Re: [Gusdev-gusdev] New LoadNRDB & Consolidated GUS install package

[<pi...@pc...>]

I recently (within the last 3 weeks) loaded an entirely new version of nrdb and
it took less than 24 hours. This should have been equivalent to a first load. I
think that something else was wrong when you ran the plugin, possibly with the
database (e.g. indexes missing, a need to update statistics).

I agree that LoadNRDB needs an upgrade but I think its poor performance in this
case is due to some other problem.

                                                    -Debbie



Quoting Ed Robinson <ed_...@be...>:

> As many of you know, we have been doing quite a few GUS installs down here,
> and this has pushed me to try and simplify this process as much as possible.
> I am now far enough along on a couple things to bring them up on the list.
>
> First, installing NRDB the first time in GUS is a horribly painful process
> using the exisintg plugin and this pain seems to be needless since it is an
> empty database.  To this end, I have written a couple scripts and a batch
> process for Oracle SQLLoader which accomplishes in about an hour what takes a
> few weeks with the plugin.  However, to make this work, I have to reserve
> early rows in a number of SRES tables for meaningful entries in columns such
> as row_alg_invocation_id.  Hence, my first discussion item:  Should we
> consider reserving early values in a number of the SRes tables to serve as
> standard values.  We already require that some rows be entered in GUS early
> on to make some-things work such as LoadReviewType.  It would seem that we
> should Pre-populate some of these tables with basic values that we can then
> refer to as standard values for bootstrapping operations such as a bulk load
> of NRDB.  Does anyone else see any value in this and, if so, what fileds
> should we create standard entries for?  Also, is there anything else that
> would be amenable to a batch process for bootstrapping?  (Note: I do NOT
> think any organisim specific data is amenable to bootstrapping.  That is what
> a (object based) pipeline is for.  Also, this batch process is only good if
> you are using Oracle, but a similar process cab be written there too.)
>
> This also gets me to some of the other scripts we use to bootstrap GUS, such
> as the predefined set of ExternalDatabases we load.  The XML which I use to
> load this is pretty messy, and not well documented.  Does anyone mind if I
> clean it up?  If the answer is yes, is there anything I should know about
> this file?  it seems that the XML for this table load is a nice one to
> clean-up and make standard for GUS installations all over since it will push
> gus to be standardized across installations.  What else should we
> standardize?
>
> Which now brings me to the last item I want to open up which is that I am
> close to completing a full GUS installation wrapper script which essentially
> makes a GUS installation a click-and-play operation.   One of our
> deliverables is supposed to be an easy to install GUS package.  Regardless of
> the state of GUS with regards to an official release, this script is going to
> make my life a whole lot easier.  I figure it might be nice to package the
> whole kit-n-kaboodle up into one nice fat tarball with a simple set of
> instructions for download from someplace.  Is anyone else interested in this?
>
> Finally, one quick question I have about the NRDB load is that working on it
> showed me that the description filed in AASequenceIMP is too short for many
> of the descriptions in NRDB.  Do we want to up the description field size for
> dots.aasequenceimp?
>
> Anyway, any feedback on this would be appreciated.
>
> -Ed R
>
>
> Ed Robinson
> 255 Deerfield Rd
> Bogart, GA 30622
> (706)425-9181
>
> --Learn more about the face of your neighbor, and less about your own.
>          -Sargent Shriver
>
>
>
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