From grazulis at ibt.lt  Mon Dec 15 09:28:27 2025
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=)
Date: Mon, 15 Dec 2025 09:28:27 +0200
Subject: [Cod-bugs] COD server down
In-Reply-To: <LO0P265MB3323E7E4658C79831E9186B4BEACA@LO0P265MB3323.GBRP265.PROD.OUTLOOK.COM>
References: <LO0P265MB3323E7E4658C79831E9186B4BEACA@LO0P265MB3323.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <b83502bc-fa87-483f-9a87-c6dced9d4617@ibt.lt>

Hi, Robert,

thank you for the inquiry!

On 2025-12-14 17:05, Robert McMeeking - STFC UKRI wrote:
>
> I notice that the COD homepage has not been available for a few days. 
> Are you experiencing a lot of problems with the ?bots? at the moments? 
> Or are there other issues. Do you have an estimate when the server 
> will be back.
>
Yes, you are right, we suffered a? very serious overload from external 
bots and lost our main disk with the server and the main repository. I'm 
an now restoring from backups, and the plan is to restart our "warm 
standby" ASAP, hopefully in a couple of days.

On that occasion, since you have diligently collected COD cifs in real 
time ? can you share you recent downloads with us? Admittedly, our 
repository backups are on month old, and a working copy in Granada 
mirror, thanks to Miguel, has a backup of 1 day old working copy, but it 
would be great to cross-check all sources including your's so that we do 
not miss any entries.

Can we access you COD CIF collection over rsync or http(s) (REST) protocols?

Regards,
Saulius

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

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From robert.mcmeeking at stfc.ac.uk  Mon Dec 15 15:45:08 2025
From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI)
Date: Mon, 15 Dec 2025 13:45:08 +0000
Subject: [Cod-bugs] COD synch
In-Reply-To: <LO0P265MB3323CB8237915C0AA97523FBBEADA@LO0P265MB3323.GBRP265.PROD.OUTLOOK.COM>
References: <LO0P265MB3323CB8237915C0AA97523FBBEADA@LO0P265MB3323.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <LO0P265MB33238413BC7E9D2184A5A14BBEADA@LO0P265MB3323.GBRP265.PROD.OUTLOOK.COM>

Hello again, Saulius

The synchronisation cron job continues to run on our server. This does not appear to cause problems whilst yourserver is out of action.

I suspect I really should be switched off until your side is fully fixed. I see potential problems if your server is restored when there is the possibility that all the data sets are not fully restored.   Do you agree?

Best Regards

Bob

From: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Sent: 15 December 2025 09:36
To: Saulius Gra?ulis <grazulis at ibt.lt>
Subject: COD synch

Hello Saulius

Sorry to hear about your server problems. I will try to give as much help as I can. I currently have limited control over our server. But assume we can sort out a mechanism to synchronise the files in question. I will talk to the powers that be here.

The latest synchronisation performed by our server was at ~4:00 GMT 12th December.

Also I notice there are current problems with the Spanish mirror. It looks like a security certificate may need updating.

Best Regards

Bob

Sent from Outlook for Android<https://aka.ms/AAb9ysg>

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From ohnishi.yusuke.corefc at osaka-u.ac.jp  Tue Dec 16 02:49:27 2025
From: ohnishi.yusuke.corefc at osaka-u.ac.jp (ohnishi.yusuke.corefc at osaka-u.ac.jp)
Date: Tue, 16 Dec 2025 00:49:27 +0000
Subject: [Cod-bugs] We cannot connect to COD
Message-ID: <TYRP286MB61596F175BB08636BDA04567A5AAA@TYRP286MB6159.JPNP286.PROD.OUTLOOK.COM>

Dear COD support,

I am Yusuke Ohnishi at the University of Osaka, Japan.

I haven't been able to connect to the COD website since last Friday.
Is there some kind of trouble going on?

I have a file I would like to deposit to COD.
If it takes a while to resolve, I'd like to deposit it via email if possible.

I apologize for the trouble, but I appreciate your help.

Best regards,
Ohnishi



????? (Ohnishi Yusuke)

The University of Osaka
Core Facility Center
Specially Appointed Assistant Professor
I-405, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
Tel: 06-6879-4815
Email: ohnishi.yusuke.corefc at osaka-u.ac.jp<mailto:ohnishi.yusuke.corefc at osaka-u.ac.jp>



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From grazulis at ibt.lt  Tue Dec 16 09:23:05 2025
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=)
Date: Tue, 16 Dec 2025 09:23:05 +0200
Subject: [Cod-bugs] We cannot connect to COD
In-Reply-To: <TYRP286MB61596F175BB08636BDA04567A5AAA@TYRP286MB6159.JPNP286.PROD.OUTLOOK.COM>
References: <TYRP286MB61596F175BB08636BDA04567A5AAA@TYRP286MB6159.JPNP286.PROD.OUTLOOK.COM>
Message-ID: <fff56102-9b64-444f-89a4-0a6439b852a0@ibt.lt>

Dear Ohnishi,

thank you for your e-mail. You are right, we experienced a server 
overload and a subsequent disk crash related to a large number of 
simultaneous bot requests. We are now busy restoring the COD server and 
loading data from backups, which, unfortunately, might take a couple of 
days.

If the deposition is urgent please sent you files to us via e-mail and I 
will handle them manually.

I apologise for this inconvenience.

Sincerely yours,
Saulius


On 2025-12-16 02:49, ohnishi.yusuke.corefc at osaka-u.ac.jp wrote:
> Dear?COD?support,
>
> I am Yusuke Ohnishi at the University of Osaka, Japan.
>
> I haven't been able to connect to the COD website since last Friday.
> Is there some kind of trouble going on?
>
> I have a file I would like to deposit to COD.
> If it takes a while to resolve, I'd like to deposit it via email if 
> possible.
>
> I apologize for the trouble, but I appreciate your help.
>
> Best regards,
> Ohnishi
>
>
> ??????(Ohnishi Yusuke)
>
> The University of Osaka
> Core Facility Center
> Specially Appointed Assistant Professor
> I-405, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
> Tel: 06-6879-4815
> Email: ohnishi.yusuke.corefc at osaka-u.ac.jp 
> <mailto:ohnishi.yusuke.corefc at osaka-u.ac.jp>
>
>
>
> -- 
> This message has been scanned for viruses and
> dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is
> believed to be clean.
>
> _______________________________________________
> Cod-bugs mailing list
> Cod-bugs at lists.crystallography.net
> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs


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

-- 
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From ohnishi.yusuke.corefc at osaka-u.ac.jp  Wed Dec 17 02:40:19 2025
From: ohnishi.yusuke.corefc at osaka-u.ac.jp (ohnishi.yusuke.corefc at osaka-u.ac.jp)
Date: Wed, 17 Dec 2025 00:40:19 +0000
Subject: [Cod-bugs] We cannot connect to COD
In-Reply-To: <fff56102-9b64-444f-89a4-0a6439b852a0@ibt.lt>
References: <TYRP286MB61596F175BB08636BDA04567A5AAA@TYRP286MB6159.JPNP286.PROD.OUTLOOK.COM>
 <fff56102-9b64-444f-89a4-0a6439b852a0@ibt.lt>
Message-ID: <TYRP286MB6159DBA92327319B96B35168A5ABA@TYRP286MB6159.JPNP286.PROD.OUTLOOK.COM>

Dear Dr. Saulius

thank you for your reply.
I apologize for taking up your time while you're busy with the recovery.
I will upload the data after the recovery is complete.

Best regards,
Ohnishi


????? (Ohnishi Yusuke)

The University of Osaka
Core Facility Center
Specially Appointed Assistant Professor
I-405, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
Tel: 06-6879-4815
Email: ohnishi.yusuke.corefc at osaka-u.ac.jp<mailto:ohnishi.yusuke.corefc at osaka-u.ac.jp>

________________________________
???: Saulius Gra?ulis <grazulis at ibt.lt>
????: 2025?12?16? 16:23
??: ????? <ohnishi.yusuke.corefc at osaka-u.ac.jp>; cod-bugs at lists.crystallography.net <cod-bugs at lists.crystallography.net>
??: Re: [Cod-bugs] We cannot connect to COD

Dear Ohnishi,

thank you for your e-mail. You are right, we experienced a server overload and a subsequent disk crash related to a large number of simultaneous bot requests. We are now busy restoring the COD server and loading data from backups, which, unfortunately, might take a couple of days.

If the deposition is urgent please sent you files to us via e-mail and I will handle them manually.

I apologise for this inconvenience.

Sincerely yours,
Saulius


On 2025-12-16 02:49, ohnishi.yusuke.corefc at osaka-u.ac.jp<mailto:ohnishi.yusuke.corefc at osaka-u.ac.jp> wrote:
Dear COD support,

I am Yusuke Ohnishi at the University of Osaka, Japan.

I haven't been able to connect to the COD website since last Friday.
Is there some kind of trouble going on?

I have a file I would like to deposit to COD.
If it takes a while to resolve, I'd like to deposit it via email if possible.

I apologize for the trouble, but I appreciate your help.

Best regards,
Ohnishi



????? (Ohnishi Yusuke)

The University of Osaka
Core Facility Center
Specially Appointed Assistant Professor
I-405, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
Tel: 06-6879-4815
Email: ohnishi.yusuke.corefc at osaka-u.ac.jp<mailto:ohnishi.yusuke.corefc at osaka-u.ac.jp>



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_______________________________________________
Cod-bugs mailing list
Cod-bugs at lists.crystallography.net<mailto:Cod-bugs at lists.crystallography.net>
http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs



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


--
This message has been scanned for viruses and
dangerous content by MailScanner<http://www.mailscanner.info/>, and is
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