[BioPython] Is BioPython thread safe?

[Brandon King]

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 at caltech.edu> 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 at biopython.org
>>>http://biopython.org/mailman/listinfo/biopython
>>>
>>>
>>>      
>>>
>>_______________________________________________
>>BioPython mailing list  -  BioPython at biopython.org
>>http://biopython.org/mailman/listinfo/biopython
>>
>>    
>>
>
>
>=====
>Mike Cariaso
>
>
>  
>