[BioMart Users] MySQL user privileges

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[BioMart Users] MySQL user privileges

Amadis Pages
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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Re: [BioMart Users] MySQL user privileges

Arek Kasprzyk-2
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. 

a

Arek Kasprzyk
Director, Bioinformatics Operations and Principal Investigator

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
     
Tel:       416-673-8559
Toll-free:           1-866-678-6427
www.oicr.on.ca


Administrative Assistant: [hidden email]

 

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.


From: Amadis Pages <[hidden email]>
Date: Tue, 3 May 2011 06:45:56 -0400
To: "[hidden email]" <[hidden email]>
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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Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] MySQL user privileges

Amadis Pages
Hi,

Thanks for your help Arek, I've been able to solve the problem.


2011/5/3 Arek Kasprzyk <[hidden email]>
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. 

a

Arek Kasprzyk
Director, Bioinformatics Operations and Principal Investigator

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
     
Tel:       416-673-8559
Toll-free:           1-866-678-6427
www.oicr.on.ca


Administrative Assistant: [hidden email]

 

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.


From: Amadis Pages <[hidden email]>
Date: Tue, 3 May 2011 06:45:56 -0400
To: "[hidden email]" <[hidden email]>
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



_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users