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

[Michael P. <mic...@ho...>]

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.
> > >
> > >
> > >
> > > _______________________________________________
> > > Genex-dev mailing list
> > > Gen...@li...
> > > http://lists.sourceforge.net/lists/listinfo/genex-dev
> > 
> > 
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