Re: [GeneX-dev] Re: CanonicalSequenceFeature is missing...

[Jiaye Z. <ze...@in...>]

Hi Michael,

  Actually, I don't think this will break the xml2db code. It will just ignore 
the missing top level xml elements which are CannonicalSequenceFeature. In fact, 
I believe that I have tested the code against files that are missing CSF, but 
that would be a while ago and I haven't done any development on the CSF end. 
  I have known of the decision on not supporting CSF, but since the Curation 
Tool has been outputing CSF, I never removed the code that handled it. Perhaps 
this is a good time for me to clean that part of the code up.

Jiaye

Quoting Michael Pear <mic...@ho...>:

> I missed the Release Notes for the DB...I see them on sourceforge
> now.
> 
> I did a quick check by doing an rgrep on the install tree and there
> are still a lot of references to CanonicalSequenceFeature in xml2db.pl
> as well, so even if the curation tool can handle it, having nothing
> there
> may break submission using xml2db.pl
> 
> Regards,
> 
> Michael Pear
> 
> ----- Original Message -----
> From: "Jason E. Stewart" <ja...@op...>
> To: "Michael Pear" <mic...@ho...>
> Cc: "Jason E. Stewart" <ja...@op...>; "Jiaye Zhou"
> <ze...@in...>;
> <gen...@li...>
> Sent: Thursday, January 25, 2001 6:56 PM
> Subject: [GeneX-dev] Re: CanonicalSequenceFeature is missing...
> 
> 
> > "Michael Pear" <mic...@ho...> writes:
> >
> > > I tried to download a control bundle on my new installation, but
> > > db2xml.pl failed because it couldn't find
> > > CanonicalSequenceFeature.pm. I don't see it or anything in
> > > Genex/CanonicalSequenceFeature in the install tree. I no longer find
> > > this table in the database either. What's up?
> >
> > This was in the Release Notes for DB v0.8.1, but for some reason, I
> > didn't include it in the Server install notes:
> >
> > From the release notes:
> >
> > * All tables related to Canonical Sequence Features were removed
> >   (CanonicalSequenceFeature, CSF_ExternalDBLink, UserCanonicalLink,
> >   RelatedCSF)
> > * the two CSF related columns in UserSequenceFeature were removed
> >   (putative_csf_fk, nonunique_flag)
> >
> > And it looks like *I* didn't debug things enough :-(
> >
> > CSF was supposed to go away a month ago, it has always been an
> > unsupported feature, and since it was never really broken, it never
> > made it high enough on my priority to remove. I did it last release.
> >
> > Todd and/or Lonny. Will the CT break without CSF in the control
> > bundle? Should I just output a blank CSF section for now?
> >
> > Mea culpa, mea culpa,
> > jas.
> >
> >
> >
> > _______________________________________________
> > Genex-dev mailing list
> > Gen...@li...
> > http://lists.sourceforge.net/lists/listinfo/genex-dev
> 
> 
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