Re: [BioPython] Is BioPython thread safe?

Hi Mike,
   Thanks for the response... I really appreciate it.  I'll look into 
the semaphor solution or just make an external command line program 
which I can call from another python program. Thanks again!

-Brandon King

Mike Cariaso wrote:

> I only use biopython occasionally, but have been
> through similar issues with perl, and will share what
> I can.
>
> I think the lack of responses indicates that no one
> can say authoritatively, since there are so many
> developers. Presumably some parts of biopython are 
> threadsafe, but that may be more a matter of luck than
> of design. 
>
> Doing threadsafe signals is considerably more complex
> than non-threadsafe. If you don't see a lot of code
> gymnastics and comments about threads, any library
> using signals for is very unlikely to be threadsafe.
>
> if you need biopython and threads, you'll probably
> have to wrap all biopython code behind a single
> semaphore, and prevent concurrent access. Depending on
> what you're doing this may serialize all your code, or
> only a portion. Manually inspect the most crucial
> biopython components and see if you can use multiple
> semaphors, perhaps one for pieces which use signals,
> and another for components which read/write class
> variables. Gradually keep decreasing the granularity
> of the semaphors. Also look for places where signals
> are used only as timeouts, and replace these with
> another thread.
>
> Its probably going to be real painful.
>
>
>
> --- Brandon King <kingb@xxxxxxxxxxx> wrote:
>
>  
>
> > Hello All,
> >    Did I not give enough information about the
> > problem? Any one have 
> > any suggestions or ideas?
> >
> > -Brandon King
> >
> > Brandon King wrote:
> >
> >    
> >
> > > Hi All,
> > >   I'm trying to use BioPython within a thread of
> > >      
> > my main program and 
> >    
> >
> > > I end up getting this error. Is BioPython intended
> > >      
> > to be thread safe?
> >    
> >
> > > TraceBack:
> > > <snip>
> > >   from Bio.Blast import NCBIStandalone
> > > File
> > >      
> > "/usr/lib/python2.3/site-packages/Bio/__init__.py",
> > line 106, in ?
> >    
> >
> > >   _load_registries()
> > > File
> > >      
> > "/usr/lib/python2.3/site-packages/Bio/__init__.py",
> > line 98, in 
> >    
> >
> > > _load_registries
> > >   module = __import__("Bio.config.%s" % module,
> > >      
> > {}, {}, 
> >    
> >
> > > ["Bio","config"])
> > > File
> > >      
> "/usr/lib/python2.3/site-packages/Bio/config/FormatRegistry.py",
>  
>
> > > line 26, in ?
> > >   import _support
> > > File
> > >      
> "/usr/lib/python2.3/site-packages/Bio/config/_support.py",
>  
>
> > line 
> >    
> >
> > > 26, in ?
> > >   from Bio.MultiProc.copen import copen_fn
> > > File
> > >      
> "/usr/lib/python2.3/site-packages/Bio/MultiProc/copen.py",
>  
>
> > line 
> >    
> >
> > > 322, in ?    signal.signal(signal.SIGTERM,
> > >      
> > _handle_sigterm)
> >    
> >
> > > ValueError: signal only works in main thread
> > >
> > > -Brandon King
> > >
> > > _______________________________________________
> > > BioPython mailing list  -  BioPython@xxxxxxxxxxxxx
> > > http://biopython.org/mailman/listinfo/biopython
> > >
> > >
> > >      
> > _______________________________________________
> > BioPython mailing list  -  BioPython@xxxxxxxxxxxxx
> > http://biopython.org/mailman/listinfo/biopython
> >
> >    
>
>
> =====
> Mike Cariaso
>
>
>  

_______________________________________________
BioPython mailing list  -  BioPython@xxxxxxxxxxxxx
http://biopython.org/mailman/listinfo/biopython