backup_mysqldb needs to dump individual tables on grunt like on tang

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---------- Forwarded message ----------
From: Cron Daemon <root@bmrb.wisc.edu>
Date: Fri, Sep 25, 2009 at 12:00 AM
Subject: Cron <docr@grunt> 
/raid/docr/workspace/wattos/scripts/backup_mysqldb.csh
To: jurgenfd@gmail.com, schulte.chris@gmail.com

Doing backup_mysqldb.csh
dump dir: /raid/backup/mr_mysql_backup
total 32600
drwxr-xr-x 2 docr users     4096 Sep 24 17:00 .
drwxr-xr-x 5 docr users     4096 Sep 24 17:00 ..
-rw-r--r-- 1 docr users 33333523 Sep 24 17:00 dump_file.sql
Done

Original issue reported on code.google.com by jurge...@gmail.com on 25 Sep 2009 at 7:55

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I miss the resource:
http://restraintsgrid.bmrb.wisc.edu/servlet_data/viavia/mr_mysql_backup/
I'm using the one in:
mr_mysql_backupAn_2009-08-03/
but that's not updated and it shouldn't.

D. can you do a weekly crontab job run both mysqldump commands in:
/big/docr/workspace/wattos/scripts/backup_mysqldb.csh
on grunt so these get in?

We refer to it from:
http://restraintsgrid.bmrb.wisc.edu/NRG/wattos/MRGridServlet/html/howto.html#Lin
k_to_the_NMR_Restraint
s_Grid
and people like RCSB and OCA and others use it (personal comm.).

Original comment by jurge...@gmail.com on 20 Oct 2009 at 1:05

• Added labels: Priority-High, Maintainability, Component-NRG
• Removed labels: Priority-Medium

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Wim mentioned the same problem for him by email so I'm adding him to the list.
D. can you take action on this issue?

Original comment by jurge...@gmail.com on 28 Oct 2009 at 10:03

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It should be showing up. 

on grunt we have:
mysqldump --master-data --tab=$DUMP_DIR -..etc.
on tang:
mysqldump --master-data --tab=$DUMP_DIR - etc.

Original comment by schulte....@gmail.com on 28 Oct 2009 at 1:50

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There's nothing at:
http://restraintsgrid.bmrb.wisc.edu/servlet_data/viavia/mr_mysql_backup/

Original comment by jurge...@gmail.com on 28 Oct 2009 at 1:55

• Changed state: Started

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Yes, we have messages about restraints updates failing.

Original comment by schulte....@gmail.com on 28 Oct 2009 at 1:59

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Short answer is "won't fix". The backup, the way you're doing it, may contain
unreleased data. Therefore we are not putting it anywhere near the public 
website,
ever.

Original comment by dmitri.m...@gmail.com on 28 Oct 2009 at 3:13

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Would it be possible to get only access to the mrfile.txt with info of the 
entries
covered by the NRG then? Or a similar file somewhere?

It's essential I have access to something like that for the weekly update of 
the PDBe
pages.

Original comment by wfvran...@gmail.com on 28 Oct 2009 at 3:21

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The file is in /raid/backup/mr_mysql_backup on grunt. However, there's still 
the issue
of unreleased entries getting out -- on PDBe pages.

What I do is go through files on PDB FTP site and make a list of "public" PDB 
IDs. Then
I select rows for these IDs only into CSV table dumps that are mirrored to 
public
servers. CSV files are in /website/admin/wattos on pike, grunt, etc.

So I can set up a direct access to mrfile.txt for you, but you'll need to make 
sure you
delete the rows for unreleased entries before you update PDBe pages. Or I can 
set up
direct access to my mrfile.csv and you'll need to adjust your script: it's a 
CSV with
fields double-quoted instead of tab-delimited/unquoted .txt.

Let me know which way works for you.

Original comment by dmitri.m...@gmail.com on 28 Oct 2009 at 3:37

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On second thought, I took the easy way out and added mysqldump to web's crontab 
on
moray and swordfish. The files should be there Thu night.

Original comment by dmitri.m...@gmail.com on 28 Oct 2009 at 4:16

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A .csv file is fine, I'll just have to modify the parser slightly. So what is 
the web
location?

Original comment by wfvran...@gmail.com on 29 Oct 2009 at 1:31

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The file you look for is again at:

http://restraintsgrid.bmrb.wisc.edu/servlet_data/viavia/mr_mysql_backup/mrfile.t
xt

Thanks D.!

Original comment by jurge...@gmail.com on 30 Oct 2009 at 8:53

• Changed state: Verified