SOLVED: problems loading data into MySQL db

[Lacey Sanderson]

Matthew:

Thanks! Changing my dsn line to

-dsn dbi:mysql:database=Medicago;host=localhost

fixed the internal errors and brought up the GBrowse page finally!

Lincoln:

I added in
mysql> grant all privileges on Medicago.* to 'dbadmin'@'128.233.29.40';
Query OK, 0 rows affected (0.02 sec)

mysql> grant select on Medicago.* to 'www-data'@'128.233.29.40';
Query OK, 0 rows affected (0.00 sec)

and then tried
dbadmin@pev024-desktop:/var/www/gbrowse/databases/Medicago$  
bp_seqfeature_load.pl -c -f -p **** -d Medicago ./ chr01_1_33214707.gff3

However I still got errors:
DBI connect('Medicago','',...) failed: Access denied for user  
'dbadmin'@'localhost' (using password: YES) at /usr/local/share/perl/
5.10.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 212

-------------------- EXCEPTION --------------------
MSG: Access denied for user 'dbadmin'@'localhost' (using password: YES)
STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/local/share/
perl/5.10.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm:212
STACK Bio::DB::SeqFeature::Store::new /usr/local/share/perl/5.10.0/Bio/
DB/SeqFeature/Store.pm:360
STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:77
-------------------------------------------

Which are the same as though I was getting before. However, using sudo  
bp_seqfeature_load did correctly load the data in.

Thanks for all the Help!!!
Lacey

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[Scott Cain-4]

Oh, fine!  I do several emails back and forth, and Matthew comes in in  
the last second and steals the glory!  :-)

Lacey, I'm glad it working for you!

Scott


On Oct 19, 2009, at 11:16 AM, Lacey Sanderson wrote:

> Matthew:
>
> Thanks! Changing my dsn line to
>
> -dsn dbi:mysql:database=Medicago;host=localhost
>
> fixed the internal errors and brought up the GBrowse page finally!
>
> Lincoln:
>
> I added in
> mysql> grant all privileges on Medicago.* to  
> 'dbadmin'@'128.233.29.40';
> Query OK, 0 rows affected (0.02 sec)
>
> mysql> grant select on Medicago.* to 'www-data'@'128.233.29.40';
> Query OK, 0 rows affected (0.00 sec)
>
> and then tried
> dbadmin@pev024-desktop:/var/www/gbrowse/databases/Medicago$
> bp_seqfeature_load.pl -c -f -p **** -d Medicago ./  
> chr01_1_33214707.gff3
>
> However I still got errors:
> DBI connect('Medicago','',...) failed: Access denied for user
> 'dbadmin'@'localhost' (using password: YES) at /usr/local/share/perl/
> 5.10.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 212
>
> -------------------- EXCEPTION --------------------
> MSG: Access denied for user 'dbadmin'@'localhost' (using password:  
> YES)
> STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/local/share/
> perl/5.10.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm:212
> STACK Bio::DB::SeqFeature::Store::new /usr/local/share/perl/5.10.0/
> Bio/
> DB/SeqFeature/Store.pm:360
> STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:77
> -------------------------------------------
>
> Which are the same as though I was getting before. However, using sudo
> bp_seqfeature_load did correctly load the data in.
>
> Thanks for all the Help!!!
> Lacey
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart  
> your
> developing skills, take BlackBerry mobile applications to market and  
> stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

-----------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research





------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse