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

[Ed R. <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
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