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

[Todd P. <tf...@nc...>]

Curation tool won't barf if the files aren't referenced in the GeneXML
external file list.

----- Original Message -----
From: "Michael Pear" <mic...@ho...>
To: "Jiaye Zhou" <ze...@in...>
Cc: <gen...@li...>
Sent: Friday, January 26, 2001 7:03 AM
Subject: Re: [GeneX-dev] Re: CanonicalSequenceFeature is missing...


> You might want to look at the code with the idea
> of ignoring any CSF section that comes in an XML file...
> If I resubmit one of my existing experiment sets from last
> week, if nothing is there to handle it, will it fail if you remove all
> mention of it? Will it fail if I use the current version? In the
long-term,
> you'll need to consider compatibility from release to release, so this
> might be a sample preparation of how to handle the situation.
>
> My guess is as the most downstream module, you should only be
> changing this after everyone else, with the only immediate action
> to ignore any tags associated with CSF as they no longer have meaning
> to the db. This probably includes a possible reference from USF.
>
> Regards,
>
> Michael Pear
>
> ----- Original Message -----
> From: "Jiaye Zhou" <ze...@in...>
> To: <gen...@li...>; "Michael Pear"
<mic...@ho...>
> Sent: Thursday, January 25, 2001 8:01 PM
> Subject: Re: [GeneX-dev] Re: CanonicalSequenceFeature is missing...
>
>
> >
> > 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.
> > > >
> > > >
> > > >
> > > > _______________________________________________
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> > > > Gen...@li...
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> > >
> > >
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> > >
>
>
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