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
# File lib/miga/cli/action/doctor/base.rb, line 14 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
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
# File lib/miga/cli/action/doctor/base.rb, line 42 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
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
# File lib/miga/cli/action/doctor/base.rb, line 56 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 if the essential genes result res
has an outdated
FastAAI index
# File lib/miga/cli/action/doctor/base.rb, line 131 def outdated_fastaai_ess(res) idx1 = res.file_path(:fastaai_index) idx2 = res.file_path(:fastaai_index_2) idx3 = res.file_path(:fastaai_crystal) idx3.nil? && !(idx1.nil? && idx2.nil?) end
Reads all the distance estimates in a
-> * for
metric
and returns them as a hash +{“b_name” => [val, sd,
…], …}+
# File lib/miga/cli/action/doctor/base.rb, line 82 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
Run command cmd
with options opts
# File lib/miga/cli/action/doctor/base.rb, line 123 def run_cmd(cmd, opts = {}) opts = { return: :output, err2out: true, raise: false }.merge(opts) cmdo = MiGA::MiGA.run_cmd(cmd, opts).chomp warn(cmdo) unless cmdo.empty? end
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
# File lib/miga/cli/action/doctor/base.rb, line 98 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
Returns all targets identified by AAI
# File lib/miga/cli/action/doctor/base.rb, line 71 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