Question: Failed To Connect To The Ensembl Mysql Database
1
gravatar for Fred Fleche
10.3 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

Hello

I am trying to connect to the mysql database available at ensembl in order to perform some query with the follwoing code but i Get a "Could not connect:" message so I am wondering if I failed because I am not allowed to perform connection out of my network for security reason.

So if someone has the time to test it and to connect successfully I would appreciate.

Thanks in advance.

<?php
$link = mysql_connect('ensembldb.ensembl.org:3306', 'anonymous', '');

if (!$link) {
    die('Could not connect: ' . mysql_error());
}
echo 'Connected successfully';
mysql_close($link);
?>
mysql ensembl • 3.6k views
ADD COMMENTlink modified 23 months ago by RamRS28k • written 10.3 years ago by Fred Fleche4.3k
2
gravatar for Giovanni M Dall'Olio
10.3 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

The port is 5306 and not 3306. I had the same problem two years ago and they answered me that:

helpdesk@ensembl.org, on May 22th 2008: From release 48 onwards the Ensembl databases are on port 5306 instead of 3306 of ensembldb …

I asked them if they could update their docs but they didn't do it yet, I don't know why.

ADD COMMENTlink written 10.3 years ago by Giovanni M Dall'Olio27k

Actually it's detailed at http://www.ensembl.org/info/data/mysql.html. The pre-v47 release is on 3306 and anything post is on 5306.

ADD REPLYlink written 10.3 years ago by Ian Simpson950

Actually it's detailed at ensembl.org/info/data/mysql.html The pre-v48 release is on 3306 and anything post is on 5306

ADD REPLYlink written 10.3 years ago by Ian Simpson950

Actually it's detailed at ensembl.org/info/data/mysql.html Version47 and prior releases are on 3306 and anything post is on 5306

ADD REPLYlink written 10.3 years ago by Ian Simpson950
1
gravatar for Ian Simpson
10.3 years ago by
Ian Simpson950
Edinburgh
Ian Simpson950 wrote:

Well this works for me so my guess would be you need to check your firewall settings (both outgoing and incoming http://www.ensembl.org/info/data/mysql.html )

<?php
$link = mysql_connect('ensembldb.ensembl.org:3306', 'anonymous', '');

if (!$link) {
    die('Could not connect: ' . mysql_error());
}
echo 'Connected successfully';

$db_list = mysql_list_dbs($link);

while ($row = mysql_fetch_object($db_list)) {
     echo $row-&gt;Database . "\n";
}

mysql_close($link);
?>
ADD COMMENTlink modified 23 months ago by RamRS28k • written 10.3 years ago by Ian Simpson950
2

Also the latest db releases are on port 5306

ADD REPLYlink written 10.3 years ago by Ian Simpson950

If you have a mysql client installed this should work :- mysql -h ensembldb.ensembl.org -P 5306 -u anonymous

ADD REPLYlink written 10.3 years ago by Ian Simpson950
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