[Biopython-dev] Faling tests

Thu Feb 17 23:36:04 EST 2005

test_Registry is "only" failing on PDB and Swissprot.

So far: we have a crippled NCBIWWW (blastn and blastp only for qblast) and
an 85% working retrieval. Not fantastic, but workable. 

Should we go ahead with the release? Any other things hitting the fan I
should know of? :)

./I

--
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://ffas.ljcrf.edu/~iddo
-------------------------------------
Automated Protein Function Prediction Meeting, June 24, 2005
http://ffas.burnham.org/AFP

On Fri, 18 Feb 2005, James Casbon wrote:

> Iddo Friedberg wrote:
> > 
> > test_Register is still failing.
> 
> Seems ebi have changed their interface or something:.  Compare:
> 
>  >>> db['pdb'].objs[0].cgi
> 'http://www.rcsb.org/pdb/cgi/export.cgi'
>  >>> h = db['pdb'].objs[0]['1BG2']
> 
> to:
> 
>  >>> db['pdb'].objs[1].url
> 'http://www.ebi.ac.uk/cgi-bin/emblfetch'
>  >>> h = db['pdb'].objs[1]['1BG2']
> ...
> KeyError: 'results do not look like PDB format'
> 
> Easiest bug fix is to remove the ebi source, but maybe someone knows how 
> to get the db object to spit out what it is receving so we can get an 
> idea of what is going wrong?
> 
> 
> Swissprot fails as well, two failiures: www.expash.ch produces a 403, 
> us.expasy.org seems to result in some more serious stuff (see below).
> 
> 
> Hope this helps,
> James
> 
>  >>> print db["swissprot"].objs[0].cgi
> http://www.expasy.ch/cgi-bin/get-sprot-raw.pl
>  >>> print db["swissprot"].objs[0][ "MTHC_DROME" ].read(100)
> <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
> <HTML><HEAD>
> <TITLE>403 Forbidden</TITLE>
> </HEAD>
>  >>> print db["swissprot"].objs[1].cgi
> http://us.expasy.org/cgi-bin/get-sprot-raw.pl
>  >>> print db["swissprot"].objs[1][ "MTHC_DROME" ].read(100)
> Traceback (most recent call last):
>    File "<stdin>", line 1, in ?
>    File "/home/james/biopython/Bio/config/DBRegistry.py", line 89, in 
> __getitem__    return self._get(key)
>    File "/home/james/biopython/Bio/config/_support.py", line 138, in 
> __call__
>      if handle.poll():
>    File "/home/james/biopython/Bio/MultiProc/copen.py", line 217, in poll
>      self._cleanup_child()
>    File "/home/james/biopython/Bio/MultiProc/copen.py", line 238, in 
> _cleanup_child
>      raise AssertionError, "Error in child process:\n\n%s" % error
> AssertionError: Error in child process:
> 
> Traceback (most recent call last):
>    File "/home/james/biopython/Bio/MultiProc/copen.py", line 70, in copen_fn
>      output = func(*args, **keywords)
>    File "/home/james/biopython/Bio/config/_support.py", line 131, in 
> _call_fn
>      retval = self.fn(*args, **keywds)
>    File "/home/james/biopython/Bio/config/_support.py", line 107, in 
> __call__
>      return self.fn(*args, **keywds)
>    File "/home/james/biopython/Bio/config/DBRegistry.py", line 310, in _get
>      handle = self._check_for_errors(handle, self.failure_cases)
>    File "/home/james/biopython/Bio/config/DBRegistry.py", line 246, in 
> _check_for_errors
>      raise KeyError, errormsg
> KeyError: 'no results'
> 