Module: MiGA::Cli::Action::Doctor::Distances

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

Instance Method Summary collapse

Instance Method Details

#check_bidir(cli) ⇒ Object

Perform bidirectional operation with MiGA::Cli cli



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# File 'lib/miga/cli/action/doctor/distances.rb', line 37

def check_bidir(cli)
  cli.say 'Checking if reference distances are bidirectional'
  project = cli.load_project
  ref_ds = project.each_dataset.select(&:ref?)

  # Read and write data
  tmp = partial_bidir_tmp(project, ref_ds)
  fixed_ds = merge_bidir_tmp(tmp)
  FileUtils.rm_rf(tmp)

  # Fix tables if needed
  unless fixed_ds.empty?
    cli.say ' - Filled datasets: %i' % fixed_ds.size
    i[aai_distances ani_distances].each do |res_name|
      res = cli.load_project.result(res_name) or next
      cli.say ' - Recalculating tables: %s' % res_name
      res.recalculate!('Distances updated for bidirectionality').save
    end
  end
end

#check_db(cli) ⇒ Object

Perform databases operation with MiGA::Cli cli



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# File 'lib/miga/cli/action/doctor/distances.rb', line 5

def check_db(cli)
  cli.say 'Checking integrity of databases'
  p = cli.load_project
  n = p.dataset_names.size
  (0 .. cli[:threads] - 1).map do |i|
    Process.fork do
      k = 0
      p.each_dataset do |d|
        k += 1
        cli.advance('Datasets:', k, n, false) if i == 0
        next unless k % cli[:threads] == i
        each_database_file(d) do |db_file, metric, result, _rank|
          check_sqlite3_database(db_file, metric) do
            cli.say(
              "  > Removing malformed database from #{d.name}:#{result}   "
            )
            File.unlink(db_file)
            r = d.result(result) or next
            [r.path(:done), r.path].each do |f|
              File.unlink(f) if File.exist?(f)
            end
          end
        end
      end
    end
  end
  Process.waitall
  cli.say
end

#check_dist(cli) ⇒ Object

Perform distances operation with MiGA::Cli cli



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# File 'lib/miga/cli/action/doctor/distances.rb', line 60

def check_dist(cli)
  p = cli.load_project
  i[ani aai].each do |dist|
    res = p.result("#{dist}_distances")
    next if res.nil?

    cli.say "Checking #{dist} table for consistent datasets"
    notok, fix = check_dist_eval(cli, p, res)
    check_dist_fix(cli, p, fix)
    check_dist_recompute(cli, res, notok)
  end
end

#merge_bidir_tmp(tmp) ⇒ Object

Read partial temporal reports of bidirectionality (located in tmp), and fill databases with missing values. Returns the names of the datasets fixed as a Set.



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# File 'lib/miga/cli/action/doctor/distances.rb', line 135

def merge_bidir_tmp(tmp)
  tmp_done = File.join(tmp, 'chunks.txt')
  chunks = File.readlines(tmp_done)[0].chomp.to_i

  lower_tr = []
  chunks.times.each do |i|
    (0 .. i).to_a.each { |j| lower_tr << [i, j] }
  end
  o = MiGA::Parallel.distribute(lower_tr, cli[:threads]) do |cell, k, thr|
    cli.advance('Writing:', k, lower_tr.size, false) if thr == 0
    done_f = File.join(tmp, "#{cell[0]}-#{cell[1]}.txt")
    next if File.exist?(done_f)

    fixed_ds = merge_bidir_tmp_pair(tmp, cell[0], cell[1])
    File.open("#{done_f}.tmp", 'w') { |fh| fixed_ds.each { |ds| fh.puts ds } }
    File.rename("#{done_f}.tmp", done_f)
  end
  cli.advance('Writing:', lower_tr.size, lower_tr.size, false)
  cli.say
  MiGA::Parallel.assess_success(o)

  lower_tr.map do |cell|
    Set.new.tap do |y|
      file = File.join(tmp, "#{cell[0]}-#{cell[1]}.txt")
      raise MiGA::Error.new(
        "Expected file missing, probably due to a thread failure: #{file}"
      ) unless File.exist?(file)
      File.open(file, 'r') { |fh| fh.each { |ln| y << ln.chomp } }
    end
  end.inject(Set.new, :+)
end

#merge_bidir_tmp_cell(dist_x, dist_y) ⇒ Object

Find missing values in a “chunks cell” and fill databases. Returns the names of the fixed datasets as a Set.



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# File 'lib/miga/cli/action/doctor/distances.rb', line 185

def merge_bidir_tmp_cell(dist_x, dist_y)
  # Find missing values
  dist = {}
  datasets = Set.new
  dist_x.each do |metric, distances_x|
    dist[metric] = {}
    distances_x.each do |qry_x, row_x|
      dist_y[metric].each do |qry_y, row_y|
        # Ignore if missing in dist_x
        next unless dist_x[metric][qry_x]&.include?(qry_y)
        # Ignore if already in dist_y
        next if dist_y[metric][qry_y]&.include?(qry_x)
        # Save otherwise
        dist[metric][qry_x] ||= {}
        dist[metric][qry_x][qry_y] = dist_x[metric][qry_x][qry_y]
        datasets << qry_y
      end
    end
  end

  # Save them in databases
  datasets.each do |ds_name|
    ds = cli.load_project.dataset(ds_name)
    save_bidirectional(ds, dist)
  end
  datasets
end

#merge_bidir_tmp_pair(tmp, x, y) ⇒ Object

Cross-reference two reports of bidirectionality (located in tmp), identified by indexes x and y, and fill databases with missing values. Returns the names of the fixed datasets as a Set.



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# File 'lib/miga/cli/action/doctor/distances.rb', line 171

def merge_bidir_tmp_pair(tmp, x, y)
  dist_x = Marshal.load(File.read(File.join(tmp, "#{x}.marshal")))
  if x == y
    merge_bidir_tmp_cell(dist_x, dist_x)
  else
    dist_y = Marshal.load(File.read(File.join(tmp, "#{y}.marshal")))
    merge_bidir_tmp_cell(dist_x, dist_y) +
    merge_bidir_tmp_cell(dist_y, dist_x)
  end
end

#partial_bidir_chunks(n) ⇒ Object

Calculates the number of chunks that should be produced during the bidirectional checks for n reference datasets (Integer)



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# File 'lib/miga/cli/action/doctor/distances.rb', line 78

def partial_bidir_chunks(n)
  y = [cli[:threads], (n / 1024).ceil].max
  y = n if y > n
  y
end

#partial_bidir_tmp(project, ref_ds) ⇒ Object

Make a temporal directory holding partial bidirectionality reports (one per thread) in a custom multi-JSON format. Requires a MiGA::Project project and the iterator of the reference datasets ref_ds. Returns the path to the temporal directory created



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# File 'lib/miga/cli/action/doctor/distances.rb', line 89

def partial_bidir_tmp(project, ref_ds)
  n = ref_ds.size
  chunks = partial_bidir_chunks(n)

  # Check first if a previous run is complete (and recover it)
  tmp = File.join(project.path, 'doctor-bidirectional.tmp')
  tmp_chunks = File.join(tmp, 'chunks.txt')
  tmp_chunks_val = [chunks, 0]
  if File.size?(tmp_chunks)
    tmp_chunks_val = File.readlines(tmp_chunks).map(&:chomp).map(&:to_i)
  end
  chunks = tmp_chunks_val[0]
  FileUtils.rm_rf(tmp) unless tmp_chunks_val[1] == n

  # Read data (threaded)
  FileUtils.mkdir_p(tmp)
  chunks_e = 0 .. chunks - 1
  o = MiGA::Parallel.distribute(chunks_e, cli[:threads]) do |chunk, k, thr|
    cli.advance('Reading:', k, chunks, false) if thr == 0
    dist = {}
    [:aai, :ani].each do |metric|
      dist[metric] = {}
      ref_ds.each_with_index do |ds, idx|
        if idx % chunks == chunk
          row = read_bidirectional(ds, metric)
          dist[metric][ds.name] = row unless row.empty?
        end
      end
    end
    file = File.join(tmp, "#{chunk}.marshal")
    File.open("#{file}.tmp", 'w') { |fh| Marshal.dump(dist, fh) }
    File.rename("#{file}.tmp", file)
  end
  cli.advance('Reading:', chunks, chunks, false)
  cli.say
  MiGA::Parallel.assess_success(o)

  # Save information to indicate that the run is complete and return
  File.open(tmp_chunks, 'w') { |fh| fh.puts(chunks, n) }
  return tmp
end