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ChemComp handling will change #127

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
I am currently reorganising the way the chemComp archive is handled to make
it more transparent (also they'll all go into a repository).

I have not checked anything in yet, but when I will I'll have to update the
installations (the allChemComps/ directory will not work any more the way
it is). I will certainly do this on /big/wim, but if you're going to do a
full run I'd advise against updating any code (except specific bug fix
files) on /big/docr.

Note that there are no changes in the XML files themselves, just in the way
the archive is organised, so this will not affect the linking process once
the new chemComp archive is present.

Original issue reported on code.google.com by wfvran...@gmail.com on 3 Oct 2008 at 3:51

GoogleCodeExporter commented 9 years ago 
Are there any more details on this? Will they be in a new directory, or is this 
just within your code? Is there going 
to be a weekly rsynch with RCSB? Could we try to mirror what you are doing here 
at BMRB, but leave the 
allChemComps directory and production software alone? That way we will have a 
better idea about how to 
trouble-shoot problems and an easier time migrating to the new server.

Original comment by schulte....@gmail.com on 3 Oct 2008 at 4:21

GoogleCodeExporter commented 9 years ago 
The chemComps will be in a new directory, and more importantly organised 
differently
(so that they're not all in the same directory - no more 12000 files in a single
one). The whole reason I'm changing this is indeed so everyone can do automatic
weekly updates.

It's not completely worked out yet how that will happen, but will be clear next 
week.
Apologies if the initial mail was vague (it was intended as early warning) - as 
I
said I'll set it all up on /big/wim/, will then mail you details and we can go 
from
there.

Original comment by wfvran...@gmail.com on 3 Oct 2008 at 6:56

GoogleCodeExporter commented 9 years ago 
Thanks for the heads up. Keep us posted...

Original comment by jurge...@gmail.com on 4 Oct 2008 at 2:41

GoogleCodeExporter commented 9 years ago 
This currently fails as noted also in comment 24 on issue 132:

http://code.google.com/p/nmrrestrntsgrid/issues/detail?
id=132&colspec=Milestone%20Priority%20ID%20Opened%20Entry%20Component%20FC%20Typ
e%20Status%20
Owner%20Summary#c24

I guess we want to have the new setup in for the milestone?

Original comment by jurge...@gmail.com on 12 Jan 2009 at 9:12

GoogleCodeExporter commented 9 years ago 
The installation on /big/wim is using the new setup - forgot to update this 
issue
sorry. Anyway don't seem to be having any problems with it for the test case, 
but as
Jurgen noted there could still be small issues with the coordinate part. This 
should
only affect dihedral constraint writing for CYANA though.

Original comment by wfvran...@gmail.com on 12 Jan 2009 at 9:37

GoogleCodeExporter commented 9 years ago 
On development side I'm waiting for the cvs system to get updated. My jurgenfd 
account was made and it was 
added to the member list so I should be able to check it out shortly.

Original comment by jurge...@gmail.com on 12 Jan 2009 at 9:56

GoogleCodeExporter commented 9 years ago 
No luck yet after waiting 60 minutes. 
Chris P., can you get in? Wim suggested me to ask you about it. Did it take a 
while (>1 hour) before access was 
up?

Original comment by jurge...@gmail.com on 12 Jan 2009 at 10:38

GoogleCodeExporter commented 9 years ago 
Ok, I got the chemp comps now. And am starting to test with it.

Original comment by jurge...@gmail.com on 13 Jan 2009 at 10:59

GoogleCodeExporter commented 9 years ago 
For my reference how to include the right new setup.

Followed Wim's instructions at the bottom of:
http://sites.google.com/site/ccpnwiki/Home/ccpnTechnical/how-to-s/installing-all
-chemcomp-
information

Then from
recoord:/python/msd/adatah/localConstants.py
I removed the lines:
allChemCompDataPath = os.path.join(dataDir,'allChemComps')
print "Defined allChemCompDataPath:" + allChemCompDataPath

I don't find the new resource being used as far as I can tell but the FC links 
the ocean 12 entries fine. So I 
guess I'll close this issue as soon as it made it into production.

Original comment by jurge...@gmail.com on 14 Jan 2009 at 8:48

GoogleCodeExporter commented 9 years ago 
Wim, how can one tell if the new compounds were taken from the new archive or 
not?
I didn't spot anything like it in the linker log file.

I presume this is working now. I'm testing with the oceans 12 entries.

Original comment by jurge...@gmail.com on 14 Jan 2009 at 12:26

GoogleCodeExporter commented 9 years ago 
You can't - the files are the same, they're just organised differently. If 
you're
using the latest code from CCPN stable, and entries with uncommon ligands are
working, then it is using the new setup.

Original comment by wfvran...@gmail.com on 14 Jan 2009 at 1:52

GoogleCodeExporter commented 9 years ago 
Wim, is it ok to do:
mv /big/docr/ccpn_tmp/data/allChemComps/ 
/big/docr/ccpn_tmp/data/allChemCompsToBeRemoved

as I did?

The place I presume is now:
/data/ l $WS/ccpn/
lrwxrwxrwx  1 docr users   23 Jan 14 05:31 ccpn-chemcomp -> 
/big/docr/ccpn-chemcomp/

Original comment by jurge...@gmail.com on 10 Feb 2009 at 1:43

GoogleCodeExporter commented 9 years ago 
Yep should be fine!

Original comment by wfvran...@gmail.com on 10 Feb 2009 at 1:54