From antanas.vaitkus90 at gmail.com  Mon Jan 27 14:08:52 2025
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Mon, 27 Jan 2025 14:08:52 +0200
Subject: [Cod-bugs] COD to sqlite3 error
In-Reply-To: <7f49e4e8-c86c-4918-909b-126705d5d65a@profex-xrd.org>
References: <f9f73af3-3ba8-4821-9b1a-843c38b01127@profex-xrd.org>
 <CALHYoX4B1CdTjTiu18ZHL0MDg-xowWAKAUHq7BEghyKzWZUMPA@mail.gmail.com>
 <7f49e4e8-c86c-4918-909b-126705d5d65a@profex-xrd.org>
Message-ID: <CALHYoX4g0CaKz3VgWh2qVD0LTxe9QSmis=Za+636T5bChN4=YQ@mail.gmail.com>

Dear Nicola,

I am glad to hear it worked. I have updated our documentation accordingly.

Sincerely
Antanas

On Mon, 27 Jan 2025 at 10:01, Nicola D?belin <support at profex-xrd.org> wrote:

> Dear Antanas,
>
> The modified script works perfectly. Thanks a lot for your help!
>
> Best regards,
> Nicola
>
>
> On 1/24/25 21:23, Antanas Vaitkus wrote:
>
> Dear Nicola,
>
> The issue seems to arise due to inline comments output by MariaDB,
> (e.g. "`time` time /* mariadb-5.3 */ DEFAULT NULL,") since sqlt MySQL
> parser does not know how to handle them.
>
> I have updated the script you sent to circumvent the issue. Please give
> it a try and let us know if this fully solves your issue. The script does
> work correctly on my machine.
>
> If this solution works for you, I will update the documentation
> accordingly.
>
> Sincerely,
> Antanas
>
> On Fri, 24 Jan 2025 at 15:22, Nicola D?belin <support at profex-xrd.org>
> wrote:
>
>> Hello,
>>
>> I am the programmer of the Rietveld refinement software Profex. In the
>> past few years, I used to convert the COD to sqlite3 to bundle it with
>> Profex. For the conversion I used the attached bash script, which I
>> created based on the information given on the COD wiki:
>>
>> https://wiki.crystallography.net/creatingSQLdatabase/
>>
>> However, this year the script no longer works and generates the
>> following error message:
>>
>> #-- begin output --
>>
>> updating svn
>> Updating '.':
>> At revision 297460.
>> converting mysql to sqlite
>>
>>        ERROR (line 13): Invalid statement: Was expecting comment, or use,
>> or
>>                         set, or drop, or create, or alter, or insert, or
>>                         delimiter, or empty statement
>> Error: translate: Error with parser 'SQL::Translator::Parser::MySQL':
>> no results at /usr/bin/sqlt line 353.
>> replacing escape sequences
>> importing data
>> CREATE TABLE data(...) failed: duplicate column name: 90
>> creating cod-250124.db
>> compressing
>>    adding: cod-250124.db3 (stored 0%)
>>
>> #-- end output --
>>
>> The resulting *.db3 file is empty. I always update the sqlite3 COD
>> version in January, so the break must have occurred some time between
>> Jan 2024 and Jan 2025. I also tried to run the script on an older Ubuntu
>> 20.04 system on which it used to work in the past, but to no avail.
>> Since I am not familiar with MySQL and have very limited experience with
>> sqlite, I would like to ask for help to create an updated sqlite version
>> of the COD that I can bundle with Profex.
>>
>> Any help will be appreciated.
>> Kind regards,
>> Nicola
>>
>> --
>> Nicola D?belin
>> Web: https://www.profex-xrd.org
>> E-Mail: support at profex-xrd.org
>>
>> --
>> 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
>>
>
>
> --
> Antanas Vaitkus,
> Vilnius University,
> Life Sciences Center,
> Institute of Biotechnology,
> room C521, Saul?tekio al. 7,
> LT-10257 Vilnius, Lithuania
>
>
>
>

-- 
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania

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From robert.mcmeeking at stfc.ac.uk  Tue Jan 28 12:29:12 2025
From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI)
Date: Tue, 28 Jan 2025 10:29:12 +0000
Subject: [Cod-bugs] Silicon Disulfide
Message-ID: <CWLP265MB0065B3DB59C2B2A2822C26AFBEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>

Good Morning,

There looks to be a problem with COD entry 9016170. The compound name, as in the article title, is "Siliciumdisulfid". But the formula is given as SiS4. There is also the COD entry 1010272 from the same paper assigned the formula SiS2.

Perhaps only the second one should be retained?

Best Regards

Bob

Dr R.F.McMeeking
STFC Daresbury Laboratory

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From antanas.vaitkus90 at gmail.com  Tue Jan 28 12:40:32 2025
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Tue, 28 Jan 2025 12:40:32 +0200
Subject: [Cod-bugs] Silicon Disulfide
In-Reply-To: <CWLP265MB0065B3DB59C2B2A2822C26AFBEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>
References: <CWLP265MB0065B3DB59C2B2A2822C26AFBEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <CALHYoX7ZJrD3zn9tWNVK2ZB1emSm_qQQYboX1XrSzHatJu-LNQ@mail.gmail.com>

Dear Robert,

On Tue, 28 Jan 2025 at 12:29, Robert McMeeking - STFC UKRI <
robert.mcmeeking at stfc.ac.uk> wrote:

> Good Morning,
>
>
>
> There looks to be a problem with COD entry 9016170. The compound name, as
> in the article title, is ?Siliciumdisulfid?. But the formula is given as
> SiS4. There is also the COD entry 1010272 from the same paper assigned the
> formula SiS2.
>

These two entries describe the same structure, but the space group
information
in entry 9016170 is most likely incorrect (for more information, see
https://projects.ibt.lt/repositories/issues/1603). The entry in question
originated
in the AMCSD database and was later synced to the COD so we are waiting
for their comments before modifying the entry.


> Perhaps only the second one should be retained?
>

While these entries are duplicates in the purest sense (same compound, same
structure,
same publication), the general policy of the COD is to not remove entries
once a COD ID
has been assigned (they might have been referenced in publications, etc.).
Instead of that,
we mark duplicate structures using the '_cod_duplicate_entry' data name.
For example, in
this case entry 9016170 contains a line "_cod_duplicate_entry
1010272" which
indicates that entry 9016170 should be excluded from calculations in favour
of entry 101027.

For more information on duplicate entries in the COD, please see
https://wiki.crystallography.net/duplicate_entry/.

Please let us know if you have any further questions.

Sincerely,
Antanas
-- 
This message has been scanned for viruses and
dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is
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> _______________________________________________
> Cod-bugs mailing list
> Cod-bugs at lists.crystallography.net
> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>


-- 
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania

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From robert.mcmeeking at stfc.ac.uk  Tue Jan 28 13:05:19 2025
From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI)
Date: Tue, 28 Jan 2025 11:05:19 +0000
Subject: [Cod-bugs] Silicon Disulfide
In-Reply-To: <CALHYoX7ZJrD3zn9tWNVK2ZB1emSm_qQQYboX1XrSzHatJu-LNQ@mail.gmail.com>
References: <CWLP265MB0065B3DB59C2B2A2822C26AFBEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>
 <CALHYoX7ZJrD3zn9tWNVK2ZB1emSm_qQQYboX1XrSzHatJu-LNQ@mail.gmail.com>
Message-ID: <CWLP265MB0065D6E9F30E9D5E162FB1BABEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>

Hello Antanas

Thank you for the prompt reply and clarification.

I have looked at the COD 9016170 in CrystalWorks. The structure looks, at first sight, quite reasonable. This seems to imply the symmetry operations used are correct and the formula corresponds to SiS2

Best Regards

Bob

From: Antanas Vaitkus <antanas.vaitkus90 at gmail.com>
Sent: 28 January 2025 10:41
To: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Cc: cod-bugs at ibt.lt
Subject: Re: [Cod-bugs] Silicon Disulfide

Dear Robert,

On Tue, 28 Jan 2025 at 12:29, Robert McMeeking - STFC UKRI <robert.mcmeeking at stfc.ac.uk<mailto:robert.mcmeeking at stfc.ac.uk>> wrote:
Good Morning,

There looks to be a problem with COD entry 9016170. The compound name, as in the article title, is ?Siliciumdisulfid?. But the formula is given as SiS4. There is also the COD entry 1010272 from the same paper assigned the formula SiS2.

These two entries describe the same structure, but the space group information
in entry 9016170 is most likely incorrect (for more information, see
https://projects.ibt.lt/repositories/issues/1603). The entry in question originated
in the AMCSD database and was later synced to the COD so we are waiting
for their comments before modifying the entry.

Perhaps only the second one should be retained?

While these entries are duplicates in the purest sense (same compound, same structure,
same publication), the general policy of the COD is to not remove entries once a COD ID
has been assigned (they might have been referenced in publications, etc.). Instead of that,
we mark duplicate structures using the '_cod_duplicate_entry' data name. For example, in
this case entry 9016170 contains a line "_cod_duplicate_entry             1010272" which
indicates that entry 9016170 should be excluded from calculations in favour of entry 101027.
For more information on duplicate entries in the COD, please see https://wiki.crystallography.net/duplicate_entry/.
Please let us know if you have any further questions.
Sincerely,
Antanas
--
This message has been scanned for viruses and
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_______________________________________________
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Cod-bugs at lists.crystallography.net<mailto:Cod-bugs at lists.crystallography.net>
http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs


--
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania


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From antanas.vaitkus90 at gmail.com  Tue Jan 28 13:55:46 2025
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Tue, 28 Jan 2025 13:55:46 +0200
Subject: [Cod-bugs] Silicon Disulfide
In-Reply-To: <CWLP265MB0065D6E9F30E9D5E162FB1BABEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>
References: <CWLP265MB0065B3DB59C2B2A2822C26AFBEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>
 <CALHYoX7ZJrD3zn9tWNVK2ZB1emSm_qQQYboX1XrSzHatJu-LNQ@mail.gmail.com>
 <CWLP265MB0065D6E9F30E9D5E162FB1BABEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <CALHYoX7PGzu35WGJNTrDVDELH0AfFEYYdctGvKRJn+ajqTAwZg@mail.gmail.com>

Hello,

When I inspect COD entry 9016170 in Jmol, I see long chains of square
pyramids with 4 S atoms at the bottom
and 1 Si atom at the top. When I inspect COD entry 1010272, the structure
instead consists of chains consisting
of flip flopping SiS2 fragments (same as reported in the original
publication and that matches the depiction on the
Wikipedia page [1]). Do the representations look the same in CrystalWorks?

[1] https://en.wikipedia.org/wiki/Silicon_disulfide

Sincerely,
Antanas

On Tue, 28 Jan 2025 at 13:05, Robert McMeeking - STFC UKRI <
robert.mcmeeking at stfc.ac.uk> wrote:

> Hello Antanas
>
>
>
> Thank you for the prompt reply and clarification.
>
>
>
> I have looked at the COD 9016170 in CrystalWorks. The structure looks, at
> first sight, quite reasonable. This seems to imply the symmetry operations
> used are correct and the formula corresponds to SiS2
>
>
>
> Best Regards
>
>
>
> Bob
>
>
>
> *From:* Antanas Vaitkus <antanas.vaitkus90 at gmail.com>
> *Sent:* 28 January 2025 10:41
> *To:* McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
> *Cc:* cod-bugs at ibt.lt
> *Subject:* Re: [Cod-bugs] Silicon Disulfide
>
>
>
> Dear Robert,
>
>
>
> On Tue, 28 Jan 2025 at 12:29, Robert McMeeking - STFC UKRI <
> robert.mcmeeking at stfc.ac.uk> wrote:
>
> Good Morning,
>
>
>
> There looks to be a problem with COD entry 9016170. The compound name, as
> in the article title, is ?Siliciumdisulfid?. But the formula is given as
> SiS4. There is also the COD entry 1010272 from the same paper assigned the
> formula SiS2.
>
>
>
> These two entries describe the same structure, but the space group
> information
> in entry 9016170 is most likely incorrect (for more information, see
> https://projects.ibt.lt/repositories/issues/1603). The entry in question
> originated
>
> in the AMCSD database and was later synced to the COD so we are waiting
>
> for their comments before modifying the entry.
>
>
>
> Perhaps only the second one should be retained?
>
>
>
> While these entries are duplicates in the purest sense (same compound,
> same structure,
> same publication), the general policy of the COD is to not remove entries
> once a COD ID
> has been assigned (they might have been referenced in publications, etc.).
> Instead of that,
> we mark duplicate structures using the '_cod_duplicate_entry' data name.
> For example, in
> this case entry 9016170 contains a line "_cod_duplicate_entry
> 1010272" which
> indicates that entry 9016170 should be excluded from calculations in
> favour of entry 101027.
>
> For more information on duplicate entries in the COD, please see
> https://wiki.crystallography.net/duplicate_entry/.
>
> Please let us know if you have any further questions.
>
> Sincerely,
>
> Antanas
> --
> 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
>
>
>
> --
>
> Antanas Vaitkus,
>
> Vilnius University,
> Life Sciences Center,
> Institute of Biotechnology,
> room C521, Saul?tekio al. 7,
> LT-10257 Vilnius, Lithuania
>
>
>


-- 
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
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From robert.mcmeeking at stfc.ac.uk  Tue Jan 28 14:39:49 2025
From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI)
Date: Tue, 28 Jan 2025 12:39:49 +0000
Subject: [Cod-bugs] Silicon Disulfide
In-Reply-To: <CALHYoX7PGzu35WGJNTrDVDELH0AfFEYYdctGvKRJn+ajqTAwZg@mail.gmail.com>
References: <CWLP265MB0065B3DB59C2B2A2822C26AFBEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>
 <CALHYoX7ZJrD3zn9tWNVK2ZB1emSm_qQQYboX1XrSzHatJu-LNQ@mail.gmail.com>
 <CWLP265MB0065D6E9F30E9D5E162FB1BABEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>
 <CALHYoX7PGzu35WGJNTrDVDELH0AfFEYYdctGvKRJn+ajqTAwZg@mail.gmail.com>
Message-ID: <CWLP265MB0065723C9E04827CDC0FA0CABEEF2@CWLP265MB0065.GBRP265.PROD.OUTLOOK.COM>

Whoops

Apologies. I got that wrong, and I omitted to include the screen captures. Yes, 9016170 does  look incorrect (corresponds to SiS4).

Many thanks

Bob

From: Antanas Vaitkus <antanas.vaitkus90 at gmail.com>
Sent: 28 January 2025 11:56
To: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk>
Cc: cod-bugs at ibt.lt
Subject: Re: [Cod-bugs] Silicon Disulfide

Hello,

When I inspect COD entry 9016170 in Jmol, I see long chains of square pyramids with 4 S atoms at the bottom
and 1 Si atom at the top. When I inspect COD entry 1010272, the structure instead consists of chains consisting
of flip flopping SiS2 fragments (same as reported in the original publication and that matches the depiction on the
Wikipedia page [1]). Do the representations look the same in CrystalWorks?

[1] https://en.wikipedia.org/wiki/Silicon_disulfide
Sincerely,
Antanas

On Tue, 28 Jan 2025 at 13:05, Robert McMeeking - STFC UKRI <robert.mcmeeking at stfc.ac.uk<mailto:robert.mcmeeking at stfc.ac.uk>> wrote:
Hello Antanas

Thank you for the prompt reply and clarification.

I have looked at the COD 9016170 in CrystalWorks. The structure looks, at first sight, quite reasonable. This seems to imply the symmetry operations used are correct and the formula corresponds to SiS2

Best Regards

Bob

From: Antanas Vaitkus <antanas.vaitkus90 at gmail.com<mailto:antanas.vaitkus90 at gmail.com>>
Sent: 28 January 2025 10:41
To: McMeeking, Robert (STFC,DL,SC) <robert.mcmeeking at stfc.ac.uk<mailto:robert.mcmeeking at stfc.ac.uk>>
Cc: cod-bugs at ibt.lt<mailto:cod-bugs at ibt.lt>
Subject: Re: [Cod-bugs] Silicon Disulfide

Dear Robert,

On Tue, 28 Jan 2025 at 12:29, Robert McMeeking - STFC UKRI <robert.mcmeeking at stfc.ac.uk<mailto:robert.mcmeeking at stfc.ac.uk>> wrote:
Good Morning,

There looks to be a problem with COD entry 9016170. The compound name, as in the article title, is ?Siliciumdisulfid?. But the formula is given as SiS4. There is also the COD entry 1010272 from the same paper assigned the formula SiS2.

These two entries describe the same structure, but the space group information
in entry 9016170 is most likely incorrect (for more information, see
https://projects.ibt.lt/repositories/issues/1603). The entry in question originated
in the AMCSD database and was later synced to the COD so we are waiting
for their comments before modifying the entry.

Perhaps only the second one should be retained?

While these entries are duplicates in the purest sense (same compound, same structure,
same publication), the general policy of the COD is to not remove entries once a COD ID
has been assigned (they might have been referenced in publications, etc.). Instead of that,
we mark duplicate structures using the '_cod_duplicate_entry' data name. For example, in
this case entry 9016170 contains a line "_cod_duplicate_entry             1010272" which
indicates that entry 9016170 should be excluded from calculations in favour of entry 101027.
For more information on duplicate entries in the COD, please see https://wiki.crystallography.net/duplicate_entry/.
Please let us know if you have any further questions.
Sincerely,
Antanas
--
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<mailto:Cod-bugs at lists.crystallography.net>
http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs


--
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania



--
Antanas Vaitkus,
Vilnius University,
Life Sciences Center,
Institute of Biotechnology,
room C521, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania


-- 
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From noreply at letsencrypt.org  Wed Jan 29 23:08:39 2025
From: noreply at letsencrypt.org (noreply at letsencrypt.org)
Date: Wed, 29 Jan 2025 21:08:39 +0000
Subject: [Cod-bugs] =?utf-8?q?Updates_on_Lets_Encrypt_Subscriber_Agreemen?=
 =?utf-8?q?t_=26_Ending_Expiration_Notification?=
Message-ID: <20250129T210839.3129094221167794029.noreply@letsencrypt.org>

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