From thomas.degen at malvernpanalytical.com  Tue May 14 10:36:47 2024
From: thomas.degen at malvernpanalytical.com (Thomas Degen)
Date: Tue, 14 May 2024 07:36:47 +0000
Subject: [Cod-bugs] FW: New Release of Search/Match database for Panalytical
 HighScore(Plus) SW
In-Reply-To: <AM6PR07MB47119927680958E181A22E87EDE52@AM6PR07MB4711.eurprd07.prod.outlook.com>
References: <HE1PR0701MB2603DE65F4746674DEE33C2CEDBD9@HE1PR0701MB2603.eurprd07.prod.outlook.com>
 <fa4ee47e-1752-71f9-9c20-ce28517ed4fb@ibt.lt>
 <AM6PR07MB47119927680958E181A22E87EDE52@AM6PR07MB4711.eurprd07.prod.outlook.com>
Message-ID: <AM6PR07MB4711D7607D06864C70FC1748EDE32@AM6PR07MB4711.eurprd07.prod.outlook.com>

Unrestricted Document

Hello COD Crew,

This is Thomas Degen from Malvern Panalytical. We typically update the Search/Match database which is calculated from the COD database once a year.
Can someone please advice me, what?s the best way to upload this latest Search/Match Database based on the COD from this May?
This is (in the meantime) a 7.1 GByte SQLite database file.

Many Thanks and best regards,

Thomas Degen



Unrestricted Document

From: Thomas Degen
Sent: Wednesday, May 8, 2024 1:29 PM
To: Saulius Gra?ulis <grazulis at ibt.lt>
Subject: RE: New Release of Search/Match database for Panalytical HighScore(Plus) SW

Hello Saulius,

Its more than a year ago that we updated the MP COD Search/Match database.
I have just compiled a new one, using the COD data from May 5th.
How can I send you that big file, is it still the same options or is there something changed/new?

Thank?s and best regards,

Thomas

From: Saulius Gra?ulis <grazulis at ibt.lt<mailto:grazulis at ibt.lt>>
Sent: Monday, March 20, 2023 12:44 PM
To: Thomas Degen <thomas.degen at malvernpanalytical.com<mailto:thomas.degen at malvernpanalytical.com>>
Subject: Re: New Release of Search/Match database for Panalytical HighScore(Plus) SW

On 2023-03-17 17:49, Thomas Degen wrote:
This is Thomas Degen from Malvern Panalytical headquarters in Almelo, the Netherlands.
I think previously you were in contact with my colleague Thomas Dortmann, concerning the Search/Match version
Of the COD database for MP HighScore(Plus) software. Thomas Dortmann retired last year and now I would like to upload a
New version of the Search/Match database, to make it available for our users on your website.
This new version is based on the COD of February this year.
Do you maybe have an upload facility for such huge files?
The SQlite (Search/Match) database file is around 7GByte.

You can send me the files using the following options:

1) using anonymous FTP on my server, 'saulius.grazulis.lt' (I have to use my own server since our university has blocked the incoming traffic to FTP port at the moment). Since my server is behind the firewall, please use PASSIVE FTP mode to upload the files. An example upload session using a CLI ftp client is provided [1].

2) Using 'rsync' to an ssh account. To use this option, please send me your ssh public key (~/.ssh/id_rsa.pub or equivalent file), I will add an account for you and send the ssh login credentials (user name and server name);

3) you can place the files on any HTTP(S) server accessible to you and send me the URL of the file(s); I will download them.

Please let me know which option is the most suitable for you.

In any case, please send me the list of the files to be published together with their crypto-checksums (SAH256), and possibly file sizes, so that I can double check the uploads. If there are any problems, please let me know and I'll do my best to help resolving them.

Sincerely yours,
Saulius

Refs.:

[1] An example upload session to the 'saulius.grazulis.lt' FTP server. The bold italic monospaced text is typed by the client operator (in the example case, by me):
saulius at tasmanijos-velnias ~/ $ ftp saulius.grazulis.lt
Connected to saulius.grazulis.lt.
220 ProFTPD 1.3.5b Server (Debian) [::ffff:192.168.1.111]
Name (saulius.grazulis.lt:saulius): anonymous
331 Anonymous login ok, send your complete email address as your password
Password:grazulis at ibt.lt<mailto:grazulis at ibt.lt>
230-Welcome, archive user anonymous at 78-60-2-35.static.zebra.lt<mailto:anonymous at 78-60-2-35.static.zebra.lt> !
230-
230-The local time is: Mon Mar 20 11:31:05 2023
230-
230-This is an experimental FTP server.  If you have any unusual problems,
230-please report them via e-mail to <root at jonvabalis>.
230-
230 Anonymous access granted, restrictions apply
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd incoming
250 CWD command successful
ftp> bin
200 Type set to I
ftp> pass
Passive mode on.
ftp> hash
Hash mark printing on (1024 bytes/hash mark).
ftp> put stack-x86.ora
local: stack-x86.ora remote: stack-x86.ora
227 Entering Passive Mode (78,62,46,183,165,93).
150 Opening BINARY mode data connection for stack-x86.ora
##############...
226 Transfer complete
6893812 bytes sent in 0.92 secs (7.1113 MB/s)
ftp> quit
221 Goodbye.



--

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 email and any files transmitted with it are confidential and maybe legally privileged. Such message is intended solely for the use of the individual or entity to whom they are addressed. Please notify the originator of the message if you are not the intended recipient and destroy all copies of the message. Please note that any use, dissemination, or reproduction is strictly prohibited and may be unlawful.

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From grazulis at ibt.lt  Tue May 14 10:49:34 2024
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=)
Date: Tue, 14 May 2024 10:49:34 +0300
Subject: [Cod-bugs] FW: New Release of Search/Match database for
 Panalytical HighScore(Plus) SW
In-Reply-To: <AM6PR07MB4711D7607D06864C70FC1748EDE32@AM6PR07MB4711.eurprd07.prod.outlook.com>
References: <HE1PR0701MB2603DE65F4746674DEE33C2CEDBD9@HE1PR0701MB2603.eurprd07.prod.outlook.com>
 <fa4ee47e-1752-71f9-9c20-ce28517ed4fb@ibt.lt>
 <AM6PR07MB47119927680958E181A22E87EDE52@AM6PR07MB4711.eurprd07.prod.outlook.com>
 <AM6PR07MB4711D7607D06864C70FC1748EDE32@AM6PR07MB4711.eurprd07.prod.outlook.com>
Message-ID: <0a7bb2d3-0152-5325-7eef-379c7dfecc71@ibt.lt>

Hi, Thomas,

great to hear from you!

I'll open the usual FTP port and send you the upload instructions this 
evening.

Sincerely yours,
Saulius

On 2024-05-14 10:36, Thomas Degen wrote:
>
> This is Thomas Degen from Malvern Panalytical. We typically update the 
> Search/Match database which is calculated from the COD database once a 
> year.
>
> Can someone please advice me, what?s the best way to upload this 
> latest Search/Match Database based on the COD from this May?
>
> This is (in the meantime) a 7.1 GByte SQLite database file.
>

-- 
Dr. Saulius Gra?ulis
Vilnius University Institute of Biotechnology, Saul?tekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / 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.

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From grazulis at ibt.lt  Wed May 15 17:29:32 2024
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=)
Date: Wed, 15 May 2024 17:29:32 +0300
Subject: [Cod-bugs] FW: New Release of Search/Match database for
 Panalytical HighScore(Plus) SW
In-Reply-To: <AM6PR07MB4711D7607D06864C70FC1748EDE32@AM6PR07MB4711.eurprd07.prod.outlook.com>
References: <HE1PR0701MB2603DE65F4746674DEE33C2CEDBD9@HE1PR0701MB2603.eurprd07.prod.outlook.com>
 <fa4ee47e-1752-71f9-9c20-ce28517ed4fb@ibt.lt>
 <AM6PR07MB47119927680958E181A22E87EDE52@AM6PR07MB4711.eurprd07.prod.outlook.com>
 <AM6PR07MB4711D7607D06864C70FC1748EDE32@AM6PR07MB4711.eurprd07.prod.outlook.com>
Message-ID: <61a771b7-2cb3-4e9c-9753-21db5d7bbbb9@ibt.lt>

Hi, Thomas,

sorry for the delay.

I have opened the FTP port on the COD server, 'crystallography.net', as 
in the previous uploads. You should be able to contact it using 'ftp 
crystallography.net' or by using other means. the disk there has 23 GB 
of free space. The example of my test session is below [1].

Please send me the file names, checksums and instructions where you 
would like to see the files under the COD archive tree, and I will 
handle the file transfer within the server.

Sincerely yours,
Saulius

On 2024-05-14 10:36, Thomas Degen wrote:
>
> Hello COD Crew,
>
> This is Thomas Degen from Malvern Panalytical. We typically update the 
> Search/Match database which is calculated from the COD database once a 
> year.
>
> Can someone please advice me, what?s the best way to upload this 
> latest Search/Match Database based on the COD from this May?
>
> This is (in the meantime) a 7.1 GByte SQLite database file.
>
> Many Thanks and best regards,
>
Refs.:

[1] FTP access to the COD server 'crystallography.net':

> saulius at pterodaktilis ~/ $ *ftp crystallography.net*
> Connected to crystallography.net.
> 220 ProFTPD Server (Debian) [::ffff:158.129.170.82]
> Name (crystallography.net:saulius): *anonymous*
> 331 Anonymous login ok, send your complete email address as your password
> Password: *_grazulis at ibt.lt_*
> 230-Welcome, archive user anonymous at 172.17.170.137 !
> 230-
> 230-The local time is: Wed May 15 17:20:38 2024
> 230-
> 230-This is an experimental FTP server.? If you have any unusual problems,
> 230-please report them via e-mail to <root at cod2.ibt.lt>.
> 230-
> 230 Anonymous access granted, restrictions apply
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> *dir*
> 229 Entering Extended Passive Mode (|||1837|)
> 150 Opening ASCII mode data connection for file list
> drwx------?? 2 ftp????? ftp????????? 4096 Aug 11? 2021 incoming
> drwxr-x---?? 2 ftp????? ftp????????? 4096 Jul 12? 2016 pub
> -rw-r--r--?? 1 ftp????? ftp?????????? 170 May 19? 2015 welcome.msg
> 226 Transfer complete
> ftp> *cd incoming*
> 250 CWD command successful
> ftp> *bin*
> 200 Type set to I
> ftp> *hash*
> Hash mark printing on (1024 bytes/hash mark).
> ftp> *passive*
> Passive mode: off; fallback to active mode: off.
> ftp> *put c-array-pointers.ora*
> local: c-array-pointers.ora remote: c-array-pointers.ora
> 200 EPRT command successful
> 150 Opening BINARY mode data connection for c-array-pointers.ora
> ###################################################################### ...
> 226 Transfer complete
> 3269103 bytes sent in 00:00 (10.71 MiB/s)
> ftp> *quit*
> 221 Goodbye.
> saulius at pterodaktilis ~/ $ *md5sum c-array-pointers.ora*
> 72c2bc90b51e9840727e5b1d83df819f? c-array-pointers.ora
> saulius at pterodaktilis ~/ $ *date*
> 2024-05-15T17:25:17 EEST

> root at cod2 etc/ # *cd /srv/ftp/*
> root at cod2 ftp/ # *ll*
> total 12
> drwx------ 2 ftp? nogroup 4096 2024-05-15 17:21 incoming/
> drwxr-x--- 2 ftp? nogroup 4096 2016-07-12 10:50 pub/
> -rw-r--r-- 1 root root???? 170 2015-05-19 14:11 welcome.msg
> root at cod2 ftp/ # *cd incoming/*
> root at cod2 incoming/ # *ll*
> total 3196
> -rw-r--r-- 1 ftp nogroup 3269103 2024-05-15 17:21 c-array-pointers.ora
> root at cod2 incoming/ # *md5sum c-array-pointers.ora*
> 72c2bc90b51e9840727e5b1d83df819f? c-array-pointers.ora
> root at cod2 incoming/ # *df -h .*
> Filesystem????? Size? Used Avail Use% Mounted on
> /dev/sda1??????? 95G?? 67G?? 23G? 75% /
> root at cod2 incoming/ # *rm c-array-pointers.ora*


-- 
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.

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