From: bwv549 <jtprince@...>
Date: 2009-12-17T14:45:12+09:00
Subject: Re: working with a slow pipe (IO.popen)

@Robert: I've looked through a lot of pymol docs and haven't found
anything on it yet, will post if I do.

The solution you post looks very intriguing.  It runs fine, but closes
before I get back the output I need.  It seems like there must be some
kind of a pause to let pymol start spitting out output.  I may play
around with it some to see if I can get it working.

@Eric: this solution works nicely and returns all the expected
output.  I will be using it unless something better comes along.

Thanks to both of you for your excellent input on this.  --John


On Dec 16, 1:05 am, Robert Klemme <shortcut...@googlemail.com> wrote:
> 2009/12/16 bwv549 <jtpri...@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 endhttp://blog.rubybestpractices.com/