[BioRuby-cvs] bioruby/lib/bio/shell core.rb,1.24,1.25
Katayama Toshiaki
k at dev.open-bio.org
Tue Jun 26 01:41:35 UTC 2007
Update of /home/repository/bioruby/bioruby/lib/bio/shell
In directory dev.open-bio.org:/tmp/cvs-serv14986/lib/bio/shell
Modified Files:
core.rb
Log Message:
* changed to Dir.chdir only on mkdir/save instead of start up time
Index: core.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/core.rb,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** core.rb 5 Apr 2007 23:35:41 -0000 1.24
--- core.rb 26 Jun 2007 01:41:33 -0000 1.25
***************
*** 11,14 ****
--- 11,16 ----
module Bio::Shell::Core
+ # chdir
+ # change to File.join for / ended dirs
SAVEDIR = "shell/session/"
CONFIG = "config"
***************
*** 41,45 ****
def datadir
! DATADIR
end
--- 43,47 ----
def datadir
! File.join(@cache[:workdir], DATADIR)
end
***************
*** 49,57 ****
def object_file
! SAVEDIR + OBJECT
end
def history_file
! SAVEDIR + HISTORY
end
--- 51,59 ----
def object_file
! File.join(@cache[:workdir], SAVEDIR, OBJECT)
end
def history_file
! File.join(@cache[:workdir], SAVEDIR, HISTORY)
end
***************
*** 88,94 ****
### save/restore the environment
! def configure
@config = {}
! @cache = {}
create_save_dir
load_config
--- 90,100 ----
### save/restore the environment
! def configure(workdir)
! savedir = File.join(Dir.pwd, workdir)
@config = {}
! @cache = {
! :workdir => workdir,
! :savedir => savedir,
! }
create_save_dir
load_config
***************
*** 115,119 ****
save_config
end
! STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
STDERR.puts "History is saved in '#{@cache[:workdir]}/#{SAVEDIR + HISTORY}'"
end
--- 121,125 ----
save_config
end
! #STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
STDERR.puts "History is saved in '#{@cache[:workdir]}/#{SAVEDIR + HISTORY}'"
end
***************
*** 128,136 ****
def create_save_dir_ask
! if File.directory?(SAVEDIR)
! @cache[:save] = true
end
! if @cache[:save].nil?
! if ask_yes_or_no("Save session in '#{SAVEDIR}' directory? [y/n] ")
create_real_dir(SAVEDIR)
create_real_dir(PLUGIN)
--- 134,144 ----
def create_save_dir_ask
! Dir.chdir(@cache[:workdir]) do |path|
! if File.directory?(SAVEDIR)
! @cache[:save] = true
! end
end
! unless @cache[:save]
! if ask_yes_or_no("Save session in '#{@cache[:workdir]}/#{SAVEDIR}' directory? [y/n] ")
create_real_dir(SAVEDIR)
create_real_dir(PLUGIN)
***************
*** 146,156 ****
def create_real_dir(dir)
! unless File.directory?(dir)
! begin
! STDERR.print "Creating directory (#{dir}) ... "
! FileUtils.mkdir_p(dir)
! STDERR.puts "done"
! rescue
! warn "Error: Failed to create directory (#{dir}) : #{$!}"
end
end
--- 154,166 ----
def create_real_dir(dir)
! Dir.chdir(@cache[:workdir]) do |path|
! unless File.directory?(dir)
! begin
! STDERR.print "Creating directory (#{path}/#{dir}) ... "
! FileUtils.mkdir_p(dir)
! STDERR.puts "done"
! rescue
! warn "Error: Failed to create directory (#{path}/#{dir}) : #{$!}"
! end
end
end
***************
*** 160,177 ****
def create_flat_dir(dbname)
! dir = BIOFLAT + dbname.to_s.strip
! unless File.directory?(dir)
! FileUtils.mkdir_p(dir)
end
! return dir
end
def find_flat_dir(dbname)
! dir = BIOFLAT + dbname.to_s.strip
! if File.exists?(dir)
! return dir
! else
! return nil
end
end
--- 170,195 ----
def create_flat_dir(dbname)
! flatdb = ""
! Dir.chdir(@cache[:workdir]) do |path|
! dir = BIOFLAT + dbname.to_s.strip
! unless File.directory?(dir)
! FileUtils.mkdir_p(dir)
! end
! flatdb = "#{path}/#{dir}"
end
! return flatdb
end
def find_flat_dir(dbname)
! flatdb = ""
! Dir.chdir(@cache[:workdir]) do |path|
! dir = BIOFLAT + dbname.to_s.strip
! if File.exists?(dir)
! flatdb = "#{path}/#{dir}"
! else
! flatdb = nil
! end
end
+ return flatdb
end
***************
*** 183,192 ****
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
--- 201,212 ----
def load_config_file(file)
! Dir.chdir(@cache[:workdir]) do |path|
! if File.exists?(file)
! STDERR.print "Loading config (#{path}/#{file}) ... "
! if hash = YAML.load(File.read(file))
! @config.update(hash)
! end
! STDERR.puts "done"
end
end
end
***************
*** 197,208 ****
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}) : #{$!}"
end
end
--- 217,230 ----
def save_config_file(file)
! Dir.chdir(@cache[:workdir]) do |path|
! begin
! STDERR.print "Saving config (#{path}/#{file}) ... "
! File.open(file, "w") do |f|
! f.puts @config.to_yaml
! end
! STDERR.puts "done"
! rescue
! warn "Error: Failed to save (#{path}/#{file}) : #{$!}"
end
end
end
***************
*** 259,267 ****
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
--- 281,291 ----
def load_plugin_dir(dir)
! Dir.chdir(@cache[:workdir]) do |path|
! if File.directory?(dir)
! Dir.glob("#{dir}/*.rb").sort.each do |file|
! STDERR.print "Loading plugin (#{path}/#{file}) ... "
! load file
! STDERR.puts "done"
! end
end
end
***************
*** 286,306 ****
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
--- 310,332 ----
def load_object_file(file)
! Dir.chdir(@cache[:workdir]) do |path|
! if File.exists?(file)
! STDERR.print "Loading object (#{path}/#{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 : #{$!}"
! end
end
+ rescue
+ warn "Error: Failed to load (#{path}/#{file}) : #{$!}"
end
! STDERR.puts "done"
end
end
end
***************
*** 311,340 ****
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 -= ["_"]
! 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}) : #{$!}"
end
end
--- 337,368 ----
def save_object_file(file)
! Dir.chdir(@cache[:workdir]) do |path|
! begin
! STDERR.print "Saving object (#{path}/#{file}) ... "
! File.rename(file, "#{file}.old") if File.exist?(file)
! File.open(file, "w") do |f|
! bind = Bio::Shell.cache[:binding]
! list = eval("local_variables", bind)
! list -= ["_"]
! hash = {}
! list.each do |elem|
! value = eval(elem, bind)
! if value
! begin
! Marshal.dump(value)
! hash[elem] = value
! rescue
! # value could not be dumped.
! end
end
end
+ Marshal.dump(hash, f)
+ @config[:marshal] = MARSHAL
end
! STDERR.puts "done"
! rescue
! File.rename("#{file}.old", file) if File.exist?("#{file}.old")
! warn "Error: Failed to save (#{file}) : #{$!}"
end
end
end
***************
*** 343,347 ****
def open_history
! @cache[:histfile] = File.open(SAVEDIR + HISTORY, "a")
@cache[:histfile].sync = true
end
--- 371,377 ----
def open_history
! Dir.chdir(@cache[:workdir]) do |path|
! @cache[:histfile] = File.open(SAVEDIR + HISTORY, "a")
! end
@cache[:histfile].sync = true
end
***************
*** 363,371 ****
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
--- 393,403 ----
def load_history_file(file)
! Dir.chdir(@cache[:workdir]) do |path|
! if File.exists?(file)
! STDERR.print "Loading history (#{path}/#{file}) ... "
! File.open(file).each do |line|
! unless line[/^# /]
! Readline::HISTORY.push line.chomp
! end
end
end
***************
*** 382,393 ****
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}) : #{$!}"
end
end
--- 414,427 ----
def save_history_file(file)
! Dir.chdir(@cache[:workdir]) do |path|
! begin
! STDERR.print "Saving history (#{path}/#{file}) ... "
! File.open(file, "w") do |f|
! f.puts Readline::HISTORY.to_a
! end
! STDERR.puts "done"
! rescue
! warn "Error: Failed to save (#{path}/#{file}) : #{$!}"
end
end
end
***************
*** 428,441 ****
def save_script
if @script_begin and @script_end and @script_begin <= @script_end
! if File.exists?(SCRIPT)
! message = "Overwrite script file (#{SCRIPT})? [y/n] "
! else
! message = "Save script file (#{SCRIPT})? [y/n] "
end
- if ask_yes_or_no(message)
- save_script_file(SCRIPT)
- else
- STDERR.puts " ... save aborted."
- end
elsif @script_begin and @script_end and @script_begin - @script_end == 1
STDERR.puts " ... script aborted."
--- 462,477 ----
def save_script
if @script_begin and @script_end and @script_begin <= @script_end
! Dir.chdir(@cache[:workdir]) do |path|
! if File.exists?(SCRIPT)
! message = "Overwrite script file (#{path}/#{SCRIPT})? [y/n] "
! else
! message = "Save script file (#{path}/#{SCRIPT})? [y/n] "
! end
! if ask_yes_or_no(message)
! save_script_file(SCRIPT)
! else
! STDERR.puts " ... save aborted."
! end
end
elsif @script_begin and @script_end and @script_begin - @script_end == 1
STDERR.puts " ... script aborted."
***************
*** 446,461 ****
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.. at script_end]
! f.puts
end
- STDERR.puts "done"
- rescue
- @script_begin = nil
- warn "Error: Failed to save (#{file}) : #{$!}"
end
end
--- 482,499 ----
def save_script_file(file)
! Dir.chdir(@cache[:workdir]) do |path|
! begin
! STDERR.print "Saving script (#{path}/#{file}) ... "
File.open(file, "w") do |f|
! f.puts "#!/usr/bin/env bioruby"
! f.puts
! f.puts Readline::HISTORY.to_a[@script_begin.. at script_end]
! f.puts
! end
! STDERR.puts "done"
! rescue
! @script_begin = nil
! warn "Error: Failed to save (#{path}/#{file}) : #{$!}"
end
end
end
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