Module: MiGA::Cli::Action::Doctor::Base

Included in:
MiGA::Cli::Action::Doctor
Defined in:
lib/miga/cli/action/doctor/base.rb

Instance Method Summary collapse

Instance Method Details

#check_dist_eval(cli, p, res) ⇒ Object

Scans the all-vs-all matrix registered in res (MiGA::Result) in search of pairs where one or both datasets are missing or inactive in the project p (MiGA::Project), and report progress through cli (MiGA::Cli). Returns an Array with two arrays: the first a list of dataset names that are no longer registered in the project or are currently inactive, and the second a list of dataset names that have registered pairs with the first list, and therefore the databases need to be cleaned. This is a subtask of check_dist



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# File 'lib/miga/cli/action/doctor/base.rb', line 54

def check_dist_eval(cli, p, res)
  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")
      names = [r[0], r[1]]
      next unless names.any? { |i| p.dataset(i).nil? }

      names.each do |i|
        if p.dataset(i).nil? || !p.dataset(i).active?
          notok[i] = true
        else
          fix[i] = true
        end
      end
    end
  end
  [notok.keys, fix.keys]
end

#check_dist_fix(cli, p, fix) ⇒ Object

Cleanup distance databases for datasets names in fix (Array: String) from project p (MiGA::Project), and report through cli (MiGA::Cli). This is a subtask of check_dist



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# File 'lib/miga/cli/action/doctor/base.rb', line 82

def check_dist_fix(cli, p, fix)
  return if fix.empty?

  cli.say("- Fixing #{fix.size} datasets")
  fix.each do |d_n|
    cli.say "  > Fixing #{d_n}."
    p.dataset(d_n).cleanup_distances!
  end
end

#check_dist_recompute(cli, res, notok) ⇒ Object

Recompute res (MiGA::Result) if notok (Array: String) has any dataset names registered, and report through cli (MiGA::Cli). This is a subtask of check_dist



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# File 'lib/miga/cli/action/doctor/base.rb', line 96

def check_dist_recompute(cli, res, notok)
  return if notok.empty?

  cli.say '- Unregistered datasets detected: '
  if notok.size <= 5
    notok.each { |i| cli.say "  > #{i}" }
  else
    cli.say "  > #{notok.size}, including #{notok.first}"
  end
  cli.say '- Removing tables, recompute'
  res.remove!
end

#check_sqlite3_database(db_file, metric, &blk) ⇒ Object

Check the database in db_file maintains integrity for the tables saving metric (:ani or :aai) and call blk if the file is corrupt or doesn’t contain the expected structure



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# File 'lib/miga/cli/action/doctor/base.rb', line 12

def check_sqlite3_database(db_file, metric, &blk)
  MiGA::SQLite.new(db_file).run("select count(*) from #{metric}")
rescue SQLite3::SQLException, SQLite3::CorruptException
  blk.call
end

#each_database_file(dataset, &blk) ⇒ Object 



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# File 'lib/miga/cli/action/doctor/base.rb', line 18

def each_database_file(dataset, &blk)
  ref_db = {
    haai: ['01.haai', :aai], aai: ['02.aai', :aai], ani: ['03.ani', :ani]
  }
  qry_db = {
    haai: ['.haai.db', :aai], aai: ['.aai.db', :aai], ani: ['.ani.db', :ani]
  }
  base = File.join(dataset.project.path, 'data', '09.distances')
  result = :distances
  if dataset.ref?
    file_db = "#{dataset.name}.db"
    ref_db.each do |rank, v|
      dir, metric = *v
      file = File.join(base, dir, file_db)
      blk[file, metric, result, rank] if File.exist? file
    end
    # Query databases for reference databases refer to taxonomy runs
    base = File.join(base, '05.taxonomy')
    result = :taxonomy
  end
  qry_db.each do |rank, v|
    ext, metric = *v
    file = File.join(base, "#{dataset.name}#{ext}")
    blk[file, metric, result, rank] if File.exist? file
  end
end

#read_bidirectional(a, metric) ⇒ Object

Reads all the distance estimates in a -> * for metric and returns them as a hash {“b_name” => [val, sd, …], …}



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# File 'lib/miga/cli/action/doctor/base.rb', line 122

def read_bidirectional(a, metric)
  db_file = a.result(:distances)&.file_path("#{metric}_db") or return {}
  sql = "select seq2, #{metric}, sd, n, omega from #{metric}"
  data = MiGA::SQLite.new(db_file).run(sql) || []
  Hash[
    data.map do |row|
      k, v = row.shift(2)
      [k, row.all?(&:zero?) ? v : [v] + row]
    end
  ]
end

#save_bidirectional(a, dist) ⇒ Object

Saves all the distance estimates in * -> a into the a databases (as a -> *), where a is a MiGA::Dataset object, with currently saved values read from the hash dist



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# File 'lib/miga/cli/action/doctor/base.rb', line 138

def save_bidirectional(a, dist)
  each_database_file(a) do |db_file, metric, result, rank|
    next if rank == :haai # No need for hAAI to be bidirectional
    next if result == :taxonomy # Taxonomy is never bidirectional

    b2a = dist[rank].map { |b_name, v| b_name if v[a.name] }.compact
    a2b = dist[rank][a.name]&.keys || []
    MiGA::SQLite.new(db_file).run do |db|
      sql = <<~SQL
        insert into #{metric}(seq1, seq2, #{metric}, sd, n, omega) \
        values(?, ?, ?, ?, ?, ?);
      SQL
      db.execute('BEGIN TRANSACTION;')
      (b2a - a2b).each do |b_name|
        val = dist[rank][b_name][a.name]
        val = [val, 0, 0, 0] unless val.is_a?(Array)
        db.execute(sql, [a.name, b_name] + val)
      end
      db.execute('COMMIT;')
    end
  end
end

#saved_targets(dataset) ⇒ Object

Returns all targets identified by AAI



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# File 'lib/miga/cli/action/doctor/base.rb', line 111

def saved_targets(dataset)
  # Return nil if distance or database are not retrievable
  dist = dataset.result(:distances) or return
  path = dist.file_path(:aai_db) or return

  MiGA::SQLite.new(path).run('select seq2 from aai').map(&:first)
end