[BioMart Users] MySQL user privileges

Arek Kasprzyk | 3 May 2011 13:46

Re: [BioMart Users] MySQL user privileges

Hi Amadis,

The user that you are using can be read only but needs to be able to connect from the host that you are running biomart server on and have access privileges to the database and tables that you want to query. First try to rule out all potential 'non-biomart' problems. The simplest test is to try to query your database from mysql client running on the same host as your biomart server. If this works writing a simple perl script querying the same tables and run it from the same host as your biomart server to make sure that the DBI/DBD install works correctly.

Arek Kasprzyk
Director, Bioinformatics Operations and Principal Investigator

Ontario Institute for Cancer Research
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Toronto, Ontario, Canada M5G 0A3

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From: Amadis Pages <amadis.pages <at> gmail.com>
Date: Tue, 3 May 2011 06:45:56 -0400
To: "users <at> biomart.org" <users <at> biomart.org>
Subject: [BioMart Users] MySQL user privileges

Hi,

I've recently installed Biomart in order to make some of my lab's data publicly available in the future.

I'm using a martDBLocation.xml-style registry file. I've created a MySQL user with USAGE privileges on the database I'm using to store the data, but when I try to run the configure.pl script, the following error shows up:

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
COULD NOT CONNECT TO DATABASE xxxxxx.CHECK YOUR SETTINGS
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

What kind of permissions should I grant to the user that appears in the registry file? I do not feel comfortable giving this user privileges to modify the database content. Below you can find a copy-paste of the registry file:

<MartDBLocation
    ...
    user         = "rgmartuser"
    password     = "xxxxxxxxxx"
    visible      = "1"
    default      = ""
    includeDatasets = ""
    martUser     = ""
/>

Thanks a lot in advance for your help. Please let me know if this is not the proper mail to send this kind of inquiries.

Best regards,
Amadís

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