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<div class="moz-cite-prefix">Dear Dean,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">thank you for your inquiry!<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 2022-04-13 12:33, Keeble, Dean
(DLSLtd,RAL,LSCI) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:PR3PR01MB8097E2EC49C9937CEBC4D07EA2EC9@PR3PR01MB8097.eurprd01.prod.exchangelabs.com">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
I'm investigating how to perform some searches in the COD
programmatically via the mysql interface. In following the
example
<a href="https://wiki.crystallography.net/howtoquerycod/"
title="https://wiki.crystallography.net/howtoquerycod/"
moz-do-not-send="true">
online </a>I'm not managing to connect, however. Do you have
any advice on how I might proceed? Below I show results of a
ping (success), the mysql (with the error) and my mysql version.
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
Many thanks in advance for your help! <br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
All the best, <br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
Dean<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<span style="font-family: "Courier New", monospace;">$
ping -c 1 sql.crystallography.net</span>
<div><span style="font-family: "Courier New",
monospace;">PING sql.crystallography.net (158.129.170.75)
56(84) bytes of data.</span></div>
<div><span style="font-family: "Courier New",
monospace;">64 bytes from 158.129.170.75 (158.129.170.75):
icmp_seq=1 ttl=46 time=47.7 ms</span></div>
<div><br>
</div>
<div><span style="font-family: "Courier New",
monospace;">--- sql.crystallography.net ping statistics ---</span></div>
<div><span style="font-family: "Courier New",
monospace;">1 packets transmitted, 1 received, 0% packet
loss, time 0ms</span></div>
<div><span style="font-family: "Courier New",
monospace;">rtt min/avg/max/mdev =
47.777/47.777/47.777/0.000 ms</span></div>
<div><span style="font-family: "Courier New",
monospace;"><br>
</span></div>
<div><span style="font-family: "Courier New",
monospace;">$ mysql -u cod_reader -h sql.crystallography.net
-e 'select count(*) from data where flags like "%has Fobs%"'
cod | cat</span></div>
<div><span style="font-family: "Courier New",
monospace;">ERROR 2003 (HY000): Can't connect to MySQL
server on 'sql.crystallography.net' (110)</span></div>
<div><span style="font-family: "Courier New",
monospace;"><br>
</span></div>
<div><span style="font-family: "Courier New",
monospace;">$ mysql --version</span></div>
<div><span style="font-family: "Courier New",
monospace;">mysql Ver 15.1 Distrib 5.5.68-MariaDB, for
Linux (x86_64) using readline 5.1</span></div>
</div>
</blockquote>
<p>All your commands seem OK. I have tested your SQL query on my
machine, and it works as expected from my location:</p>
<p>
<blockquote type="cite"><font face="monospace">saulius@tasmanijos-velnias
2022-USNC-Cr-Database-Workshop-III/ $ mysql -u cod_reader -h
sql.crystallography.net -e 'select count(*) from data where
flags like "%has Fobs%"' cod | cat<br>
count(*)<br>
57568</font><br>
</blockquote>
</p>
<p>As Andrius pointed out, the reason why the command does not work
for you might be a firewall. <br>
</p>
<p>I could add to that that need the TCP port 3306 open to be able
to access mysql directly:</p>
<p>
<blockquote type="cite"><font face="monospace">saulius@tasmanijos-velnias
2022-USNC-Cr-Database-Workshop-III/ $ grep mysql /etc/services
<br>
mysql 3306/tcp</font><br>
</blockquote>
</p>
<p>Please check with your site admin if they have blocked that port
(if you are in Diamond, this could be the case – the sysadmins are
simtimes be extra-cautious at large facilities...); if they have,
maybe they can open the port for you. In addition to that, you may
want to check the same command though your home Internet provide
or via you mobile phone.<br>
</p>
<p>HTH,<br>
Saulius<br>
</p>
<pre class="moz-signature" cols="72">--
Dr. Saulius Gražulis
Vilnius University, Life Science Center, Institute of Biotechnology
Saulėtekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)
phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366
</pre>
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