From sakurabayashi26 at sanken.osaka-u.ac.jp Mon Apr 21 08:29:46 2025 From: sakurabayashi26 at sanken.osaka-u.ac.jp (sakurabayashi26 at sanken.osaka-u.ac.jp) Date: Mon, 21 Apr 2025 14:29:46 +0900 Subject: [Cod-bugs] Regarding the section "manage/release prepublications" Message-ID: <002401dbb27e$650e48e0$2f2adaa0$@sanken.osaka-u.ac.jp> Dear COD team, I am Shuhei Sakurabayashi in Osaka University, Japan. I previously deposited a CIF file to the Crystallography Open Database (COD ID: 3000497), and it is currently on hold for prepublication. Recently, the corresponding paper has been accepted for publication. I would now like to update the entry to include the "Journal of publication" information and make it publicly available. However, when I try to access the update page, I encounter an error (HTTP ERROR 500) and cannot proceed. I would greatly appreciate it if you could advise me on how to resolve this issue. Thank you very much for your support. Best regards, Shuhei Sakurabayashi -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Tue Apr 22 08:23:47 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Tue, 22 Apr 2025 08:23:47 +0300 Subject: [Cod-bugs] Regarding the section "manage/release prepublications" In-Reply-To: <002401dbb27e$650e48e0$2f2adaa0$@sanken.osaka-u.ac.jp> References: <002401dbb27e$650e48e0$2f2adaa0$@sanken.osaka-u.ac.jp> Message-ID: <85f596c4-45a2-4695-8ea2-ad6d4f390729@ibt.lt> Dear Sakurabayashi, I have checked the release management Web page, and it works for me at the moment. We have recently experienced an increased activity of bots that used to crash our server; it could be that you were also hit by this incident. At the moment our software is fixed and the COD web site seems to function as expected; may I ask you to try once more to release your structure? If this still does not work, please send us the URL you were using and a screen-shot with the error message/error page. Sincerely yours, Saulius On 2025-04-21 08:29, sakurabayashi26 at sanken.osaka-u.ac.jp wrote: > > Dear COD team, > > I am Shuhei Sakurabayashi in Osaka University, Japan. > > I previously deposited a CIF file to the Crystallography Open Database > (COD ID: 3000497), and it is currently on hold for prepublication. > > Recently, the corresponding paper has been accepted for publication. > > I would now like to update the entry to include the "Journal of > publication" information and make it publicly available. > > However, when I try to access the update page, I encounter an error > (HTTP ERROR 500) and cannot proceed. > > I would greatly appreciate it if you could advise me on how to resolve > this issue. > > Thank you very much for your support. > > Best regards, > > Shuhei Sakurabayashi > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sakurabayashi26 at sanken.osaka-u.ac.jp Tue Apr 22 08:43:18 2025 From: sakurabayashi26 at sanken.osaka-u.ac.jp (sakurabayashi26 at sanken.osaka-u.ac.jp) Date: Tue, 22 Apr 2025 14:43:18 +0900 Subject: [Cod-bugs] Regarding the section "manage/release prepublications" In-Reply-To: <85f596c4-45a2-4695-8ea2-ad6d4f390729@ibt.lt> References: <002401dbb27e$650e48e0$2f2adaa0$@sanken.osaka-u.ac.jp> <85f596c4-45a2-4695-8ea2-ad6d4f390729@ibt.lt> Message-ID: <0c7901dbb349$734667a0$59d336e0$@sanken.osaka-u.ac.jp> Dear Saulius, ? Thank you for your response. ? I tried accessing the release management page again, but it still does not work on my end. I have attached the URL I was using as well as a screenshot of the error page for your reference. ? COD: https://www.crystallography.net/cod/my_depositions.php?CODSESSION=e2gl6l2hv0o5dicj4bru8cr5s2 &filter=prepublications ? Update page: https://www.crystallography.net/cod/edit.php?CODSESSION=lt8pnionim0obv2c72bug566nv &id=3000497&type=cif ? Best regards, Sakurabayashi ? From: Saulius Gra?ulis Sent: Tuesday, April 22, 2025 2:24 PM To: sakurabayashi26 at sanken.osaka-u.ac.jp; cod-bugs at ibt.lt Subject: Re: [Cod-bugs] Regarding the section "manage/release prepublications" ? Dear Sakurabayashi, ? I have checked the release management Web page, and it works for me at the moment. We have recently experienced an increased activity of bots that used to crash our server; it could be that you were also hit by this incident. At the moment our software is fixed and the COD web site seems to function as expected; may I ask you to try once more to release your structure? ? If this still does not work, please send us the URL you were using and a screen-shot with the error message/error page. ? Sincerely yours, Saulius ? On 2025-04-21 08:29, sakurabayashi26 at sanken.osaka-u.ac.jp wrote: Dear COD team, ? I am Shuhei Sakurabayashi in Osaka University, Japan. ? I previously deposited a CIF file to the Crystallography Open Database (COD ID: 3000497), and it is currently on hold for prepublication. ? Recently, the corresponding paper has been accepted for publication. I would now like to update the entry to include the "Journal of publication" information and make it publicly available. However, when I try to access the update page, I encounter an error (HTTP ERROR 500) and cannot proceed. ? I would greatly appreciate it if you could advise me on how to resolve this issue. ? Thank you very much for your support. ? Best regards, Shuhei Sakurabayashi -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 87141 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 13502 bytes Desc: not available URL: From grazulis at ibt.lt Tue Apr 22 08:45:01 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Tue, 22 Apr 2025 08:45:01 +0300 Subject: [Cod-bugs] Regarding the section "manage/release prepublications" In-Reply-To: <0c7901dbb349$734667a0$59d336e0$@sanken.osaka-u.ac.jp> References: <002401dbb27e$650e48e0$2f2adaa0$@sanken.osaka-u.ac.jp> <85f596c4-45a2-4695-8ea2-ad6d4f390729@ibt.lt> <0c7901dbb349$734667a0$59d336e0$@sanken.osaka-u.ac.jp> Message-ID: <0e39ccb6-1ec0-4a8f-9b6b-e045ee7ebfd4@ibt.lt> Dear Sakurabayashi, thank you for your update! I see the problem. We'll investigate and come back to you shortly. Sincerely yours, Saulius On 2025-04-22 08:43, sakurabayashi26 at sanken.osaka-u.ac.jp wrote: > > Dear Saulius, > > Thank you for your response. > > I tried accessing the release management page again, but it still does > not work on my end. > > I have attached the URL I was using as well as a screenshot of the > error page for your reference. > > COD: > > https://www.crystallography.net/cod/my_depositions.php?CODSESSION=e2gl6l2hv0o5dicj4bru8cr5s2&filter=prepublications > > > Update page: > > https://www.crystallography.net/cod/edit.php?CODSESSION=lt8pnionim0obv2c72bug566nv&id=3000497&type=cif > > > Best regards, > > Sakurabayashi > > *From:*Saulius Gra?ulis > *Sent:* Tuesday, April 22, 2025 2:24 PM > *To:* sakurabayashi26 at sanken.osaka-u.ac.jp; cod-bugs at ibt.lt > *Subject:* Re: [Cod-bugs] Regarding the section "manage/release > prepublications" > > Dear Sakurabayashi, > > I have checked the release management Web page, and it works for me at > the moment. We have recently experienced an increased activity of bots > that used to crash our server; it could be that you were also hit by > this incident. At the moment our software is fixed and the COD web > site seems to function as expected; may I ask you to try once more to > release your structure? > > If this still does not work, please send us the URL you were using and > a screen-shot with the error message/error page. > > Sincerely yours, > Saulius > > On 2025-04-21 08:29, sakurabayashi26 at sanken.osaka-u.ac.jp wrote: > > Dear COD team, > > I am Shuhei Sakurabayashi in Osaka University, Japan. > > I previously deposited a CIF file to the Crystallography Open > Database (COD ID: 3000497), and it is currently on hold for > prepublication. > > Recently, the corresponding paper has been accepted for publication. > > I would now like to update the entry to include the "Journal of > publication" information and make it publicly available. > > However, when I try to access the update page, I encounter an > error (HTTP ERROR 500) and cannot proceed. > > I would greatly appreciate it if you could advise me on how to > resolve this issue. > > Thank you very much for your support. > > Best regards, > > Shuhei Sakurabayashi > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , > 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 > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. -- 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, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 87141 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.png Type: image/png Size: 13502 bytes Desc: not available URL: From grazulis at ibt.lt Wed Apr 23 09:10:02 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Wed, 23 Apr 2025 09:10:02 +0300 Subject: [Cod-bugs] Regarding the section "manage/release prepublications" In-Reply-To: <0c7901dbb349$734667a0$59d336e0$@sanken.osaka-u.ac.jp> References: <002401dbb27e$650e48e0$2f2adaa0$@sanken.osaka-u.ac.jp> <85f596c4-45a2-4695-8ea2-ad6d4f390729@ibt.lt> <0c7901dbb349$734667a0$59d336e0$@sanken.osaka-u.ac.jp> Message-ID: Dear Sakurabayashi, it seems that we have found the reason why your reposition release did not work. The file "3000497.cif" is relatively large, about 34M, and it overflows our server memory. The reason for such size is a larger than usual SHELX data set (which is great! and understandable given the electron diffraction experiment). If you do not mind, for a quick fix I will release the file manually (i.e. without using the Web site) and send you a COD link for confirmation that it looks as you intended. In future, we'll have to solve the problem with large files somehow. Are you OK with such plan? Sincerely yours, Saulius On 2025-04-22 08:43, sakurabayashi26 at sanken.osaka-u.ac.jp wrote: > > Dear Saulius, > > Thank you for your response. > > I tried accessing the release management page again, but it still does > not work on my end. > > I have attached the URL I was using as well as a screenshot of the > error page for your reference. > > COD: > > https://www.crystallography.net/cod/my_depositions.php?CODSESSION=e2gl6l2hv0o5dicj4bru8cr5s2&filter=prepublications > > > Update page: > > https://www.crystallography.net/cod/edit.php?CODSESSION=lt8pnionim0obv2c72bug566nv&id=3000497&type=cif > > > Best regards, > > Sakurabayashi > > *From:*Saulius Gra?ulis > *Sent:* Tuesday, April 22, 2025 2:24 PM > *To:* sakurabayashi26 at sanken.osaka-u.ac.jp; cod-bugs at ibt.lt > *Subject:* Re: [Cod-bugs] Regarding the section "manage/release > prepublications" > > Dear Sakurabayashi, > > I have checked the release management Web page, and it works for me at > the moment. We have recently experienced an increased activity of bots > that used to crash our server; it could be that you were also hit by > this incident. At the moment our software is fixed and the COD web > site seems to function as expected; may I ask you to try once more to > release your structure? > > If this still does not work, please send us the URL you were using and > a screen-shot with the error message/error page. > > Sincerely yours, > Saulius > > On 2025-04-21 08:29, sakurabayashi26 at sanken.osaka-u.ac.jp wrote: > > Dear COD team, > > I am Shuhei Sakurabayashi in Osaka University, Japan. > > I previously deposited a CIF file to the Crystallography Open > Database (COD ID: 3000497), and it is currently on hold for > prepublication. > > Recently, the corresponding paper has been accepted for publication. > > I would now like to update the entry to include the "Journal of > publication" information and make it publicly available. > > However, when I try to access the update page, I encounter an > error (HTTP ERROR 500) and cannot proceed. > > I would greatly appreciate it if you could advise me on how to > resolve this issue. > > Thank you very much for your support. > > Best regards, > > Shuhei Sakurabayashi > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , > 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 > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. -- 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, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... 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