Module | Bio::Shell::Ghost |
In: |
lib/bio/shell/core.rb
|
cache | [RW] | A hash to store temporal (per session) configurations |
config | [RW] | A hash to store persistent configurations |
object
# File lib/bio/shell/core.rb, line 299 299: def check_marshal 300: if @config[:marshal] and @config[:marshal] != MARSHAL 301: raise "Marshal version mismatch" 302: end 303: end
# File lib/bio/shell/core.rb, line 381 381: def close_history 382: if @cache[:histfile] 383: STDERR.print "Saving history (#{history_file}) ... " 384: @cache[:histfile].close 385: STDERR.puts "done" 386: end 387: end
# File lib/bio/shell/core.rb, line 565 565: def closing_splash 566: STDERR.puts 567: STDERR.puts 568: if @config[:color] 569: STDERR.print splash_message_color 570: else 571: STDERR.print splash_message 572: end 573: STDERR.puts 574: STDERR.puts 575: end
# File lib/bio/shell/core.rb, line 251 251: def config_color 252: bind = Bio::Shell.cache[:binding] 253: flag = ! @config[:color] 254: @config[:color] = flag 255: if flag 256: IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR 257: eval("conf.prompt_mode = :BIORUBY_COLOR", bind) 258: else 259: IRB.conf[:PROMPT_MODE] = :BIORUBY 260: eval("conf.prompt_mode = :BIORUBY", bind) 261: end 262: end
# File lib/bio/shell/core.rb, line 243 243: def config_echo 244: bind = Bio::Shell.cache[:binding] 245: flag = ! @config[:echo] 246: @config[:echo] = IRB.conf[:ECHO] = flag 247: eval("conf.echo = #{flag}", bind) 248: STDERR.puts "Echo #{flag ? 'on' : 'off'}" 249: end
# File lib/bio/shell/core.rb, line 275 275: def config_message(str = nil) 276: str ||= MESSAGE 277: @config[:message] = str 278: opening_splash 279: end
# File lib/bio/shell/core.rb, line 264 264: def config_pager(cmd = nil) 265: @config[:pager] = cmd 266: end
# File lib/bio/shell/core.rb, line 237 237: def config_show 238: @config.each do |k, v| 239: STDERR.puts "#{k}\t= #{v.inspect}" 240: end 241: end
# File lib/bio/shell/core.rb, line 268 268: def config_splash 269: flag = ! @config[:splash] 270: @config[:splash] = flag 271: STDERR.puts "Splash #{flag ? 'on' : 'off'}" 272: opening_splash 273: end
save/restore the environment
# File lib/bio/shell/core.rb, line 115 115: def configure(savedir) 116: @config = {} 117: @cache = { 118: :savedir => savedir, 119: :workdir => Dir.pwd, 120: } 121: create_save_dir 122: load_config 123: load_plugin 124: end
bioflat
# File lib/bio/shell/core.rb, line 188 188: def create_flat_dir(dbname) 189: dir = File.join(bioflat_dir, dbname.to_s.strip) 190: unless File.directory?(dir) 191: FileUtils.makedirs(dir) 192: end 193: return dir 194: end
# File lib/bio/shell/core.rb, line 174 174: def create_real_dir(dir) 175: unless File.directory?(dir) 176: begin 177: STDERR.print "Creating directory (#{dir}) ... " 178: FileUtils.makedirs(dir) 179: STDERR.puts "done" 180: rescue 181: warn "Error: Failed to create directory (#{dir}) : #{$!}" 182: end 183: end 184: end
directories
# File lib/bio/shell/core.rb, line 150 150: def create_save_dir 151: create_real_dir(session_dir) 152: create_real_dir(plugin_dir) 153: create_real_dir(data_dir) 154: end
# File lib/bio/shell/core.rb, line 156 156: def create_save_dir_ask 157: if File.directory?(session_dir) 158: @cache[:save] = true 159: end 160: unless @cache[:save] 161: if ask_yes_or_no("Save session in '#{@cache[:workdir]}' directory? [y/n] ") 162: create_real_dir(session_dir) 163: create_real_dir(plugin_dir) 164: create_real_dir(data_dir) 165: create_real_dir(bioflat_dir) 166: @cache[:save] = true 167: else 168: @cache[:save] = false 169: end 170: end 171: return @cache[:save] 172: end
# File lib/bio/shell/core.rb, line 196 196: def find_flat_dir(dbname) 197: dir = File.join(bioflat_dir, dbname.to_s.strip) 198: if File.exists?(dir) 199: return dir 200: else 201: return nil 202: end 203: end
config
# File lib/bio/shell/core.rb, line 207 207: def load_config 208: load_config_file(config_file) 209: end
# File lib/bio/shell/core.rb, line 211 211: def load_config_file(file) 212: if File.exists?(file) 213: STDERR.print "Loading config (#{file}) ... " 214: if hash = YAML.load(File.read(file)) 215: @config.update(hash) 216: end 217: STDERR.puts "done" 218: end 219: end
# File lib/bio/shell/core.rb, line 389 389: def load_history 390: if @cache[:readline] 391: load_history_file(history_file) 392: end 393: end
# File lib/bio/shell/core.rb, line 395 395: def load_history_file(file) 396: if File.exists?(file) 397: STDERR.print "Loading history (#{file}) ... " 398: File.open(file).each do |line| 399: unless line[/^# /] 400: Readline::HISTORY.push line.chomp 401: end 402: end 403: STDERR.puts "done" 404: end 405: end
# File lib/bio/shell/core.rb, line 305 305: def load_object 306: begin 307: check_marshal 308: load_object_file(object_file) 309: rescue 310: warn "Error: Load aborted : #{$!}" 311: end 312: end
# File lib/bio/shell/core.rb, line 314 314: def load_object_file(file) 315: if File.exists?(file) 316: STDERR.print "Loading object (#{file}) ... " 317: begin 318: bind = Bio::Shell.cache[:binding] 319: hash = Marshal.load(File.read(file)) 320: hash.each do |k, v| 321: begin 322: Thread.current[:restore_value] = v 323: eval("#{k} = Thread.current[:restore_value]", bind) 324: rescue 325: STDERR.puts "Warning: object '#{k}' couldn't be loaded : #{$!}" 326: end 327: end 328: rescue 329: warn "Error: Failed to load (#{file}) : #{$!}" 330: end 331: STDERR.puts "done" 332: end 333: end
plugin
# File lib/bio/shell/core.rb, line 283 283: def load_plugin 284: load_plugin_dir(plugin_dir) 285: end
# File lib/bio/shell/core.rb, line 287 287: def load_plugin_dir(dir) 288: if File.directory?(dir) 289: Dir.glob("#{dir}/*.rb").sort.each do |file| 290: STDERR.print "Loading plugin (#{file}) ... " 291: load file 292: STDERR.puts "done" 293: end 294: end 295: end
# File lib/bio/shell/core.rb, line 126 126: def load_session 127: load_object 128: unless @cache[:mode] == :script 129: load_history 130: opening_splash 131: open_history 132: end 133: end
history
# File lib/bio/shell/core.rb, line 371 371: def open_history 372: @cache[:histfile] = File.open(history_file, "a") 373: @cache[:histfile].sync = true 374: end
# File lib/bio/shell/core.rb, line 543 543: def opening_splash 544: STDERR.puts 545: if @config[:splash] 546: if @config[:color] 547: splash_message_action_color 548: else 549: splash_message_action 550: end 551: end 552: if @config[:color] 553: STDERR.print splash_message_color 554: else 555: STDERR.print splash_message 556: end 557: STDERR.puts 558: STDERR.puts 559: STDERR.print " Version : BioRuby #{Bio::BIORUBY_VERSION_ID}" 560: STDERR.print " / Ruby #{RUBY_VERSION}" 561: STDERR.puts 562: STDERR.puts 563: end
# File lib/bio/shell/core.rb, line 221 221: def save_config 222: save_config_file(config_file) 223: end
# File lib/bio/shell/core.rb, line 225 225: def save_config_file(file) 226: begin 227: STDERR.print "Saving config (#{file}) ... " 228: File.open(file, "w") do |f| 229: f.puts @config.to_yaml 230: end 231: STDERR.puts "done" 232: rescue 233: warn "Error: Failed to save (#{file}) : #{$!}" 234: end 235: end
not used (use open_history/close_history instead)
# File lib/bio/shell/core.rb, line 408 408: def save_history 409: if @cache[:readline] 410: save_history_file(history_file) 411: end 412: end
# File lib/bio/shell/core.rb, line 414 414: def save_history_file(file) 415: begin 416: STDERR.print "Saving history (#{file}) ... " 417: File.open(file, "w") do |f| 418: f.puts Readline::HISTORY.to_a 419: end 420: STDERR.puts "done" 421: rescue 422: warn "Error: Failed to save (#{file}) : #{$!}" 423: end 424: end
# File lib/bio/shell/core.rb, line 335 335: def save_object 336: save_object_file(object_file) 337: end
# File lib/bio/shell/core.rb, line 339 339: def save_object_file(file) 340: begin 341: STDERR.print "Saving object (#{file}) ... " 342: File.rename(file, "#{file}.old") if File.exist?(file) 343: File.open(file, "w") do |f| 344: bind = Bio::Shell.cache[:binding] 345: list = eval("local_variables", bind) 346: list -= ["_"] 347: hash = {} 348: list.each do |elem| 349: value = eval(elem, bind) 350: if value 351: begin 352: Marshal.dump(value) 353: hash[elem] = value 354: rescue 355: # value could not be dumped. 356: end 357: end 358: end 359: Marshal.dump(hash, f) 360: @config[:marshal] = MARSHAL 361: end 362: STDERR.puts "done" 363: rescue 364: File.rename("#{file}.old", file) if File.exist?("#{file}.old") 365: warn "Error: Failed to save (#{file}) : #{$!}" 366: end 367: end
# File lib/bio/shell/core.rb, line 459 459: def save_script 460: if @script_begin and @script_end and @script_begin <= @script_end 461: if File.exists?(script_file) 462: message = "Overwrite script file (#{script_file})? [y/n] " 463: else 464: message = "Save script file (#{script_file})? [y/n] " 465: end 466: if ask_yes_or_no(message) 467: save_script_file(script_file) 468: else 469: STDERR.puts " ... save aborted." 470: end 471: elsif @script_begin and @script_end and @script_begin - @script_end == 1 472: STDERR.puts " ... script aborted." 473: else 474: STDERR.puts "Error: Script range #{@script_begin}..#{@script_end} is invalid" 475: end 476: end
# File lib/bio/shell/core.rb, line 478 478: def save_script_file(file) 479: begin 480: STDERR.print "Saving script (#{file}) ... " 481: File.open(file, "w") do |f| 482: f.puts "#!/usr/bin/env bioruby" 483: f.puts 484: f.puts Readline::HISTORY.to_a[@script_begin..@script_end] 485: f.puts 486: end 487: STDERR.puts "done" 488: rescue 489: @script_begin = nil 490: warn "Error: Failed to save (#{file}) : #{$!}" 491: end 492: end
# File lib/bio/shell/core.rb, line 135 135: def save_session 136: unless @cache[:mode] == :script 137: closing_splash 138: end 139: if create_save_dir_ask 140: #save_history # changed to use our own... 141: close_history 142: save_object 143: save_config 144: end 145: #STDERR.puts "Leaving directory '#{@cache[:workdir]}'" 146: end
# File lib/bio/shell/core.rb, line 428 428: def script(mode = nil) 429: case mode 430: when :begin, "begin", :start, "start" 431: @cache[:script] = true 432: script_begin 433: when :end, "end", :stop, "stop" 434: @cache[:script] = false 435: script_end 436: save_script 437: else 438: if @cache[:script] 439: @cache[:script] = false 440: script_end 441: save_script 442: else 443: @cache[:script] = true 444: script_begin 445: end 446: end 447: end
# File lib/bio/shell/core.rb, line 449 449: def script_begin 450: STDERR.puts "-- 8< -- 8< -- 8< -- Script -- 8< -- 8< -- 8< --" 451: @script_begin = Readline::HISTORY.size 452: end
# File lib/bio/shell/core.rb, line 454 454: def script_end 455: STDERR.puts "-- >8 -- >8 -- >8 -- Script -- >8 -- >8 -- >8 --" 456: @script_end = Readline::HISTORY.size - 2 457: end
splash
# File lib/bio/shell/core.rb, line 496 496: def splash_message 497: @config[:message] ||= MESSAGE 498: @config[:message].to_s.split(//).join(" ") 499: end
# File lib/bio/shell/core.rb, line 508 508: def splash_message_action(message = nil) 509: s = message || splash_message 510: l = s.length 511: x = " " 512: 0.step(l,2) do |i| 513: l1 = l-i; l2 = l1/2; l4 = l2/2 514: STDERR.print "#{s[0,i]}#{x*l1}#{s[i,1]}\r" 515: sleep(0.001) 516: STDERR.print "#{s[0,i]}#{x*l2}#{s[i,1]}#{x*(l1-l2)}\r" 517: sleep(0.002) 518: STDERR.print "#{s[0,i]}#{x*l4}#{s[i,1]}#{x*(l2-l4)}\r" 519: sleep(0.004) 520: STDERR.print "#{s[0,i+1]}#{x*l4}\r" 521: sleep(0.008) 522: end 523: end
# File lib/bio/shell/core.rb, line 525 525: def splash_message_action_color(message = nil) 526: s = message || splash_message 527: l = s.length 528: c = colors 529: x = " " 530: 0.step(l,2) do |i| 531: l1 = l-i; l2 = l1/2; l4 = l2/2 532: STDERR.print "#{c[:n]}#{s[0,i]}#{x*l1}#{c[:y]}#{s[i,1]}\r" 533: sleep(0.001) 534: STDERR.print "#{c[:n]}#{s[0,i]}#{x*l2}#{c[:g]}#{s[i,1]}#{x*(l1-l2)}\r" 535: sleep(0.002) 536: STDERR.print "#{c[:n]}#{s[0,i]}#{x*l4}#{c[:r]}#{s[i,1]}#{x*(l2-l4)}\r" 537: sleep(0.004) 538: STDERR.print "#{c[:n]}#{s[0,i+1]}#{x*l4}\r" 539: sleep(0.008) 540: end 541: end
# File lib/bio/shell/core.rb, line 501 501: def splash_message_color 502: str = splash_message 503: ruby = colors[:ruby] 504: none = colors[:none] 505: return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" } 506: end