Module: Bio::Shell::Ghost

Includes:
Core
Included in:
Bio::Shell
Defined in:
lib/bio/shell/core.rb

Constant Summary

Constant Summary

Constants included from Core

Core::BIOFLAT, Core::CONFIG, Core::DATADIR, Core::ESC_SEQ, Core::HISTORY, Core::MARSHAL, Core::MESSAGE, Core::OBJECT, Core::PLUGIN, Core::SCRIPT, Core::SESSION, Core::SHELLDIR

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Core

#ask_yes_or_no, #bioflat_dir, #colors, #config_file, #data_dir, #history_file, #object_file, #plugin_dir, #script_dir, #script_file, #session_dir, #shell_dir

Instance Attribute Details

#cacheObject

A hash to store temporal (per session) configurations



111
112
113
# File 'lib/bio/shell/core.rb', line 111

def cache
  @cache
end

#configObject

A hash to store persistent configurations



108
109
110
# File 'lib/bio/shell/core.rb', line 108

def config
  @config
end

Instance Method Details

#check_marshalObject

object



299
300
301
302
303
# File 'lib/bio/shell/core.rb', line 299

def check_marshal
  if @config[:marshal] and @config[:marshal] != MARSHAL
    raise "Marshal version mismatch"
  end
end

#close_historyObject



382
383
384
385
386
387
388
# File 'lib/bio/shell/core.rb', line 382

def close_history
  if @cache[:histfile]
    STDERR.print "Saving history (#{history_file}) ... "
    @cache[:histfile].close
    STDERR.puts "done"
  end
end

#closing_splashObject



566
567
568
569
570
571
572
573
574
575
576
# File 'lib/bio/shell/core.rb', line 566

def closing_splash
  STDERR.puts
  STDERR.puts
  if @config[:color]
    STDERR.print splash_message_color
  else
    STDERR.print splash_message
  end
  STDERR.puts
  STDERR.puts
end

#config_colorObject



251
252
253
254
255
256
257
258
259
260
261
262
# File 'lib/bio/shell/core.rb', line 251

def config_color
  bind = Bio::Shell.cache[:binding]
  flag = ! @config[:color]
  @config[:color] = flag
  if flag
    IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
    eval("conf.prompt_mode = :BIORUBY_COLOR", bind)
  else
    IRB.conf[:PROMPT_MODE] = :BIORUBY
    eval("conf.prompt_mode = :BIORUBY", bind)
  end
end

#config_echoObject



243
244
245
246
247
248
249
# File 'lib/bio/shell/core.rb', line 243

def config_echo
  bind = Bio::Shell.cache[:binding]
  flag = ! @config[:echo]
  @config[:echo] = IRB.conf[:ECHO] = flag
  eval("conf.echo = #{flag}", bind)
  STDERR.puts "Echo #{flag ? 'on' : 'off'}"
end

#config_message(str = nil) ⇒ Object



275
276
277
278
279
# File 'lib/bio/shell/core.rb', line 275

def config_message(str = nil)
  str ||= MESSAGE
  @config[:message] = str
  opening_splash
end

#config_pager(cmd = nil) ⇒ Object



264
265
266
# File 'lib/bio/shell/core.rb', line 264

def config_pager(cmd = nil)
  @config[:pager] = cmd
end

#config_showObject



237
238
239
240
241
# File 'lib/bio/shell/core.rb', line 237

def config_show
  @config.each do |k, v|
    STDERR.puts "#{k}\t= #{v.inspect}"
  end
end

#config_splashObject



268
269
270
271
272
273
# File 'lib/bio/shell/core.rb', line 268

def config_splash
  flag = ! @config[:splash]
  @config[:splash] = flag
  STDERR.puts "Splash #{flag ? 'on' : 'off'}"
  opening_splash
end

#configure(savedir) ⇒ Object

save/restore the environment



115
116
117
118
119
120
121
122
123
124
# File 'lib/bio/shell/core.rb', line 115

def configure(savedir)
  @config = {}
  @cache  = {
    :savedir => savedir,
    :workdir => Dir.pwd,
  }
  create_save_dir
  load_config
  load_plugin
end

#create_flat_dir(dbname) ⇒ Object

bioflat



188
189
190
191
192
193
194
# File 'lib/bio/shell/core.rb', line 188

def create_flat_dir(dbname)
  dir = File.join(bioflat_dir, dbname.to_s.strip)
  unless File.directory?(dir)
    FileUtils.makedirs(dir)
  end
  return dir
end

#create_real_dir(dir) ⇒ Object



174
175
176
177
178
179
180
181
182
183
184
# File 'lib/bio/shell/core.rb', line 174

def create_real_dir(dir)
  unless File.directory?(dir)
    begin
      STDERR.print "Creating directory (#{dir}) ... "
      FileUtils.makedirs(dir)
      STDERR.puts "done"
    rescue
      warn "Error: Failed to create directory (#{dir}) : #{$!}"
    end
  end
end

#create_save_dirObject

directories



150
151
152
153
154
# File 'lib/bio/shell/core.rb', line 150

def create_save_dir
  create_real_dir(session_dir)
  create_real_dir(plugin_dir)
  create_real_dir(data_dir)
end

#create_save_dir_askObject



156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
# File 'lib/bio/shell/core.rb', line 156

def create_save_dir_ask
  if File.directory?(session_dir)
    @cache[:save] = true
  end
  unless @cache[:save]
    if ask_yes_or_no("Save session in '#{@cache[:workdir]}' directory? [y/n] ")
      create_real_dir(session_dir)
      create_real_dir(plugin_dir)
      create_real_dir(data_dir)
      create_real_dir(bioflat_dir)
      @cache[:save] = true
    else
      @cache[:save] = false
    end
  end
  return @cache[:save]
end

#find_flat_dir(dbname) ⇒ Object



196
197
198
199
200
201
202
203
# File 'lib/bio/shell/core.rb', line 196

def find_flat_dir(dbname)
  dir = File.join(bioflat_dir, dbname.to_s.strip)
  if File.exists?(dir)
    return dir
  else
    return nil
  end
end

#load_configObject

config



207
208
209
# File 'lib/bio/shell/core.rb', line 207

def load_config
  load_config_file(config_file)
end

#load_config_file(file) ⇒ Object



211
212
213
214
215
216
217
218
219
# File 'lib/bio/shell/core.rb', line 211

def load_config_file(file)
  if File.exists?(file)
    STDERR.print "Loading config (#{file}) ... "
    if hash = YAML.load(File.read(file))
      @config.update(hash)
    end
    STDERR.puts "done"
  end
end

#load_historyObject



390
391
392
393
394
# File 'lib/bio/shell/core.rb', line 390

def load_history
  if @cache[:readline]
    load_history_file(history_file)
  end
end

#load_history_file(file) ⇒ Object



396
397
398
399
400
401
402
403
404
405
406
# File 'lib/bio/shell/core.rb', line 396

def load_history_file(file)
  if File.exists?(file)
    STDERR.print "Loading history (#{file}) ... "
    File.open(file).each do |line|
      unless line[/^# /]
        Readline::HISTORY.push line.chomp
      end
    end
    STDERR.puts "done"
  end
end

#load_objectObject



305
306
307
308
309
310
311
312
# File 'lib/bio/shell/core.rb', line 305

def load_object
  begin
    check_marshal
    load_object_file(object_file)
  rescue
    warn "Error: Load aborted : #{$!}"
  end
end

#load_object_file(file) ⇒ Object



314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
# File 'lib/bio/shell/core.rb', line 314

def load_object_file(file)
  if File.exists?(file)
    STDERR.print "Loading object (#{file}) ... "
    begin
      bind = Bio::Shell.cache[:binding]
      hash = Marshal.load(File.read(file))
      hash.each do |k, v|
        begin
          Thread.current[:restore_value] = v
          eval("#{k} = Thread.current[:restore_value]", bind)
        rescue
          STDERR.puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
        end
      end
    rescue
      warn "Error: Failed to load (#{file}) : #{$!}"
    end
    STDERR.puts "done"
  end
end

#load_pluginObject

plugin



283
284
285
# File 'lib/bio/shell/core.rb', line 283

def load_plugin
  load_plugin_dir(plugin_dir)
end

#load_plugin_dir(dir) ⇒ Object



287
288
289
290
291
292
293
294
295
# File 'lib/bio/shell/core.rb', line 287

def load_plugin_dir(dir)
  if File.directory?(dir)
    Dir.glob("#{dir}/*.rb").sort.each do |file|
      STDERR.print "Loading plugin (#{file}) ... "
      load file
      STDERR.puts "done"
    end
  end
end

#load_sessionObject



126
127
128
129
130
131
132
133
# File 'lib/bio/shell/core.rb', line 126

def load_session
  load_object
  unless @cache[:mode] == :script
    load_history
    opening_splash
    open_history
  end
end

#open_historyObject

history



372
373
374
375
# File 'lib/bio/shell/core.rb', line 372

def open_history
  @cache[:histfile] = File.open(history_file, "a")
  @cache[:histfile].sync = true
end

#opening_splashObject



544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
# File 'lib/bio/shell/core.rb', line 544

def opening_splash
  STDERR.puts
  if @config[:splash]
    if @config[:color]
      splash_message_action_color
    else
      splash_message_action
    end
  end
  if @config[:color]
    STDERR.print splash_message_color
  else
    STDERR.print splash_message
  end
  STDERR.puts
  STDERR.puts
  STDERR.print "  Version : BioRuby #{Bio::BIORUBY_VERSION_ID}"
  STDERR.print " / Ruby #{RUBY_VERSION}"
  STDERR.puts
  STDERR.puts
end

#save_configObject



221
222
223
# File 'lib/bio/shell/core.rb', line 221

def save_config
  save_config_file(config_file)
end

#save_config_file(file) ⇒ Object



225
226
227
228
229
230
231
232
233
234
235
# File 'lib/bio/shell/core.rb', line 225

def save_config_file(file)
  begin
    STDERR.print "Saving config (#{file}) ... "
    File.open(file, "w") do |f|
      f.puts @config.to_yaml
    end
    STDERR.puts "done"
  rescue
    warn "Error: Failed to save (#{file}) : #{$!}"
  end
end

#save_historyObject

not used (use open_history/close_history instead)



409
410
411
412
413
# File 'lib/bio/shell/core.rb', line 409

def save_history
  if @cache[:readline]
    save_history_file(history_file)
  end
end

#save_history_file(file) ⇒ Object



415
416
417
418
419
420
421
422
423
424
425
# File 'lib/bio/shell/core.rb', line 415

def save_history_file(file)
  begin
    STDERR.print "Saving history (#{file}) ... "
    File.open(file, "w") do |f|
      f.puts Readline::HISTORY.to_a
    end
    STDERR.puts "done"
  rescue
    warn "Error: Failed to save (#{file}) : #{$!}"
  end
end

#save_objectObject



335
336
337
# File 'lib/bio/shell/core.rb', line 335

def save_object
  save_object_file(object_file)
end

#save_object_file(file) ⇒ Object



339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
# File 'lib/bio/shell/core.rb', line 339

def save_object_file(file)
  begin
    STDERR.print "Saving object (#{file}) ... "
    File.rename(file, "#{file}.old") if File.exist?(file)
    File.open(file, "w") do |f|
      bind = Bio::Shell.cache[:binding]
      list = eval("local_variables", bind)
      list.collect! { |x| x.to_s }
      list -= ["_"]
      hash = {}
      list.each do |elem|
        value = eval(elem, bind)
        if value
          begin
            Marshal.dump(value)
            hash[elem] = value
          rescue
            # value could not be dumped.
          end
        end
      end
      Marshal.dump(hash, f)
      @config[:marshal] = MARSHAL
    end
    STDERR.puts "done"
  rescue
    File.rename("#{file}.old", file) if File.exist?("#{file}.old")
    warn "Error: Failed to save (#{file}) : #{$!}"
  end
end

#save_scriptObject



460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
# File 'lib/bio/shell/core.rb', line 460

def save_script
  if @script_begin and @script_end and @script_begin <= @script_end
    if File.exists?(script_file)
      message = "Overwrite script file (#{script_file})? [y/n] "
    else
      message = "Save script file (#{script_file})? [y/n] "
    end
    if ask_yes_or_no(message)
      save_script_file(script_file)
    else
      STDERR.puts " ... save aborted."
    end
  elsif @script_begin and @script_end and @script_begin - @script_end == 1
    STDERR.puts " ... script aborted."
  else
    STDERR.puts "Error: Script range #{@script_begin}..#{@script_end} is invalid"
  end
end

#save_script_file(file) ⇒ Object



479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
# File 'lib/bio/shell/core.rb', line 479

def save_script_file(file)
  begin
    STDERR.print "Saving script (#{file}) ... "
    File.open(file, "w") do |f|
      f.puts "#!/usr/bin/env bioruby"
      f.puts
      f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
      f.puts
    end
    STDERR.puts "done"
  rescue
    @script_begin = nil
    warn "Error: Failed to save (#{file}) : #{$!}"
  end
end

#save_sessionObject



135
136
137
138
139
140
141
142
143
144
145
146
# File 'lib/bio/shell/core.rb', line 135

def save_session
  unless @cache[:mode] == :script
    closing_splash
  end
  if create_save_dir_ask
    #save_history	# changed to use our own...
    close_history
    save_object
    save_config
  end
  #STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
end

#script(mode = nil) ⇒ Object

script



429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
# File 'lib/bio/shell/core.rb', line 429

def script(mode = nil)
  case mode
  when :begin, "begin", :start, "start"
    @cache[:script] = true
    script_begin
  when :end, "end", :stop, "stop"
    @cache[:script] = false
    script_end
    save_script
  else
    if @cache[:script]
      @cache[:script] = false
      script_end
      save_script
    else
      @cache[:script] = true
      script_begin
    end
  end
end

#script_beginObject



450
451
452
453
# File 'lib/bio/shell/core.rb', line 450

def script_begin
  STDERR.puts "-- 8< -- 8< -- 8< --  Script  -- 8< -- 8< -- 8< --"
  @script_begin = Readline::HISTORY.size
end

#script_endObject



455
456
457
458
# File 'lib/bio/shell/core.rb', line 455

def script_end
  STDERR.puts "-- >8 -- >8 -- >8 --  Script  -- >8 -- >8 -- >8 --"
  @script_end = Readline::HISTORY.size - 2
end

#splash_messageObject

splash



497
498
499
500
# File 'lib/bio/shell/core.rb', line 497

def splash_message
  @config[:message] ||= MESSAGE
  @config[:message].to_s.split(//).join(" ")
end

#splash_message_action(message = nil) ⇒ Object



509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
# File 'lib/bio/shell/core.rb', line 509

def splash_message_action(message = nil)
  s = message || splash_message
  l = s.length
  x = " "
  0.step(l,2) do |i|
    l1 = l-i;  l2 = l1/2;  l4 = l2/2
    STDERR.print "#{s[0,i]}#{x*l1}#{s[i,1]}\r"
    sleep(0.001)
    STDERR.print "#{s[0,i]}#{x*l2}#{s[i,1]}#{x*(l1-l2)}\r"
    sleep(0.002)
    STDERR.print "#{s[0,i]}#{x*l4}#{s[i,1]}#{x*(l2-l4)}\r"
    sleep(0.004)
    STDERR.print "#{s[0,i+1]}#{x*l4}\r"
    sleep(0.008)
  end
end

#splash_message_action_color(message = nil) ⇒ Object



526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
# File 'lib/bio/shell/core.rb', line 526

def splash_message_action_color(message = nil)
  s = message || splash_message
  l = s.length
  c = colors
  x = " "
  0.step(l,2) do |i|
    l1 = l-i;  l2 = l1/2;  l4 = l2/2
    STDERR.print "#{c[:n]}#{s[0,i]}#{x*l1}#{c[:y]}#{s[i,1]}\r"
    sleep(0.001)
    STDERR.print "#{c[:n]}#{s[0,i]}#{x*l2}#{c[:g]}#{s[i,1]}#{x*(l1-l2)}\r"
    sleep(0.002)
    STDERR.print "#{c[:n]}#{s[0,i]}#{x*l4}#{c[:r]}#{s[i,1]}#{x*(l2-l4)}\r"
    sleep(0.004)
    STDERR.print "#{c[:n]}#{s[0,i+1]}#{x*l4}\r"
    sleep(0.008)
  end
end

#splash_message_colorObject



502
503
504
505
506
507
# File 'lib/bio/shell/core.rb', line 502

def splash_message_color
  str = splash_message
  ruby = colors[:ruby]
  none = colors[:none]
  return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
end

#store_history(line) ⇒ Object



377
378
379
380
# File 'lib/bio/shell/core.rb', line 377

def store_history(line)
  Bio::Shell.cache[:histfile].puts "# #{Time.now}"
  Bio::Shell.cache[:histfile].puts line
end