Class: MiGA::MiGA

Inherits:
Object
  • Object
show all
Extended by:
Common::Format, Common::Net, Common::Path, Common::SystemCall
Includes:
MiGA, Common
Defined in:
lib/miga/common.rb,
lib/miga/version.rb,
lib/miga/common/base.rb

Overview

Generic class used to handle system-wide information and methods, and parent of all other MiGA::* classes.

Constant Summary

Constants included from MiGA

CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes included from Common::Net

#remote_connection_uri

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Common::Path

root_path, script_path

Methods included from Common::Format

clean_fasta_file, seqs_length, tabulate

Methods included from Common::Net

data_server, download_file_ftp, http_request, known_hosts, main_server, net_method, normalize_encoding, remote_connection

Methods included from Common::SystemCall

run_cmd, run_cmd_opts

Class Method Details

.CITATION ⇒ Object

Reference of MiGA



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# File 'lib/miga/version.rb', line 70

def self.CITATION
  CITATION.map { |i| "- #{i}" }.join
end

.CITATION_ARRAY ⇒ Object 



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# File 'lib/miga/version.rb', line 74

def self.CITATION_ARRAY
  CITATION
end

.DEBUG(*args) ⇒ Object

Send debug message



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# File 'lib/miga/common/base.rb', line 31

def DEBUG(*args)
  $stderr.puts(*args) if debug?
  $stderr.puts(
    caller.map { |v| v.gsub(/^/, '     ') }.join("\n")
  ) if debug_trace?
end

.debug? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/miga/common/base.rb', line 38

def debug?
  @@DEBUG ||= false
end

.DEBUG_OFF ⇒ Object

Turn off debugging



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# File 'lib/miga/common/base.rb', line 12

def DEBUG_OFF
  @@DEBUG = false
end

.DEBUG_ON ⇒ Object

Turn on debugging



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# File 'lib/miga/common/base.rb', line 6

def DEBUG_ON
  @@DEBUG = true
end

.debug_trace? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/miga/common/base.rb', line 42

def debug_trace?
  @@DEBUG_TRACE ||= false
end

.DEBUG_TRACE_OFF ⇒ Object

Turn off debug tracing (but not debugging)



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# File 'lib/miga/common/base.rb', line 25

def DEBUG_TRACE_OFF
  @@DEBUG_TRACE = false
end

.DEBUG_TRACE_ON ⇒ Object

Turn on debug tracing (and debugging)



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# File 'lib/miga/common/base.rb', line 18

def DEBUG_TRACE_ON
  @@DEBUG_TRACE = true
  DEBUG_ON()
end

.FULL_VERSION ⇒ Object

Complete version as string



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# File 'lib/miga/version.rb', line 52

def self.FULL_VERSION
  VERSION.join('.')
end

.initialized? ⇒ Boolean

Has MiGA been initialized?

Returns:

  • (Boolean) 


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# File 'lib/miga/common.rb', line 36

def self.initialized?
  File.exist?(rc_path) &&
    File.exist?(File.join(ENV['MIGA_HOME'], '.miga_daemon.json'))
end

.LONG_VERSION ⇒ Object

Complete version with nickname and date as string



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# File 'lib/miga/version.rb', line 58

def self.LONG_VERSION
  "MiGA #{VERSION.join('.')} - #{VERSION_NAME} - #{VERSION_DATE}"
end

.rc_path ⇒ Object

Path to the .miga_rc file



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# File 'lib/miga/common.rb', line 30

def self.rc_path
  File.join(ENV['MIGA_HOME'], '.miga_rc')
end

.VERSION ⇒ Object

Major.minor version as Float



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# File 'lib/miga/version.rb', line 46

def self.VERSION
  VERSION[0]
end

.VERSION_DATE ⇒ Object

Date of the current gem release



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# File 'lib/miga/version.rb', line 64

def self.VERSION_DATE
  VERSION_DATE
end

Instance Method Details

#advance(step, n = 0, total = nil, bin = true) ⇒ Object

Reports the advance of a task at step (String), the n out of total. The advance is reported in powers of 1,024 if bin is true, or powers of 1,000 otherwise. The report goes to $stderr iff –verbose



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# File 'lib/miga/common.rb', line 65

def advance(step, n = 0, total = nil, bin = true)
  # Initialize advance timing
  @_advance_time ||= { last: nil, n: 0, avg: nil, total: total }
  if @_advance_time[:n] > n || total != @_advance_time[:total]
    @_advance_time[:last] = nil
    @_advance_time[:n] = 0
    @_advance_time[:avg]  = nil
    @_advance_time[:total] = total
  end

  # Estimate timing
  adv_n = n - @_advance_time[:n]
  if total.nil? || @_advance_time[:last].nil? || adv_n.negative?
    # Initial report
    @_advance_time[:last] = Time.now
    @_advance_time[:n] = n
  elsif adv_n > 0.001 * total
    # Advance report (if change > 0.1% change and time > 1 second)
    this_time = (Time.now - @_advance_time[:last]).to_f
    return if this_time < 1.0 && n < total

    this_avg = this_time / adv_n
    @_advance_time[:avg] ||= this_avg
    @_advance_time[:avg] = 0.9 * @_advance_time[:avg] + 0.1 * this_avg
    @_advance_time[:last] = Time.now
    @_advance_time[:n] = n
  else
    # Final report (if the last update was too small) or ignore update
    return if n < total
  end

  # Report
  adv =
    if total.nil?
      (n == 0 ? '' : num_suffix(n, bin))
    else
      vals = [100.0 * n / total, num_suffix(n, bin), num_suffix(total, bin)]
      ('%.1f%% (%s/%s)' % vals)
    end
  left =
    if @_advance_time[:avg].nil?
      ''
    else
      left_time = @_advance_time[:avg] * (total - n) / 60 # <- in minutes
      left_time   < 0.01 ? '' :
        left_time < 1    ? ('%.0fs left' % (left_time * 60))   :
        left_time > 1440 ? ('%.1fd left' % (left_time / 1440)) :
        left_time > 60   ? ('%.1fh left' % (left_time / 60))   :
        ('%.1fm left' % left_time)
    end
  $stderr.print("[%s] %s %s %-12s   \r" % [Time.now, step, adv, left])
end

#like_io?(obj) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/miga/common.rb', line 134

def like_io?(obj)
  obj.is_a?(IO) || obj.is_a?(StringIO)
end

#num_suffix(n, bin = false) ⇒ Object

Return formatted number n with the appropriate units as powers of 1,000 (if bin if false) or 1,024 (otherwise)



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# File 'lib/miga/common.rb', line 121

def num_suffix(n, bin = false)
  p = ''
  { T: 4, G: 3, M: 2, K: 1 }.each do |k, x|
    v = (bin ? 1024 : 1e3)**x
    if n > v
      n = '%.1f' % (n.to_f / v)
      p = k
      break
    end
  end
  "#{n}#{p}"
end

#result_files_exist?(base, ext) ⇒ Boolean

Check if the result files exist with base name (String) followed by the ext values (Array of String).

Returns:

  • (Boolean) 


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# File 'lib/miga/common.rb', line 44

def result_files_exist?(base, ext)
  ext = [ext] unless ext.is_a? Array
  MiGA::MiGA.DEBUG("Assserting files for result: #{ext}")
  ext.all? { |f| File.exist?(base + f) or File.exist?("#{base}#{f}.gz") }
end

#say(*par) ⇒ Object

Print par ensuring new line at the end. Date/time-stamp each line. If the first parameter is IO or StringIO the output is sent there, otherwise it’s sent to $stderr



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# File 'lib/miga/common.rb', line 55

def say(*par)
  io = like_io?(par.first) ? par.shift : $stderr
  io.puts(*par.map { |i| "[#{Time.now}] #{i}" })
end