From grazulis at ibt.lt  Fri Jul 22 11:48:42 2022
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=)
Date: Fri, 22 Jul 2022 11:48:42 +0300
Subject: [Cod-bugs] COD updates
In-Reply-To: <LOYP265MB2318C5E6EF81F73BA765AC13BE909@LOYP265MB2318.GBRP265.PROD.OUTLOOK.COM>
References: <32fb1a84bffe4ae08896e31c0c6dc67b@stfc.ac.uk>
 <a9e9a840-280c-9262-16a6-c836af86dbd5@ibt.lt>
 <LO0P265MB2604BAB72490633A8CDF44E6BE159@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
 <LO0P265MB2604D2A7B2B1BECC82B46773BEE19@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
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 <LO0P265MB26041AFF7E932CB670C0DF6ABE859@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
 <LO0P265MB2604A0BA4914F3AE3D563107BE869@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
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Message-ID: <b7b501f2-09a3-957a-12a3-28e131da5d96@ibt.lt>

On 2022-07-22 11:22, Robert McMeeking - STFC UKRI wrote:
> I have just noticed that there currently appear to be COD update problems similar to as in the past (see below).
>
> As I recall this may have been related to making inadvertent changes to protection to files/directories after you performed a system upgrade.

Thanks for the e-mail ? yo are write, we have a technical problem, I'm
already investigating it and it seems that we have run out of disk space
on the scraper machine...

It that is the only reason then I'll start the reposition soon and we'll
catch up.

Sincerely,
Saulius

-- 
Dr. Saulius Gra?ulis
Vilnius University, Life Science Center, Institute of Biotechnology
Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)
phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366


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From robert.mcmeeking at stfc.ac.uk  Fri Jul 22 11:22:30 2022
From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI)
Date: Fri, 22 Jul 2022 08:22:30 +0000
Subject: [Cod-bugs] COD updates
References: <32fb1a84bffe4ae08896e31c0c6dc67b@stfc.ac.uk>
 <a9e9a840-280c-9262-16a6-c836af86dbd5@ibt.lt>
 <LO0P265MB2604BAB72490633A8CDF44E6BE159@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
 <LO0P265MB2604D2A7B2B1BECC82B46773BEE19@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
 <25011402-3ea5-ddbe-0557-dca9023d56ae@ibt.lt>
 <LO0P265MB26041AFF7E932CB670C0DF6ABE859@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
 <LO0P265MB2604A0BA4914F3AE3D563107BE869@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <LOYP265MB2318C5E6EF81F73BA765AC13BE909@LOYP265MB2318.GBRP265.PROD.OUTLOOK.COM>

Dear Saulius

I have just noticed that there currently appear to be COD update problems similar to as in the past (see below).

As I recall this may have been related to making inadvertent changes to protection to files/directories after you performed a system upgrade.

Best Regards

Bob



-----Original Message-----
From: McMeeking, Robert (STFC,DL,SC) 
Sent: 28 October 2021 10:28
To: 'cod-bugs at ibt.lt' <cod-bugs at ibt.lt>
Cc: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Subject: FW: COD updates

Apologies

I got the incorrect email address!

-----Original Message-----
From: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Sent: 28 October 2021 10:25
To: Saulius Gra?ulis <grazulis at ibt.lt>; cod-bug at ibt.lt
Cc: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Subject: RE: COD updates

Good Morning

I have just noticed that no new COD entries have appeared on the COD site since the 25th October. Is there a problem with the COD update pipeline?

Best Regards

Bob

-----Original Message-----
From: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Sent: 27 October 2021 10:49
To: Saulius Gra?ulis <grazulis at ibt.lt>
Cc: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Subject: RE: COD updates

Good Morning, Saulius

I hope you are well.

We continue to use the COD within our CrystalWorks system, and the SVN downloads appear to be working fine.

However, I have noticed that in the last day or so there appear to have been less entries from the journals you normally harvest for structures. Do you know of any current problems? I see structures, but suspect that these may have been entered manually by contributors.

Actually I have had some interactions with a recent contributor, and I have a related question. What is the recommended procedure to amend/update an already contributed CIF? The CIF in question has been created manually. It, however, lacks some details such as temperature, pressure, radiation used, etc. It would be very useful to get these into the database without creating a new entry.

Best Regards

Bob

===================================================

R.F. McMeeking
STFC Daresbury Laboratory

-----Original Message-----
From: Saulius Gra?ulis <grazulis at ibt.lt>
Sent: 03 August 2021 16:12
To: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Subject: Re: COD updates

On 2021-07-19 17:37, Robert McMeeking - STFC UKRI wrote:
> I am now back from holiday with greater access to our CrystalWorks server.
>
> It looks like there may have been problems with the SVN transfer which cause a disk quota knock on effect. I have been able to perform an 'svn cleanup". This freed up a lot of disk space. The SVN update now runs fine.  So it does look like the main problems has been at our end. I need to keep a closer eye on available disk space!
>
Hi, Bob,

thank you for your messages. I'm glad that you have found the solution to the problem.

I have checked our side quickly and it seems that the SQL dumps get updated:

> saulius at tasmanijos-velnias cod/ $ svn log 
> svn://www.crystallography.net/cod/mysql -l 1 -v
> ----------------------------------------------------------------------
> --
> r267895 | coder | 2021-08-03 00:40:54 +0300 (Tue, 03 Aug 2021) | 1 
> line Changed paths:
> ?? M /mysql/data.txt
> ?? M /mysql/numbers.txt
>
> Adding automatic MySQL table dump for the database `cod`.

Actually, as indicated in this example, you can always run 'svn log' on the repository directly, without using you working copy. That should give you full log messages and the latest revision numbers also in the case when the local working copy is outdated or has problems (e.g. when there is not enough of disk space, or when some SVN files are corrupt).

Sincerely yours,
Saulius

--
Dr. Saulius Gra?ulis
Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366



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From robert.mcmeeking at stfc.ac.uk  Fri Jul 22 11:53:32 2022
From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI)
Date: Fri, 22 Jul 2022 08:53:32 +0000
Subject: [Cod-bugs] COD updates
In-Reply-To: <b7b501f2-09a3-957a-12a3-28e131da5d96@ibt.lt>
References: <32fb1a84bffe4ae08896e31c0c6dc67b@stfc.ac.uk>
 <a9e9a840-280c-9262-16a6-c836af86dbd5@ibt.lt>
 <LO0P265MB2604BAB72490633A8CDF44E6BE159@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
 <LO0P265MB2604D2A7B2B1BECC82B46773BEE19@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
 <25011402-3ea5-ddbe-0557-dca9023d56ae@ibt.lt>
 <LO0P265MB26041AFF7E932CB670C0DF6ABE859@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
 <LO0P265MB2604A0BA4914F3AE3D563107BE869@LO0P265MB2604.GBRP265.PROD.OUTLOOK.COM>
 <LOYP265MB2318C5E6EF81F73BA765AC13BE909@LOYP265MB2318.GBRP265.PROD.OUTLOOK.COM>
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Message-ID: <LOYP265MB231840476645EE92A6D120D8BE909@LOYP265MB2318.GBRP265.PROD.OUTLOOK.COM>

Thanks,  Saulius

Hopefully the fix will be quite straightforward.

Best Regards

Bob

-----Original Message-----
From: Saulius Gra?ulis <grazulis at ibt.lt> 
Sent: 22 July 2022 09:49
To: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Cc: cod-bugs at ibt.lt
Subject: Re: COD updates

On 2022-07-22 11:22, Robert McMeeking - STFC UKRI wrote:
> I have just noticed that there currently appear to be COD update problems similar to as in the past (see below).
>
> As I recall this may have been related to making inadvertent changes to protection to files/directories after you performed a system upgrade.

Thanks for the e-mail ? yo are write, we have a technical problem, I'm already investigating it and it seems that we have run out of disk space on the scraper machine...

It that is the only reason then I'll start the reposition soon and we'll catch up.

Sincerely,
Saulius

--
Dr. Saulius Gra?ulis
Vilnius University, Life Science Center, Institute of Biotechnology Saul?tekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania) phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.


This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses.

-- 
This message has been scanned for viruses and
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