[MOBY-dev] where are all signature URLs?

[mark wilkinson]

Thanks for your forgiveness - I was quite embarrassed by it, actually!  The reason I didn't fix it right away was that it was the last operation I did that day, so to roll-back would have re-introduced all of the crap that I had just spent the morning removing.  I just kicked myself and decided that I would only script the replacement of the sigURL's if someone asked me to... I have night-terrors when I have to edit the main registry database by hand!!  Over the past three years it had picked up a lot of junk from various code bugs and such, so the cleaning needed to happen, but I messed it up... And I sincerely apologize for that!!!

Vv changing the timestamp:  that was an even bigger problem.  Last week eddie mentioned to me that, sor some reason that we still don't understand, many of the namespace terms ended up with an underscore appended to them ("EMBL_").  This happened before the LSID timestamp was added, and so our LSID's ended up with this underscore in them as well!  This caused a problem (that nobody seemed to notice??) That namespaces registered for a service were no longer valid namespaces (the lsid is used as the primary key, and it no longer matched with the namespace in the namespaces database tables).  The only solutiuon was to modify the lsid in the namespace table (remove the underscore) but keep the same timestamp, since that was the timestamp that the service was registered under.  Again, I apologize for any frustration that caused, but in this case I couldn't see a good alternative that didn't involve changing the registration of every service (and that terrifies me!)... I wish I knew where those underscores came from in the first place, though...??????

Anyway, that's the full history of the manual registry database edits from last week...

M

-----Original Message-----
From: Martin Senger <senger at ebi.ac.uk>
Date: Sat, 25 Feb 2006 03:43:32 
To:mark wilkinson <markw at illuminae.com>
Cc:Core developer announcements <moby-dev at biomoby.org>
Subject: Re: [MOBY-dev] where are all signature URLs?

It happens to all of us... :-)
   But it reminds me something else: if you do anytime a manual change in
the registry, please do not forget always to change also the timestamp
field (unless it's done automatically by the RDBS) - otherwise the
software relying on the new LSID versioning will not notice the change and
cannot update various caches properly.

Thanks,
Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

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--
Mark Wilkinson
...on the road!