[Biopython-dev] Bio.File

[Michiel de Hoon]

OK, done.

Best,
--Michiel

--- On Wed, 10/19/11, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> From: Peter Cock <p.j.a.cock at googlemail.com>
> Subject: Re: [Biopython-dev] Bio.File
> To: "Michiel de Hoon" <mjldehoon at yahoo.com>
> Cc: biopython-dev at biopython.org
> Date: Wednesday, October 19, 2011, 4:49 AM
> On Wed, Oct 19, 2011 at 3:39 AM,
> Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
> > Hi Peter,
> >
> >> That leaves Bio/SCOP/__init__.py as the only
> existing or
> >> imminent code using Bio.File, so if we can sort
> that out,
> >> we can deprecate Bio.File as you suggested.
> >
> > In Bio/SCOP/__init__.py, Bio.File.UndoHandle is used
> in the _open
> > function, which is an internal function used in the
> "search" function
> > in Bio.SCOP. The UndoHandle is used to wrap a handle
> returned
> > by urllib.urlopen.
> 
> Should we change that to use urllib2 for better error
> handling,
> as in Bio.Entrez's _open?
> 
> > This search function returns a handle to data in HTML
> format.
> > I don't think we have a parser for it. This suggests
> that there is
> > no specific purpose for UndoHandle in Bio.SCOP._open.
> 
> I wonder if that is a sign of URL rot, it would make more
> sense
> to get plain text back. Sadly there were no unit tests for
> this at
> all until now, and I don't yet do anything with the handle
> other
> than confirm we get one!
> 
> https://github.com/biopython/biopython/commit/10b94a7b5611edde5fe05f95406d927e5a6a02d9
> 
> > So I would suggest to just remove the UndoHandle from
> > Bio.SCOP._open and return the urllib.urlopen handle
> directly.
> >
> > Any objections?
> 
> Sounds fine.
> 
> Peter
>