Thank you. I can understand that.

 

[chado:database]

db_adaptor           = Bio::DB::Das::Chado

db_args                     = -adaptor Bio::DB::Das::Chado

                     -dsn dbi:Pg:dbname=tripal;host=localhost

                     -user tripaldemo

                     -pass tripal2demo

psql= ALTER USER tripaldemo SET search_path TO chado;  <-

 

This line I put here in both the Gbrowse and Chado conf should get it to look through chado first right?

 

Also, the server the postgres database is on is port 5432 for localhost, is that information needed?

 

David Jeang

 

From: Scott Cain [mailto:scott <at> scottcain.net]
Sent: Wednesday, July 25, 2012 9:17 AM
To: Jeang, David - ARS
Cc: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org

Subject: Re: [Gmod-gbrowse] establishing chado connections

 

Hi David,

Sorry about the radio silence; I've been traveling a lot the last few weeks so a few things have slipped.

I'd say the fact that it is complaining about not finding the cv table means two things:

1. It is successfully connecting to the database (that's a good thing), and

2. You don't have the search path set appropriately for the user that's connecting to the database. 

Since you're using GBrowse with Tripal, you have to set the search path for the user that is connecting so that it searches the chado schema first.

Scott

On Fri, Jul 20, 2012 at 2:58 PM, Jeang, David - ARS <David.Jeang-yPPU2dwoW2ufRvmTrFJqzg@public.gmane.org> wrote:

I’ve managed to adjust some permissions that clear up the DBD::Pg problem, now I have this error in the log:

 

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] DBD::Pg::st execute failed: ERROR:  relation "cv" does not exist

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] LINE 1: select cv_id from cv where name in (

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67]                           ^ at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das/

Chado.pm line 843.

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] Could not open database:

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] ------------- EXCEPTION: Bio::Root::Exception -------------

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] MSG: trying to find SOFA

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Error::throw

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::sofa_id /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB

/Das/Chado.pm:843

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::DB::Das::Chado::new /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/DB/Das

/Chado.pm:242

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataBase::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux

-thread-multi/Bio/Graphics/Browser2/DataBase.pm:44

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::DataSource::open_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-lin

ux-thread-multi/Bio/Graphics/Browser2/DataSource.pm:981

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init_database /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-t

hread-multi/Bio/Graphics/Browser2/Render.pm:1084

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::init /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mul

ti/Bio/Graphics/Browser2/Render.pm:343

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: Bio::Graphics::Browser2::Render::run /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-mult

i/Bio/Graphics/Browser2/Render.pm:285

[Fri Jul 20 13:17:23 2012] [error] [client 10.12.20.67] STACK: /var/www/cgi-bin/gb2/gbrowse:50

 

Can anyone tell me what is means?

 

David Jeang

 

From: Jeang, David - ARS [mailto:David.Jeang-pPx96Vez9UE3g5lI6rsm2w@public.gmane.org]
Sent: Thursday, July 19, 2012 9:24 AM
To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
Subject: Re: [Gmod-gbrowse] establishing chado connections

 

Update: after getting GCI::Toggle to work, the error log now states:

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: install_driver(Pg) failed: Can't locate loadable object for module DBD::Pg in <at> INC ( <at> INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at (eval 139) line 3.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 139) line 3.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Perhaps a module that DBD::Pg requires hasn't been fully installed

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67]  at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Das/Chado.pm line 234.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::dr::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 1240.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Had to create DBD::Pg::db::imp_data_size unexpectedly at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBI.pm line 1270.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 131.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 141.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/DataSource.pm line 1048.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Use of uninitialized value in hash element at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/RegionSearch.pm line 404.

[Thu Jul 19 09:14:38 2012] [error] [client 10.12.20.67] Can't call method "segment" on an undefined value at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Region.pm line 357.

[Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] which: no inkscape in (/sbin:/usr/sbin:/bin:/usr/bin)

[Thu Jul 19 09:14:39 2012] [error] [client 10.12.20.67] Could not open database: Undefined subroutine &DBD::Pg::db::_login called at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/DBD/Pg.pm line 224.

[Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico

[Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico

[Thu Jul 19 09:14:40 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico

 

The browser says

Can't call method "segment" on an undefined value.

 

I’m wondering…am I going about the connection wrong? The chado schema I want to connect to is in a tripal database, that I’ve already accounted for. But the tripal database is on a PostgreSQL 8.4.12 server running on localhost:5432, and it’s the server that needs the password, not the database. Also, an additional password and username is used to access the site http://i5k.nal.usda.gov/phppgadmin/, where I can see the server, is that relevant to the conf files?

 

David Jeang

 

From: Jeang, David - ARS [mailto:David.Jeang-pPx96Vez9UE3g5lI6rsm2w@public.gmane.org]
Sent: Wednesday, July 18, 2012 3:21 PM
To: gmod-gbrowse-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f@public.gmane.org
Subject: [Gmod-gbrowse] establishing chado connections

 

I’m attempting to connect to Chado with Gbrowse 2.49.

 

My Gbrowse conf is at its defaults when installed with these edits:

[GENERAL]

db_adaptor           = Bio::DB::Das::Chado

db_args                     = -adaptor Bio::DB::Das::Chado

                     -dsn dbi:Pg:dbname=tripal;host=localhost

                     -user tripaldemo

                     -pass tripal2demo

psql= ALTER USER tripaldemo SET search_path TO chado;

config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF

htdocs_base            = /var/www/html/gbrowse2

url_base               = /gbrowse2

tmp_base               = /var/tmp/gbrowse2

persistent_base        = /var/lib/gbrowse2

userdata_base          = /var/lib/gbrowse2/userdata

db_base                = /var/www/cgi-bin/gb2/gbrowse

 

###############################################################################################

#

# DATASOURCE DEFINITIONS

# One stanza for each configured data source

#

###############################################################################################

 

[chado]

description   = Chado Database

path          = Chado.conf

 

My chado conf is:

[GENERAL]

description   = Chado database

database      = chado

 

initial landmark = chrI:143000..180000

plugins       = FilterTest RestrictionAnnotator TrackDumper FastaDumper

autocomplete  = 1

 

default tracks = Genes

                 ORFs

                 tRNAs

                 CDS

                 Transp

                 Centro:overview

                 GC:region

 

# examples to show in the introduction

examples = chrI

          chrII

          chrI:80,000..120,000

          "membrane trafficking"

          NUT21

          YAL063C

 

# "automatic" classes to try when an unqualified identifier is given

automatic classes = Symbol Gene Clone

 

#################################

# database definitions

#################################

 

[chado:database]

db_adaptor           = Bio::DB::Das::Chado

db_args                     = -adaptor Bio::DB::Das::Chado

                     -dsn dbi:Pg:dbname=tripal;host=localhost

                     -user tripaldemo

                     -pass tripal2demo

 

When I attempt to connect I get Undefined subroutine &DBD::Pg::db::_login called on the browser,

and my apache error log shows:

 

[Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Can't locate CGI/Toggle.pm in <at> INC ( <at> INC contains: /usr/lib/perl5/5.8.8 /usr/lib/perl5 /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 64, <DATA> line 192.

[Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 64, <DATA> line 192.

[Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Compilation failed in require at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192.

[Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] BEGIN failed--compilation aborted at /var/www/cgi-bin/gbrowse line 18, <DATA> line 192.

[Wed Jul 18 15:16:44 2012] [error] [client 66.249.72.81] Premature end of script headers: gbrowse

 

I appreciate any advice or help that can be given to solve this problem.

 

David Jeang

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