+
       cli.puts d.name
       q.import_dataset(d, cli[:method])
     end

data/lib/miga/cli/action/ls.rb

@@ -4,7 +4,6 @@
 require 'miga/cli/action'
 
 class MiGA::Cli::Action::Ls < MiGA::Cli::Action
-
   def parse_cli
     cli.defaults = { info: false, processing: false, silent: false }
     cli.parse do |opt|
@@ -51,7 +50,7 @@ class MiGA::Cli::Action::Ls < MiGA::Cli::Action
     exit(ds.empty? ? 1 : 0) if cli[:silent]
     if !cli[:datum].nil?
       cli[:tabular] = true
-      format_table(ds, [nil,nil]) { |d| [d.name, d.metadata[cli[:datum]]] }
+      format_table(ds, [nil, nil]) { |d| [d.name, d.metadata[cli[:datum]]] }
     elsif !cli[:fields].nil?
       format_table(ds, [:name] + cli[:fields]) do |d|
         [d.name] + cli[:fields].map { |f| d.metadata[f] }

data/lib/miga/cli/action/ncbi_get.rb

@@ -53,6 +53,7 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
       end
     end
     return unless cli[:unlink]
+
     unlink = p.dataset_names - d
     unlink.each { |i| p.unlink_dataset(i).remove! }
     cli.say "Datasets unlinked: #{unlink.size}"
@@ -105,14 +106,16 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
     ) { |v| cli[:ignore_until] = v }
     cli.opt_flag(
       opt, 'get-metadata',
-      'Only download and update metadata for existing datasets', :get_md)
+      'Only download and update metadata for existing datasets', :get_md
+    )
   end
 
   def cli_save_actions(opt)
     cli.opt_flag(
       opt, 'only-metadata',
       'Create datasets without input data but retrieve all metadata',
-      :only_md)
+      :only_md
+    )
     opt.on(
       '--save-every INT', Integer,
       'Save project every this many downloaded datasets',
@@ -139,6 +142,7 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
     unless tasks.any? { |i| cli[i.to_sym] }
       raise 'No action requested: pick at least one type of genome'
     end
+
     cli[:save_every] = 1 if cli[:dry]
   end
 
@@ -151,12 +155,13 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
       asm = r['assembly']
       next if asm.nil? || asm.empty? || asm == '-'
       next unless r['ftp_path_genbank']
+
       rep = remote_row_replicons(r)
       n = remote_row_name(r, rep, asm)
 
       # Register for download
       fna_url = '%s/%s_genomic.fna.gz' %
-        [r['ftp_path_genbank'], File.basename(r['ftp_path_genbank'])]
+                [r['ftp_path_genbank'], File.basename(r['ftp_path_genbank'])]
       ds[n] = {
         ids: [fna_url], db: :assembly_gz, universe: :web,
         md: {
@@ -173,6 +178,7 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
 
   def remote_row_replicons(r)
     return if r['replicons'].nil?
+
     r['replicons']
       .split('; ')
       .map { |i| i.gsub(/.*:/, '') }
@@ -181,6 +187,7 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
 
   def remote_row_name(r, rep, asm)
     return r['#organism'].miga_name if cli[:legacy_name] && cli[:reference]
+
     if cli[:legacy_name] && ['Complete', ' Chromosome'].include?(r['level'])
       acc = rep.nil? ? '' : rep.first
     else
@@ -240,6 +247,7 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
       cli.puts name
       ignore = false if ignore && name == cli[:ignore_until]
       next if ignore || p.dataset(name).nil? == cli[:get_md]
+
       downloaded += 1
       unless cli[:dry]
         save_entry(name, body, p)

data/lib/miga/cli/action/new.rb

@@ -4,7 +4,6 @@
 require 'miga/cli/action'
 
 class MiGA::Cli::Action::New < MiGA::Cli::Action
-
   def parse_cli
     cli.parse do |opt|
       cli.opt_object(opt, [:project, :project_type_req])
@@ -36,13 +35,14 @@ class MiGA::Cli::Action::New < MiGA::Cli::Action
   def perform
     cli.ensure_type(MiGA::Project)
     cli.ensure_par(project: '-P')
-    unless File.exist? "#{ENV["HOME"]}/.miga_rc" and
-          File.exist? "#{ENV["HOME"]}/.miga_daemon.json"
+    unless File.exist?(File.join(ENV['HOME'], '.miga_rc')) &&
+           File.exist?(File.join(ENV['HOME'], '.miga_daemon.json'))
       raise "You must initialize MiGA before creating the first project.\n" +
-        'Please use "miga init".'
+            'Please use "miga init".'
     end
     cli.say "Creating project: #{cli[:project]}"
     raise 'Project already exists, aborting.' if Project.exist? cli[:project]
+
     p = Project.new(cli[:project], false)
     p = cli.add_metadata(p)
     if cli[:fast]

data/lib/miga/cli/action/next_step.rb

@@ -4,7 +4,6 @@
 require 'miga/cli/action'
 
 class MiGA::Cli::Action::NextStep < MiGA::Cli::Action
-
   def parse_cli
     cli.parse do |opt|
       cli.opt_object(opt, [:project, :dataset_opt])

data/lib/miga/cli/action/preproc_wf.rb

@@ -15,14 +15,14 @@ class MiGA::Cli::Action::PreprocWf < MiGA::Cli::Action
       opt.on(
         '-i', '--input-type STRING',
         '(Mandatory) Type of input data, one of the following:',
-        *MiGA::Cli::Action::Add.INPUT_TYPES.map{ |k,v| "~ #{k}: #{v[0]}" }
+        *MiGA::Cli::Action::Add.INPUT_TYPES.map { |k, v| "~ #{k}: #{v[0]}" }
       ) { |v| cli[:input_type] = v.downcase.to_sym }
       opt.on(
         '-m', '--mytaxa_scan',
         'Perform MyTaxa scan analysis'
       ) { |v| cli[:mytaxa] = v }
       opts_for_wf(opt, 'Input files as defined by --input-type',
-        multi: true, cleanup: false, ncbi: false)
+                  multi: true, cleanup: false, ncbi: false)
     end
   end
 
@@ -31,7 +31,7 @@ class MiGA::Cli::Action::PreprocWf < MiGA::Cli::Action
     cli.ensure_par(input_type: '-i')
     p_metadata = Hash[
       %w[project_stats haai_distances aai_distances ani_distances clade_finding]
-        .map { |i| ["run_#{i}", false] }
+                 .map { |i| ["run_#{i}", false] }
     ]
     d_metadata = { run_distances: false }
     unless cli[:mytaxa]

data/lib/miga/cli/action/quality_wf.rb

@@ -23,7 +23,7 @@ class MiGA::Cli::Action::QualityWf < MiGA::Cli::Action
     # Input data
     p_metadata = Hash[
       %w[project_stats haai_distances aai_distances ani_distances clade_finding]
-        .map { |i| ["run_#{i}", false] }
+                 .map { |i| ["run_#{i}", false] }
     ]
     d_metadata = { run_distances: false }
     d_metadata[:run_mytaxa_scan] = false unless cli[:mytaxa]

data/lib/miga/cli/action/rm.rb

@@ -4,16 +4,15 @@
 require 'miga/cli/action'
 
 class MiGA::Cli::Action::Rm < MiGA::Cli::Action
-
   def parse_cli
-    cli.defaults = {remove: false}
+    cli.defaults = { remove: false }
     cli.parse do |opt|
       cli.opt_object(opt)
       opt.on(
         '-r', '--remove',
         'Also remove all associated files',
         'By default, only unlinks from metadata'
-        ){ |v| cli[:remove] = v }
+      ) { |v| cli[:remove] = v }
     end
   end