From: Robert Klemme <shortcutter@...>
Date: 2009-12-16T17:05:54+09:00
Subject: Re: working with a slow pipe (IO.popen)

2009/12/16 bwv549 <jtprince@gmail.com>:
> On Dec 15, 11:32 pm, Eric Wong <normalper...@yhbt.net> wrote:
>> bwv549 <jtpri...@gmail.com> wrote:
>> > I'm doing some work with pymol and having trouble getting all the
>> > pymol output out:
>>
>> > # I open it in quiet/commandline mode with a pipe:
>> > IO.popen("pymol -cq -p", 'w+') do |pipe|
>> >   pipe.puts "load file.pdb, mymodel\n"
>> >   pipe.puts "run my_script.py"
>> >   # this command will generate a whole bunch of output to stdout
>> >   pipe.puts "my_script mymodel"
>> >   sleep(5)  # <--- this is what I have to do in order to get the
>> > output
>> >   pipe.close_write
>> >   output = pipe.read
>> > end
>>
>> > What is annoying is that unless I sleep for 2-5 seconds I don't get
>> > output or (even worse) my output is cut off.  There has to be a way
>> > besides arbitrarily sleeping to ensure that the command is finished.
>> > I've tried things like piping in "quit", but that doesn't seem to
>> > work.  Anybody know how to solve this?  I'm happy to use a different
>> > approach if it means I can be sure I get all of my output out.   --
>> > Thanks!
>>
>> Hi,
>>
>> I don't know about pymol, but some apps do not respond well to having
>> its stdin closed on it with close_write.  pipe.read should just block
>> until you get output, otherwise put an IO.select([pipe) in front of it.
>>
>> Does this work?
>>
>>   IO.popen("pymol -cq -p", 'w+') do |pipe|
>>     pipe.puts "load file.pdb, mymodel\n"
>>     pipe.puts "run my_script.py"
>>     pipe.puts "my_script mymodel"
>>
>>     # IO.select([pipe]) # you shouldn't need to uncomment this...
>>
>>     output = pipe.read
>>   end
>>
>> --
>> Eric Wong
>
> both of those hang indefinitely.  It doesn't hang if I add the line:
>
>   pipe.puts "quit"
>
> but that doesn't give me all the output either.  So maybe pymol
> behaves differently than many commandline programs?

What does the documentation of "pymol" say?

> Here is what I've worked out for the time being.  It opens a thread
> for reading the output and asks if there is any output every 1/2
> second.  Once we go 1/2 second without output we kill the thread.
>
> my_string = ""
> Open3.popen3("pymol -cq -p") do |si, so, se|
>  si.puts "load file.pdb, mymodel\n"
>  si.puts "run my_script.py\n"
>  si.puts "myscript mymodel\n"
>
>  forstdout = Thread.new do
>    Thread.current['lines'] = []
>    while line = so.gets
>      Thread.current['lines'] << line
>    end
>  end

You don't need the thread local for this to work.  Note there is also
Thread#value!

How does this work:

output = IO.popen("pymol -cq -p", 'w+') do |pipe|
  reader = Thread.new { pipe.to_a }

  pipe.puts "load file.pdb, mymodel"
  pipe.puts "run my_script.py"
  # this command will generate a whole bunch of output to stdout
  pipe.puts "my_script mymodel"

  pipe.close_write
  reader.value
end

Kind regards

robert

-- 
remember.guy do |as, often| as.you_can - without end
http://blog.rubybestpractices.com/