[GeneX-dev] Conf call summary

[<ja...@op...>]

Michael, Harry, and I had a call today about the status of the data
loader. 

Security
========
Michael had a good suggestion as to how to fix the three way circle of
fkeys between UserSec --> Contact --> Security --> UserSec ...  I'm
including the jpg of his ER diagram. The solution involves normalizing
the Contact table to remove the redundant information into a separate
table, Source (perhaps a better name??), which holds the security
info, and creating a view that unifies Source and Contact. That way no
circle of fkeys, no redundant user info in Contact (previously, a
users could have all their contact info repeated for each entry --
login, experiment_provider, sample_provider, etc.). Now they just have
multiple source entries, with one set of Contact info.

We decided not to go with using the Postgres user-level security for
now, as it would involve big changes to late in the game.

Thank you Michael, thank you OpenSource ...

Loader
======
Next, we identified the pieces which are critical for the entry of
ArrayLayouts:

* Assuming that the SequenceFeature information is not present already
  in the DB, the SF info will be taken from the layout file.
* the spot type for each layout spot (blank, sequence_feature, control)
* the species to which all the SF belong, or a listing of species on
  a per-SF basis.
* a unique identifier for each SF (and we need to add
  unique_identifier to the SF_Type controlled vocab).
* a unique identifier for each layout spot

Also, new (optional) additions for sample and quality tracking:

- The plate where the spotted stuff came from:
* plate identifier (a barcode)
* plate row
* plate column

- The order in which the spotting mechanism laid down the spots:
* source visit
* print sequence
* pin

Assignments
===========
Jason:
- list all the available information slots for
  layout/layout-spots. This involves a combination of SequenceFeature,
  ArrayLayout, Sample, and AL_Spots.
- load new tdscripts into genex2 DB
- re-write the scripts to load Contact and UserSec info 
- load test Contact, UserSec, GroupSec, GroupLink, and Security into
  genex2 DB
- load Species, Spotter, Scanner, and Software info into genex2 DB
- load CV into genex2 DB
- write first loader for simple yeast file

Michael:
- Modify embperl script to use new Security table to retrieve all
  ExperimentSet's visible by a given user
- get CVS working

Harry:
- Modify existing scripts to use genex2 DB


Harry and Michael, please fill in what I've forgotten.
jas.