upload user settings for GB 2.08?

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upload user settings for GB 2.08?

okeeffe
Hi all,
I'm trying to upload external user gff data onto our 2.08 system here.
I'm getting a user denied error in the browser.
*
test.gff*: Access denied for user 'okeeffe'@'localhost' (using password: NO)

Now though I am user 'okeeffe', I shouldn't be as I've configured the
datasource to be user gbrowse and the upload users to be www-data:

# from the mouse conf file
..
[gbrowse2_NCBIM37:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                  -dsn
dbi:mysql:database=gbrowse2_NCBIM37;host=genome.molgen.mpg.de;user=gbrowse;password=gbrowse;
search options = all
..

# from the global gbrowse conf file
..
userdb_adaptor = DBI::mysql
userdb_host    = localhost
userdb_user    = www-data
userdb_pass    = gbrowse
..

I have set up the database to allow the browser to create userdata_%
databases as follows:

grant create on `userdata\_%`.* to 'www-data'@genome.molgen.mpg.de
identified by 'gbrowse';

I just can't figure why I'm user 'okeeffe'.
Am I missing some settings here?
Thx,

Sean.

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Re: upload user settings for GB 2.08?

Lincoln Stein
Hi Sean,

Is there perhaps a userdb_user option located in the datasource configuration file? That will override the setting.

If this isn't happening it is possible that there's a bug in the code that opens up the user database. Is the web server running as user "okeefe"?

Lincoln

On Tue, Jun 15, 2010 at 8:46 AM, Sean O'Keeffe <[hidden email]> wrote:
Hi all,
I'm trying to upload external user gff data onto our 2.08 system here.
I'm getting a user denied error in the browser.
*
test.gff*: Access denied for user 'okeeffe'@'localhost' (using password: NO)

Now though I am user 'okeeffe', I shouldn't be as I've configured the
datasource to be user gbrowse and the upload users to be www-data:

# from the mouse conf file
..
[gbrowse2_NCBIM37:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                 -dsn
dbi:mysql:database=gbrowse2_NCBIM37;host=genome.molgen.mpg.de;user=gbrowse;password=gbrowse;
search options = all
..

# from the global gbrowse conf file
..
userdb_adaptor = DBI::mysql
userdb_host    = localhost
userdb_user    = www-data
userdb_pass    = gbrowse
..

I have set up the database to allow the browser to create userdata_%
databases as follows:

grant create on `userdata\_%`.* to '[hidden email]
identified by 'gbrowse';

I just can't figure why I'm user 'okeeffe'.
Am I missing some settings here?
Thx,

Sean.

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
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Re: upload user settings for GB 2.08?

Jayaraman, Pushkala

I think there is a problem with your conf file

 

[gbrowse2_NCBIM37:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                 -dsn DBI:mysql:database=gbrowse2_NCBIM37;host=genome.molgen.mpg.de

-user gbrowse

-pass gbrowse

search options = all

try this format …..

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, June 15, 2010 9:39 AM
To: Sean O'Keeffe
Cc: Gbrowse Mailing List
Subject: Re: [Gmod-gbrowse] upload user settings for GB 2.08?

 

Hi Sean,

 

Is there perhaps a userdb_user option located in the datasource configuration file? That will override the setting.

 

If this isn't happening it is possible that there's a bug in the code that opens up the user database. Is the web server running as user "okeefe"?

 

Lincoln

On Tue, Jun 15, 2010 at 8:46 AM, Sean O'Keeffe <[hidden email]> wrote:

Hi all,
I'm trying to upload external user gff data onto our 2.08 system here.
I'm getting a user denied error in the browser.
*
test.gff*: Access denied for user 'okeeffe'@'localhost' (using password: NO)

Now though I am user 'okeeffe', I shouldn't be as I've configured the
datasource to be user gbrowse and the upload users to be www-data:

# from the mouse conf file
..
[gbrowse2_NCBIM37:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                 -dsn
dbi:mysql:database=gbrowse2_NCBIM37;host=genome.molgen.mpg.de;user=gbrowse;password=gbrowse;
search options = all
..

# from the global gbrowse conf file
..
userdb_adaptor = DBI::mysql
userdb_host    = localhost
userdb_user    = www-data
userdb_pass    = gbrowse
..

I have set up the database to allow the browser to create userdata_%
databases as follows:

grant create on `userdata\_%`.* to '[hidden email]
identified by 'gbrowse';

I just can't figure why I'm user 'okeeffe'.
Am I missing some settings here?
Thx,

Sean.

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
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Re: upload user settings for GB 2.08?

Jayaraman, Pushkala
In reply to this post by okeeffe
I am not sure.. but I think it is not able to read your conf file
right...
I've had the same problems and Changing the format of the -dsn argument
in the conf file helped set it right.
But then,
It is worth a try..
Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Sean O'Keeffe [mailto:[hidden email]]
Sent: Tuesday, June 15, 2010 7:46 AM
To: Gbrowse Mailing List
Subject: [Gmod-gbrowse] upload user settings for GB 2.08?

Hi all,
I'm trying to upload external user gff data onto our 2.08 system here.
I'm getting a user denied error in the browser.
*
test.gff*: Access denied for user 'okeeffe'@'localhost' (using password:
NO)

Now though I am user 'okeeffe', I shouldn't be as I've configured the
datasource to be user gbrowse and the upload users to be www-data:

# from the mouse conf file
..
[gbrowse2_NCBIM37:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                  -dsn
dbi:mysql:database=gbrowse2_NCBIM37;host=genome.molgen.mpg.de;user=gbrow
se;password=gbrowse;
search options = all
..

# from the global gbrowse conf file
..
userdb_adaptor = DBI::mysql
userdb_host    = localhost
userdb_user    = www-data
userdb_pass    = gbrowse
..

I have set up the database to allow the browser to create userdata_%
databases as follows:

grant create on `userdata\_%`.* to 'www-data'@genome.molgen.mpg.de
identified by 'gbrowse';

I just can't figure why I'm user 'okeeffe'.
Am I missing some settings here?
Thx,

Sean.

------------------------------------------------------------------------
------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse