miga-base 0.7.22.0 → 0.7.25.0

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

@@ -1,5 +1,4 @@
-# @package MiGA
-# @license Artistic-2.0
+# frozen_string_literal: true
 
 ##
 # Helper module with daemon configuration functions for MiGA::Cli::Action::Init

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

@@ -0,0 +1,119 @@
+# frozen_string_literal: true
+
+##
+# Helper module with files configuration functions for MiGA::Cli::Action::Init
+module MiGA::Cli::Action::Init::FilesHelper
+  def open_rc_file
+    rc_path = File.expand_path('.miga_rc', ENV['HOME'])
+    if File.exist? rc_path
+      if cli.ask_user(
+        'I found a previous configuration. Do you want to continue?',
+        'yes', %w(yes no)
+      ) == 'no'
+        cli.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
+    rc_fh
+  end
+
+  def close_rc_file(rc_fh)
+    rc_fh.puts <<~FOOT
+
+      MIGA_CONFIG_VERSION='#{MiGA::MiGA.FULL_VERSION}'
+      MIGA_CONFIG_LONGVERSION='#{MiGA::MiGA.LONG_VERSION}'
+      MIGA_CONFIG_DATE='#{Time.now}'
+
+    FOOT
+    rc_fh.close
+  end
+
+  def check_configuration_script(rc_fh)
+    unless File.exist? cli[:config]
+      cli[:config] = cli.ask_user(
+        'Is there a script I need to load at startup?',
+        cli[:config]
+      )
+    end
+    if File.exist? cli[:config]
+      cli[:config] = File.expand_path(cli[:config])
+      cli.puts "Found bash configuration script: #{cli[:config]}"
+      rc_fh.puts "MIGA_STARTUP='#{cli[:config]}'"
+      rc_fh.puts '. "$MIGA_STARTUP"'
+    else
+      cli[:config] = '/dev/null'
+    end
+    cli.puts ''
+  end
+
+  def check_additional_files(paths)
+    if cli[:mytaxa]
+      check_mytaxa_scores(paths)
+      check_mytaxa_database(paths)
+    end
+    check_rdp_classifier if cli[:rdp]
+    check_phyla_lite
+    cli.puts ''
+  end
+
+  def check_mytaxa_scores(paths)
+    cli.print 'Looking for MyTaxa scores... '
+    mt = File.dirname(paths['MyTaxa'])
+    unless Dir.exist?(File.join(mt, 'db'))
+      cli.puts "no\nExecute 'python2 #{mt}/utils/download_db.py'"
+      raise 'Incomplete MyTaxa installation'
+    end
+    cli.puts 'yes'
+  end
+
+  def check_mytaxa_database(paths)
+    cli.print 'Looking for MyTaxa DB... '
+    mt = File.dirname(paths['MyTaxa'])
+    dmnd_db = 'AllGenomes.faa.dmnd'
+    miga_db = File.join(ENV['MIGA_HOME'], '.miga_db')
+    home_db = File.join(miga_db, dmnd_db)
+    mt_db = File.join(mt, 'AllGenomes.faa.dmnd')
+    if File.exist?(home_db)
+      cli.puts 'yes'
+    elsif File.exist?(mt_db)
+      cli.puts 'yes, sym-linking'
+      File.symlink(mt_db, home_db)
+    else
+      cli.puts 'no, downloading'
+      MiGA::MiGA.download_file_ftp(:miga_dist, dmnd_db, home_db) do |n, size|
+        cli.advance("#{dmnd_db}:", n, size)
+      end
+      cli.puts
+    end
+  end
+
+  def check_rdp_classifier
+    cli.print 'Looking for RDP classifier... '
+    miga_db = File.join(ENV['MIGA_HOME'], '.miga_db')
+    file = 'classifier.jar'
+    path = File.join(miga_db, file)
+    if File.size?(path)
+      cli.puts 'yes'
+    else
+      cli.puts 'no, downloading'
+      arch = 'classifier.tar.gz'
+      MiGA::MiGA.download_file_ftp(
+        :miga_dist, arch, File.join(miga_db, arch)
+      ) { |n, size| cli.advance("#{arch}:", n, size) }
+      `cd '#{miga_db}' && tar zxf '#{arch}' && rm '#{arch}'`
+      cli.puts
+    end
+  end
+
+  def check_phyla_lite
+    cli.puts 'Looking for Phyla Lite... '
+    cmd = ['get_db', '-n', 'Phyla_Lite', '--no-overwrite']
+    MiGA::Cli.new(cmd).launch(true)
+  end
+end

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

@@ -269,7 +269,7 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
     else
       cli.say '  Creating dataset'
       rd.save_to(p, name, !cli[:query], body[:md])
-      cli.add_metadata(p.add_dataset(name)).save
+      cli.add_metadata(p.add_dataset(name))
     end
   end
 end

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

@@ -24,6 +24,11 @@ class MiGA::Cli::Action::New < MiGA::Cli::Action
         'Use faster identity engines (Diamond-AAI and FastANI)',
         'Equivalent to: -m aai_p=diamond,ani_p=fastani'
       ) { |v| cli[:fast] = v }
+      opt.on(
+        '--sensitive',
+        'Use more sensitive identity engines (BLAST+)',
+        'Equivalent to: -m aai_p=blast+,ani_p=blast+'
+      ) { |v| cli[:sensitive] = v }
       opt.on(
         '-m', '--metadata STRING',
         'Metadata as key-value pairs separated by = and delimited by comma',
@@ -35,20 +40,21 @@ class MiGA::Cli::Action::New < MiGA::Cli::Action
   def perform
     cli.ensure_type(MiGA::Project)
     cli.ensure_par(project: '-P')
-    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".'
+    unless MiGA::MiGA.initialized?
+      raise 'MiGA has not been initialized, please use "miga init" first'
     end
     cli.say "Creating project: #{cli[:project]}"
-    raise 'Project already exists, aborting.' if Project.exist? 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]
-      p.metadata[:aai_p] = 'diamond'
-      p.metadata[:ani_p] = 'fastani'
+
+    if cli[:sensitive]
+      p.set_option(:aai_p, 'blast+')
+      p.set_option(:ani_p, 'blast+')
+    elsif cli[:fast]
+      p.set_option(:aai_p, 'diamond')
+      p.set_option(:ani_p, 'fastani')
     end
-    p.save
   end
 end

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

@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+require 'miga/cli/action'
+
+##
+# CLI: `miga option`
+class MiGA::Cli::Action::Option < MiGA::Cli::Action
+  def parse_cli
+    cli.parse do |opt|
+      cli.opt_object(opt, %i[project dataset_opt])
+      opt.on(
+        '-k', '--key STRING',
+        'Option name to get or set (by default, all options are printed)'
+      ) { |v| cli[:key] = v }
+      opt.on(
+        '--value STRING',
+        'Value of the option to set (by default, option value is not changed)',
+        'Recognized tokens: nil, true, false'
+      ) { |v| cli[:value] = v }
+      opt.on(
+        '-o', '--output PATH',
+        'Create output file instead of returning to STDOUT'
+      ) { |v| cli[:output] = v }
+    end
+  end
+
+  def perform
+    unless cli[:value].nil?
+      cli.ensure_par(
+        { key: '-k' },
+        '%<name>s is mandatory when --value is set: please provide %<flag>s'
+      )
+    end
+    obj = cli.load_project_or_dataset
+    io = cli[:output].nil? ? $stdout : File.open(cli[:output], 'w')
+    if cli[:key].nil?
+      cli.table(%w[Key Value], obj.all_options.to_a, io)
+    else
+      obj.set_option(cli[:key], cli[:value], true) unless cli[:value].nil?
+      io.puts obj.option(cli[:key])
+    end
+    io.close unless cli[:output].nil?
+  end
+end

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

@@ -21,18 +21,20 @@ class MiGA::Cli::Action::PreprocWf < MiGA::Cli::Action
         '-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)
+      opts_for_wf(
+        opt, 'Input files as defined by --input-type',
+        multi: true, cleanup: false, ncbi: false, project_type: true
+      )
     end
   end
 
   def perform
     # Input data
     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] }
+    norun = %w[
+      project_stats haai_distances aai_distances ani_distances clade_finding
     ]
+    p_metadata = Hash[norun.map { |i| ["run_#{i}", false] }]
     d_metadata = { run_distances: false }
     unless cli[:mytaxa]
       d_metadata[:run_mytaxa_scan] = false

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

@@ -21,10 +21,10 @@ class MiGA::Cli::Action::QualityWf < MiGA::Cli::Action
 
   def perform
     # Input data
-    p_metadata = Hash[
-      %w[project_stats haai_distances aai_distances ani_distances clade_finding]
-                 .map { |i| ["run_#{i}", false] }
+    norun = %w[
+      project_stats haai_distances aai_distances ani_distances clade_finding
     ]
+    p_metadata = Hash[norun.map { |i| ["run_#{i}", false] }]
     d_metadata = { run_distances: false }
     d_metadata[:run_mytaxa_scan] = false unless cli[:mytaxa]
     p = create_project(:assembly, p_metadata, d_metadata)

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

@@ -47,7 +47,7 @@ class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
 
   def read_distances
     p = cli.load_project
-    cli[:metric] ||= p.is_clade? ? 'ani' : 'aai'
+    cli[:metric] ||= p.clade? ? 'ani' : 'aai'
     res_n = "#{cli[:metric]}_distances"
     cli.say "Reading distances: 1-#{cli[:metric].upcase}"
     res = p.result(res_n)

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

@@ -59,7 +59,7 @@ class MiGA::Cli::Action::TaxTest < MiGA::Cli::Action
     cli.puts "Closest relative: #{cr[0]} with AAI: #{cr[1]}."
     p = cli.load_project
     if cli[:ref_project]
-      if (ref = p.metadata[:ref_project]).nil?
+      if (ref = p.option(:ref_project)).nil?
         raise '--ref-project requested but no reference project has been set'
       end
       if (q = MiGA::Project.load(ref)).nil?

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

@@ -7,9 +7,8 @@ module MiGA::Cli::Action::Wf
   def default_opts_for_wf
     cli.expect_files = true
     cli.defaults = {
-      clean: false, regexp: MiGA::Cli.FILE_REGEXP,
-      project_type: :genomes, dataset_type: :popgenome,
-      ncbi_draft: true, min_qual: 25.0
+      clean: false, project_type: :genomes, dataset_type: :popgenome,
+      ncbi_draft: true, min_qual: MiGA::Project.OPTIONS[:min_qual][:default]
     }
   end
 
@@ -56,28 +55,10 @@ module MiGA::Cli::Action::Wf
     opt.on(
       '-R', '--name-regexp REGEXP', Regexp,
       'Regular expression indicating how to extract the name from the path',
-      "By default: '#{cli[:regexp]}'"
+      "By default: '#{MiGA::Cli.FILE_REGEXP}'"
     ) { |v| cli[:regexp] = v }
-    opt.on(
-      '--type STRING',
-      "Type of datasets. By default: #{cli[:dataset_type]}",
-      'Recognized types:',
-      *MiGA::Dataset.KNOWN_TYPES
-        .map do |k, v|
-          "~ #{k}: #{v[:description]}" unless !params[:multi] && v[:multi]
-        end.compact
-    ) { |v| cli[:dataset_type] = v.downcase.to_sym }
-    if params[:project_type]
-      opt.on(
-        '--project-type STRING',
-        "Type of project. By default: #{cli[:project_type]}",
-        'Recognized types:',
-        *MiGA::Project.KNOWN_TYPES
-          .map do |k, v|
-            "~ #{k}: #{v[:description]}" unless !params[:multi] && v[:multi]
-          end.compact
-      ) { |v| cli[:project_type] = v.downcase.to_sym }
-    end
+    opt_object_type(opt, :dataset, params[:multi])
+    opt_object_type(opt, :project, params[:multi]) if params[:project_type]
     opt.on(
       '--daemon PATH',
       'Use custom daemon configuration in JSON format',
@@ -124,33 +105,42 @@ module MiGA::Cli::Action::Wf
       project_type: '--project-type',
       dataset_type: '--dataset-type'
     )
+    paired = cli[:input_type].to_s.include?('_paired')
+    cli[:regexp] ||= MiGA::Cli.FILE_REGEXP(paired)
+
     # Create empty project
-    call_cli([
-               'new',
-               '-P', cli[:outdir],
-               '-t', cli[:project_type]
-             ]) unless MiGA::Project.exist? cli[:outdir]
+    call_cli(
+      ['new', '-P', cli[:outdir], '-t', cli[:project_type]]
+    ) unless MiGA::Project.exist? cli[:outdir]
+
     # Define project metadata
     p = cli.load_project(:outdir, '-o')
-    %i[haai_p aai_p ani_p ess_coll min_qual].each { |i| p_metadata[i] = cli[i] }
     p_metadata[:type] = cli[:project_type]
     transfer_metadata(p, p_metadata)
+    %i[haai_p aai_p ani_p ess_coll min_qual].each do |i|
+      p.set_option(i, cli[i])
+    end
+
     # Download datasets
-    call_cli([
-               'ncbi_get',
-               '-P', cli[:outdir],
-               '-T', cli[:ncbi_taxon],
-               (cli[:ncbi_draft] ? '--all' : '--complete')
-             ]) unless cli[:ncbi_taxon].nil?
+    unless cli[:ncbi_taxon].nil?
+      what = cli[:ncbi_draft] ? '--all' : '--complete'
+      call_cli(
+        ['ncbi_get', '-P', cli[:outdir], '-T', cli[:ncbi_taxon], what]
+      )
+    end
+
     # Add datasets
-    call_cli([
-      'add',
-      '--ignore-dups',
-      '-P', cli[:outdir],
-      '-t', cli[:dataset_type],
-      '-i', stage,
-      '-R', cli[:regexp]
-    ] + cli.files) unless cli.files.empty?
+    call_cli(
+      [
+        'add',
+        '--ignore-dups',
+        '-P', cli[:outdir],
+        '-t', cli[:dataset_type],
+        '-i', stage,
+        '-R', cli[:regexp]
+      ] + cli.files
+    ) unless cli.files.empty?
+
     # Define datasets metadata
     p.load
     d_metadata[:type] = cli[:dataset_type]
@@ -161,13 +151,13 @@ module MiGA::Cli::Action::Wf
   def summarize(which = %w[cds assembly essential_genes ssu])
     which.each do |r|
       cli.say "Summary: #{r}"
-      call_cli([
-                 'summary',
-                 '-P', cli[:outdir],
-                 '-r', r,
-                 '-o', File.expand_path("#{r}.tsv", cli[:outdir]),
-                 '--tab', '--ref', '--active'
-               ])
+      call_cli(
+        [
+          'summary',
+          '-P', cli[:outdir], '-r', r, '--tab', '--ref', '--active',
+          '-o', File.join(cli[:outdir], "#{r}.tsv")
+        ]
+      )
     end
     call_cli(['browse', '-P', cli[:outdir]])
   end
@@ -193,17 +183,45 @@ module MiGA::Cli::Action::Wf
     cmd += ['--max-jobs', cli[:jobs]] unless cli[:jobs].nil?
     cmd += ['--ppn', cli[:threads]] unless cli[:threads].nil?
     cwd = Dir.pwd
-    call_cli cmd
+    call_cli(cmd)
     Dir.chdir(cwd)
   end
 
   def transfer_metadata(obj, md)
     # Clear old metadata
     obj.metadata.each do |k, v|
-      obj.metadata[k] = nil if k.to_s =~ /^run_/ || k == :ref_project
+      obj.metadata[k] = nil if k.to_s =~ /^run_/ || obj.option?(k)
     end
     # Transfer and save
     md.each { |k, v| obj.metadata[k] = v }
     obj.save
   end
+
+  private
+
+  ##
+  # Add option --type or --project-type to +opt+
+  def opt_object_type(opt, obj, multi)
+    conf =
+      case obj
+      when :dataset
+        ['type', 'datasets', :dataset_type, MiGA::Dataset]
+      when :project
+        ['project-type', 'project', :project_type, MiGA::Project]
+      else
+        raise "Unrecognized object type: #{obj}"
+      end
+
+    options =
+      conf[3].KNOWN_TYPES.map do |k, v|
+        "~ #{k}: #{v[:description]}" unless !multi && v[:multi]
+      end.compact
+
+    opt.on(
+      "--#{conf[0]} STRING",
+      "Type of #{conf[1]}. By default: #{cli[conf[2]]}",
+      'Recognized types:',
+      *options
+    ) { |v| cli[conf[2]] = v.downcase.to_sym }
+  end
 end