Re: [GeneX-dev] Re: Starting from a scratch

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

"Ron Ophir" <Ls...@wi...> writes:

> "Ron Ophir" <ls...@wi...> writes:
> 
> >> I'm trying to upload data from a scratch. I empty the entire genex
> >> database by TRUNCATE for all tables. Then I used the cml file of the
> >> control bundle you provided as a start (from the disk) and
> >> remove/add record in contact, softaware etc... lisCo ntactts. In the
> >> XML2DB step I got the following error ": SELECT con_pk from Contact
> >> where contact_person = 'genex' AND at ../../bin/xml2db.pl line
> >> 1650."  What do you think is the best way for starting from the
> >> scratch?  
> 
> >Ouch. Hey Ron.
> 
> No Ouch. I have a backup, however I do think that MEta data is
> something that should be editable.

Hey Ron,

If you look in the GeneX/scripts directory in the installer, you will
notice a number of (potentially) useful scripts. Look especially at
the *_insert.pl ones. They are for editing XML versions of the GeneX
metadata and inserting/updating your GeneX DB. Also notice CV_check.pl
for ensuring that you are properly setting controlled vocabulary
fields in your DB.

Some of these are better documented than others, I'll be happy to
answer questions.

Now, in terms of editing the metadata associated with an experiment,
that was to be the role of the curation tool. As far as I know,
however, todd and others, have not solved the issue of updates.

My goal was to develop WWW based tools that enable you to modify the
metadata for your own experiment. The MGED programming jamboree in
Sept will be working on this problem, and the tools we develop will be
very useful for GeneX. The issue right now is funding. If I receive
funding to continue this work it will get done soon.

> >There is a quick and simple way to start from scratch:
> 
> >* drop your DB using dropdb
> >* re-create your DB using createdb
> >* get the starting genex-init Pg dump which you may already, if not
> >  you can download it from the genex-server download at genex.ncgr.org
> >* load the dump into the DB (su to user postgres and run:
>    'gunzip --stdout path_to_dump_file.gz |psql genex_db_name'
> 
> >Or if you want, just run the init-dump.pl script (it lives in the
> >top-level directory of the GeneX-Server installation package) as user
> >postgres. It automates the whole process I listed above.

Were you able to recreate the DB?

> >> Would you care of organize a workshop on GeneX?  
> 
> >That's a wonderful idea. I'm hoping we can do just that at the
> >upcoming O'Reilly Open Source Bioinformatics conference (Jan 2002, in
> >Tucson Arizona). I'm including Jennifer Weller on this reply, she is a
> >co-organizer of the conference, as well as having been the GeneX
> >project leader while she was at NCGR, so I'm sure she'll look
> >favorably on your request.
> 
> >If Tucson is too far to travel from Israel, you can always invite me
> >to the Weizmann Institute for a visit. 
> 
> I'll try that, but the problem as always is money not the distance
> so I'm not promises anything. In any case, I would like very much to
> be informed about any workshop you give on GeneX.

If you would like to see a GeneX workshop, please email Jennifer and
request it from her (jew...@vt...). She can't do anything until
it's requested by someone else.

> You so well documented GeneX.pm and other tools. What about XML2DB
> and DB2XML?  

Well...

I didn't write xml2db. so all bets are off.

I did write db2xml, and there is documentation. Trying runing:
'pod2text db2xml.pl' or pod2man db2xml.pl on the command line from
within the GeneX/scripts directory in the installer directory.

Also, in the GeneX/html directory you should have db2xml.html which is
an html version of the same thing. This page should be installed in
your WWW server directory alongside all the other Genex.pm html pages.

And yes, the documentation should be better. Suggestions on what to
add would be appreciated.

jas.