gbrowse doesn't display my new config dataset

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gbrowse doesn't display my new config dataset

JINGJING JIN-2
Dear all,

I have run successfully on the test dataset.

However, after I load my own dataset into mysql database using
bp_sequence_load.

When I try to access it on network,
http://localhost/cgi-bin/gb2/gbrowse/oilpalm
it display The server encountered an internal error or misconfiguration and
was unable to complete your request.

I have checked the access log about apache, it is about:

::1 - - [08/Apr/2013:19:47:48 -0400] "GET /cgi-bin/gb2/gbrowse/oilpalm
HTTP/1.1" 500 631 "-" "Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:19.0)
Gecko/20100101 Firefox/19.0"

The error about apache is about:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: syntax error at line 75: '['
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472
STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_feature
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:629
STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_indexed_feature
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:616
STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::handle_feature
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:491
STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::load_line
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:430
STACK: Bio::Graphics::FeatureFile::parse_data_line
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:904
STACK: Bio::Graphics::FeatureFile::parse_line
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:822
STACK: Bio::Graphics::FeatureFile::parse_fh
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:773
STACK: Bio::Graphics::FeatureFile::parse_file
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:760
STACK: Bio::Graphics::FeatureFile::_new
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:395
STACK: Bio::Graphics::FeatureFile::new_from_cache
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:443
STACK: Bio::Graphics::Browser2::DataSource::new
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm:67
STACK: Bio::Graphics::Browser2::create_data_source
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2.pm:390
STACK: Bio::Graphics::Browser2::Render::new
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:74
STACK: /usr/lib/cgi-bin/gb2/gbrowse:56
-----------------------------------------------------------
[Mon Apr 08 19:47:49 2013] [error] [client ::1] Premature end of script
headers: gbrowse

In fact, after I load my dataset into mysql, i have already added

[oilpalm]
description  = oilpalm database
path         = oilpalm.conf

to the Gbrowse.conf file.

The database information in oilpalm.conf is like this:

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn     oilpalm
                -user    nobody

Can anyone give me some suggestion about how to fix this problem?

Thanks!

JIngjing





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Re: gbrowse doesn't display my new config dataset

Scott Cain
Hi Jingjing,

My initial guess is that you've got a syntax error in your oilpalm configuration file, probably on or about line 75 based on the error message in your error message.  You didn't send your whole configuration file, so I can't say for sure.

Scott



On Tue, Apr 9, 2013 at 12:50 AM, jjjscuedu <[hidden email]> wrote:
Dear all,

I have run successfully on the test dataset.

However, after I load my own dataset into mysql database using
bp_sequence_load.

When I try to access it on network,
http://localhost/cgi-bin/gb2/gbrowse/oilpalm
it display The server encountered an internal error or misconfiguration and
was unable to complete your request.

I have checked the access log about apache, it is about:

::1 - - [08/Apr/2013:19:47:48 -0400] "GET /cgi-bin/gb2/gbrowse/oilpalm
HTTP/1.1" 500 631 "-" "Mozilla/5.0 (X11; Ubuntu; Linux i686; rv:19.0)
Gecko/20100101 Firefox/19.0"

The error about apache is about:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: syntax error at line 75: '['
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472
STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_feature
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:629
STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_indexed_feature
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:616
STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::handle_feature
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:491
STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::load_line
/usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm:430
STACK: Bio::Graphics::FeatureFile::parse_data_line
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:904
STACK: Bio::Graphics::FeatureFile::parse_line
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:822
STACK: Bio::Graphics::FeatureFile::parse_fh
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:773
STACK: Bio::Graphics::FeatureFile::parse_file
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:760
STACK: Bio::Graphics::FeatureFile::_new
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:395
STACK: Bio::Graphics::FeatureFile::new_from_cache
/usr/local/share/perl/5.10.1/Bio/Graphics/FeatureFile.pm:443
STACK: Bio::Graphics::Browser2::DataSource::new
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/DataSource.pm:67
STACK: Bio::Graphics::Browser2::create_data_source
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2.pm:390
STACK: Bio::Graphics::Browser2::Render::new
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:74
STACK: /usr/lib/cgi-bin/gb2/gbrowse:56
-----------------------------------------------------------
[Mon Apr 08 19:47:49 2013] [error] [client ::1] Premature end of script
headers: gbrowse

In fact, after I load my dataset into mysql, i have already added

[oilpalm]
description  = oilpalm database
path         = oilpalm.conf

to the Gbrowse.conf file.

The database information in oilpalm.conf is like this:

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                -dsn     oilpalm
                -user    nobody

Can anyone give me some suggestion about how to fix this problem?

Thanks!

JIngjing





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View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/gbrowse-doesn-t-display-my-new-config-dataset-tp5711080.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
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--
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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

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse