module MiGA::Cli::Action::Doctor::Databases

# File lib/miga/cli/action/doctor/databases.rb, line 7
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

# File lib/miga/cli/action/doctor/databases.rb, line 13
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