I setup WebGBrowse but when I try to test it (@ http://localhost/webgbrowse/ it redirects me to http://localhost/cgi-bin/webgbrowse/uploadData where) I get the 500 Internal Sever Error page. There's only GBrowse 2.0 installed on the server. The Server Settings in WebGB.pm are: our @GBR_VER = ("1.70", "2.0"); our $TMP = '/usr/lib/tmp'; our $YAML_LIB = '/usr/lib/files/yamlib'; our $SEND_MAIL = '/usr/sbin/sendmail'; our $CONF = ''; our $WWW = '/var/www'; our $WWW2 = '/var/lib'; our $CONF2 = '/etc/gbrowse2'; The databases have write permission for the apache user: $ ls -lh /var/lib/gbrowse2/databases total 40K drwxr-xr-x 2 www-data www-data 4.0K Apr 9 14:40 admin_uploads drwxr-xr-x 5 www-data www-data 4.0K Apr 9 14:40 gbrowse_syn drwxr-xr-x 2 www-data www-data 4.0K Apr 9 14:40 ideograms drwxr-xr-x 2 www-data www-data 4.0K Apr 9 14:40 pop_demo -rw-r--r-- 1 www-data www-data 16K Apr 9 14:40 users.sqlite drwxr-xr-x 2 www-data www-data 4.0K Apr 9 14:40 yeast_chr1+2 drwxr-xr-x 2 www-data www-data 4.0K Apr 9 14:40 yeast_scaffolds How can I address this issue? Nic ------------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
Hi Nic,
Can you provide me the message in apache error log? Thanks, Ram On 04/15/2013 01:54 PM, Nic Herndon wrote:
------------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
I'm away from that machine right now and it's turned off. I can send you the error log later today. The error message is
------------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
Attached is the log file and a couple of files I modified. From: "Nicolae Herndon" <[hidden email]> To: "Ram Podicheti" <[hidden email]> Cc: [hidden email] Sent: Tuesday, April 16, 2013 10:07:47 AM Subject: Re: [Gmod-webgbrowse] 500 Internal Server Error I'm away from that machine right now and it's turned off. I can send you the error log later today. The error message is
------------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse ![]() ![]() ![]() |
<base href="x-msg://14/">
Nic,
I see the problem is with the detection of the location of the WebGBrowse modules. The CGI scripts have a line in them that reads
use lib '../../lib';
where the "lib" folder is expected to have all the WebGB perl modules (a folder WebGB and its contents and the WebGB.pm file). The solution would be to make the lib folder available at the above location relative to the cgi-bin folder or to alter the use
lib line in each of the cgi scripts.
Please let me know if this helps.
Thanks,
Ram
On Apr 16, 2013, at 2:28 PM, Nic Herndon wrote:
------------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
Oh, if it was only that easy. After I commented out the use lib '../../lib' line and added on the next line use lib '/usr/lib' in all files in /usr/lib/cgi-bin/webgbrowse/, the contents of /var/log/apache2/error.log are: [Wed Apr 17 06:29:16 2013] [notice] Apache/2.2.22 (Ubuntu) mod_fcgid/2.3.6 mod_perl/2.0.5 Perl/v5.14.2 configured -- resuming normal operations Can't locate Exception/Class.pm in @INC (@INC contains: /usr/lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/lib/WebGB/Exceptions.pm line 48. BEGIN failed--compilation aborted at /usr/lib/WebGB/Exceptions.pm line 48. Compilation failed in require at /usr/lib/WebGB/GFFData.pm line 17. BEGIN failed--compilation aborted at /usr/lib/WebGB/GFFData.pm line 17. Compilation failed in require at /usr/lib/cgi-bin/webgbrowse/uploadData line 11. BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 11. [Wed Apr 17 14:05:44 2013] [error] [client myClient] Premature end of script headers: uploadData, referer: http://localhost/webgbrowse/ [Wed Apr 17 14:05:44 2013] [error] [client myClient] File does not exist: /var/www/favicon.ico, referer: http://localhost/cgi-bin/webgbrowse/uploadData Can't locate Exception/Class.pm in @INC (@INC contains: /usr/lib /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/lib/WebGB/Exceptions.pm line 48. BEGIN failed--compilation aborted at /usr/lib/WebGB/Exceptions.pm line 48. Compilation failed in require at /usr/lib/WebGB/GFFData.pm line 17. BEGIN failed--compilation aborted at /usr/lib/WebGB/GFFData.pm line 17. Compilation failed in require at /usr/lib/cgi-bin/webgbrowse/uploadData line 11. BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 11. [Wed Apr 17 14:19:24 2013] [error] [client myClient] Premature end of script headers: uploadData, referer: http://localhost/webgbrowse/ This would suggest to me that the issue is with /usr/lib/WebGB/Exceptions.pm. Attached are copies of /usr/lib/WebGB/GFFData.pm and /usr/lib/WebGB/Exceptions.pm. Any other suggestions? From: "Ram Podicheti" <[hidden email]> To: "Nic Herndon" <[hidden email]> Cc: "<[hidden email]>" <[hidden email]> Sent: Wednesday, April 17, 2013 2:00:54 PM Subject: Re: [Gmod-webgbrowse] 500 Internal Server Error Nic, I see the problem is with the detection of the location of the WebGBrowse modules. The CGI scripts have a line in them that reads
use lib '../../lib';
where the "lib" folder is expected to have all the WebGB perl modules (a folder WebGB and its contents and the WebGB.pm file). The solution would be to make the lib folder available at the above location relative to the cgi-bin folder or to alter the use
lib line in each of the cgi scripts.
Please let me know if this helps.
Thanks,
Ram
On Apr 16, 2013, at 2:28 PM, Nic Herndon wrote:
------------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
<base href="x-msg://26/">
You need to install Exception::Class (http://search.cpan.org/~drolsky/Exception-Class-1.37/lib/Exception/Class.pm) on your system. This modules helps define custom
exceptions in perl. Please let me know if this resolves the issue.
Ram
On Apr 17, 2013, at 3:33 PM, Nic Herndon wrote:
------------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
It's already installed. cpan[1]> i Exception::Class Module id = Exception::Class DESCRIPTION Declare exception class hierarchies CPAN_USERID DROLSKY (Dave Rolsky <[hidden email]>) CPAN_VERSION 1.37 CPAN_FILE D/DR/DROLSKY/Exception-Class-1.37.tar.gz UPLOAD_DATE 2013-02-24 DSLIP_STATUS RdpOp (released,developer,perl,object-oriented,Standard-Perl) MANPAGE Exception::Class - A module that allows you to declare real exception classes in Perl INST_FILE /usr/local/lib/perl5/site_perl/5.17.4/Exception/Class.pm INST_VERSION 1.37 From: "Ram Podicheti" <[hidden email]> To: "Nic Herndon" <[hidden email]> Cc: "gmod-webgbrowse" <[hidden email]> Sent: Wednesday, April 17, 2013 2:42:49 PM Subject: Re: [Gmod-webgbrowse] 500 Internal Server Error You need to install Exception::Class (http://search.cpan.org/~drolsky/Exception-Class-1.37/lib/Exception/Class.pm) on your system. This modules helps define custom
exceptions in perl. Please let me know if this resolves the issue.
Ram
On Apr 17, 2013, at 3:33 PM, Nic Herndon wrote:
------------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
Also $ perl -e "print \"@INC\"" /usr/local/lib/perl5/site_perl/5.17.4/x86_64-linux /usr/local/lib/perl5/site_perl/5.17.4 /usr/local/lib/perl5/5.17.4/x86_64-linux /usr/local/lib/perl5/5.17.4 . From: "Nic Herndon" <[hidden email]> To: "Ram Podicheti" <[hidden email]> Cc: "gmod-webgbrowse" <[hidden email]> Sent: Wednesday, April 17, 2013 2:49:55 PM Subject: Re: [Gmod-webgbrowse] 500 Internal Server Error It's already installed. cpan[1]> i Exception::Class Module id = Exception::Class DESCRIPTION Declare exception class hierarchies CPAN_USERID DROLSKY (Dave Rolsky <[hidden email]>) CPAN_VERSION 1.37 CPAN_FILE D/DR/DROLSKY/Exception-Class-1.37.tar.gz UPLOAD_DATE 2013-02-24 DSLIP_STATUS RdpOp (released,developer,perl,object-oriented,Standard-Perl) MANPAGE Exception::Class - A module that allows you to declare real exception classes in Perl INST_FILE /usr/local/lib/perl5/site_perl/5.17.4/Exception/Class.pm INST_VERSION 1.37 From: "Ram Podicheti" <[hidden email]> To: "Nic Herndon" <[hidden email]> Cc: "gmod-webgbrowse" <[hidden email]> Sent: Wednesday, April 17, 2013 2:42:49 PM Subject: Re: [Gmod-webgbrowse] 500 Internal Server Error You need to install Exception::Class (http://search.cpan.org/~drolsky/Exception-Class-1.37/lib/Exception/Class.pm) on your system. This modules helps define custom
exceptions in perl. Please let me know if this resolves the issue.
Ram
On Apr 17, 2013, at 3:33 PM, Nic Herndon wrote:
------------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
Yes, but is /usr/local/lib/... in Apache's @INC? I bet not. Look at mod_env: So that you can use SetEnv in you apache config to set the PERL5LIB to include it.http://httpd.apache.org/docs/2.2/mod/mod_env.html On Wed, Apr 17, 2013 at 3:52 PM, Nic Herndon <[hidden email]> wrote:
-- ------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
How can I check/change the contents of Apache's @INC? From: "Scott Cain" <[hidden email]> To: "Nic Herndon" <[hidden email]> Cc: "Ram Podicheti" <[hidden email]>, "gmod-webgbrowse" <[hidden email]> Sent: Wednesday, April 17, 2013 2:56:50 PM Subject: Re: [Gmod-webgbrowse] 500 Internal Server Error Yes, but is /usr/local/lib/... in Apache's @INC? I bet not. Look at mod_env: So that you can use SetEnv in you apache config to set the PERL5LIB to include it.http://httpd.apache.org/docs/2.2/mod/mod_env.html On Wed, Apr 17, 2013 at 3:52 PM, Nic Herndon <[hidden email]> wrote:
-- ------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
I added SetEnv PERL5LIB /usr/local/lib/perl5/site_perl/5.17.4 to /etc/apache2/httpd.conf, restarted Apache and now http://localhost/cgi-bin/webgbrowse/uploadData loads fine. Thank you, Nic From: "Nic Herndon" <[hidden email]> To: "Scott Cain" <[hidden email]> Cc: "Ram Podicheti" <[hidden email]>, "gmod-webgbrowse" <[hidden email]> Sent: Wednesday, April 17, 2013 3:08:12 PM Subject: Re: [Gmod-webgbrowse] 500 Internal Server Error How can I check/change the contents of Apache's @INC? From: "Scott Cain" <[hidden email]> To: "Nic Herndon" <[hidden email]> Cc: "Ram Podicheti" <[hidden email]>, "gmod-webgbrowse" <[hidden email]> Sent: Wednesday, April 17, 2013 2:56:50 PM Subject: Re: [Gmod-webgbrowse] 500 Internal Server Error Yes, but is /usr/local/lib/... in Apache's @INC? I bet not. Look at mod_env: So that you can use SetEnv in you apache config to set the PERL5LIB to include it.http://httpd.apache.org/docs/2.2/mod/mod_env.html On Wed, Apr 17, 2013 at 3:52 PM, Nic Herndon <[hidden email]> wrote:
-- ------------------------------------------------------------------------ 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-webgbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse |
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