[Bioperl-l] bioperl-db bugs

[Elia Stupka]

> All of these changes have no effect on the Sequence database (Seqdb)
> modules - we just decided to cram everything related to a relationaldb in
> one cvs module.  There is a stable tagged version of the working markerdb
> but I don't know that it would be useful to anyone esp if we plan to
> migrate to the new schema that is in the repository.  So options are to
> continue to leave the HEAD broken and comment out the tests or try and
> micro-fix things that are probably going to change soon.

Glad to hear from you, was getting a bit too stuck in the code.... Even if
in flux I guess we should not break our rule that tests should pass,
right? I went for the same conclusion as you, I am fixing really obvious
things, and skipping other tests. Will commit soon, because there is other
tets that are failing.

Elia

> 
> -jason
> 
> On Fri, 19 Oct 2001, Elia Stupka wrote:
> 
> > Hello there,
> >
> > I am trying to fix the bugs that Alex reported.
> > There is quite a few:
> >
> > 1)There is a strange one, Jason tell me if you seewhat you were trying to
> > do here:
> >
> > In Bio/DB/Map/SQL/MarkerAdaptor.pm you write:
> >
> > my (undef,$chrom) = ( $marker->chrom =~ /(chr)?(X|Y|UL|\d+)/ );
> >
> > which perl doesn't like. I changed it to:
> >
> > my ($go,$chrom) = ( $marker->chrom =~ /(chr)?(X|Y|UL|\d+)/ );
> >
> > 2)Also, the marker-db.sql file had lots of commas on the last lines of the
> > create statements, which made mysql die, I have fixed that.
> >
> > 3)The sql statements in the Adaptor were failing because statements were
> > made on columns named mapid rather than map_id, name rather than map_name
> > as in the sql file
> >
> > 4)The marker schema seems to have changed radically , but not the
> > MarkerAdaptor.
> >
> > I am making fixes as we speak, but Jason maybe there is stuff you have not
> > committed?
> >
> > Elia
> >
> >
> >
> > ******************************
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> 
> -- 
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
> 
> 

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