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=A0am, Robert Klemme <[e-mail]> wrote:
> 2009/12/16 bwv549 <[e-mail]>:
>
>
>
> > On Dec 15, 11:32=A0pm, Eric Wong <[e-mail]> wrote:
> >> bwv549 <[e-mail]> 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|
> >> > =A0 pipe.puts "load file.pdb, mymodel\n"
> >> > =A0 pipe.puts "run my_script.py"
> >> > =A0 # this command will generate a whole bunch of output to stdout
> >> > =A0 pipe.puts "my_script mymodel"
> >> > =A0 sleep(5) =A0# <--- this is what I have to do in order to get the
> >> > output
> >> > =A0 pipe.close_write
> >> > =A0 output =3D 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. =A0There has to be a wa=
y
> >> > 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. =A0Anybody know how to solve this? =A0I'm happy to use a diffe=
rent
> >> > approach if it means I can be sure I get all of my output out. =A0 -=
-
> >> > 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. =A0pipe.read should just bloc=
k
> >> until you get output, otherwise put an IO.select([pipe) in front of it=
.
>
> >> Does this work?
>
> >> =A0 IO.popen("pymol -cq -p", 'w+') do |pipe|
> >> =A0 =A0 pipe.puts "load file.pdb, mymodel\n"
> >> =A0 =A0 pipe.puts "run my_script.py"
> >> =A0 =A0 pipe.puts "my_script mymodel"
>
> >> =A0 =A0 # IO.select([pipe]) # you shouldn't need to uncomment this...
>
> >> =A0 =A0 output =3D pipe.read
> >> =A0 end
>
> >> --
> >> Eric Wong
>
> > both of those hang indefinitely. =A0It doesn't hang if I add the line:
>
> > =A0 pipe.puts "quit"
>
> > but that doesn't give me all the output either. =A0So 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. =A0It opens a thread
> > for reading the output and asks if there is any output every 1/2
> > second. =A0Once we go 1/2 second without output we kill the thread.
>
> > my_string =3D ""
> > Open3.popen3("pymol -cq -p") do |si, so, se|
> > =A0si.puts "load file.pdb, mymodel\n"
> > =A0si.puts "run my_script.py\n"
> > =A0si.puts "myscript mymodel\n"
>
> > =A0forstdout =3D Thread.new do
> > =A0 =A0Thread.current['lines'] =3D []
> > =A0 =A0while line =3D so.gets
> > =A0 =A0 =A0Thread.current['lines'] << line
> > =A0 =A0end
> > =A0end
>
> You don't need the thread local for this to work. =A0Note there is also
> Thread#value!
>
> How does this work:
>
> output =3D IO.popen("pymol -cq -p", 'w+') do |pipe|
> =A0 reader =3D Thread.new { pipe.to_a }
>
> =A0 pipe.puts "load file.pdb, mymodel"
> =A0 pipe.puts "run my_script.py"
> =A0 # this command will generate a whole bunch of output to stdout
> =A0 pipe.puts "my_script mymodel"
>
> =A0 pipe.close_write
> =A0 reader.value
> end
>
> Kind regards
>
> robert
>
> --
> remember.guy do |as, often| as.you_can - without endhttp://blog.rubybestp=
ractices.com/