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500 Internal Server Error

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Nicolae Herndon

500 Internal Server Error

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

Ram Podicheti-2

Re: 500 Internal Server Error

Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:

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

Nicolae Herndon

Re: 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

Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.

On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:

Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:
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

Nicolae Herndon

Re: 500 Internal Server Error

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

Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.

On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:

Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:
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

error.log (21K) Download Attachment

uploadData (17K) Download Attachment

WebGB.pm (8K) Download Attachment

Ram Podicheti-2

Re: 500 Internal Server Error

<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:

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
Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.
On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:
Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:
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
<error.log><uploadData><WebGB.pm>

Nicolae Herndon

Re: 500 Internal Server Error

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

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';

Please let me know if this helps.

Thanks,

Ram

On Apr 16, 2013, at 2:28 PM, Nic Herndon wrote:

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
Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.
On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:
Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:
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
<error.log><uploadData><WebGB.pm>

GFFData.pm (9K) Download Attachment

Exceptions.pm (2K) Download Attachment

Ram Podicheti-2

Re: 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:

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.pmand /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:

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

Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.

On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:

Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:

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

<error.log><uploadData><WebGB.pm>

<GFFData.pm><Exceptions.pm>

Nicolae Herndon

Re: 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

Ram

On Apr 17, 2013, at 3:33 PM, Nic Herndon wrote:

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.pmand /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:
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
Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.
On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:
Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:
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
<error.log><uploadData><WebGB.pm>
<GFFData.pm><Exceptions.pm>

Nicolae Herndon

Re: 500 Internal Server Error

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

Ram

On Apr 17, 2013, at 3:33 PM, Nic Herndon wrote:

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.pmand /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:
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
Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.
On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:
Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:
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
<error.log><uploadData><WebGB.pm>
<GFFData.pm><Exceptions.pm>

Scott Cain

Re: 500 Internal Server Error

Yes, but is /usr/local/lib/... in Apache's @INC? I bet not. Look at mod_env:

http://httpd.apache.org/docs/2.2/mod/mod_env.html

So that you can use SetEnv in you apache config to set the PERL5LIB to include it.

Scott

On Wed, Apr 17, 2013 at 3:52 PM, Nic Herndon <[hidden email]> wrote:

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:
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.pmand /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:
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
Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.
On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:
Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:
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
<error.log><uploadData><WebGB.pm>
<GFFData.pm><Exceptions.pm>
------------------------------------------------------------------------------
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

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

Nicolae Herndon

Re: 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:

http://httpd.apache.org/docs/2.2/mod/mod_env.html

So that you can use SetEnv in you apache config to set the PERL5LIB to include it.

Scott

On Wed, Apr 17, 2013 at 3:52 PM, Nic Herndon <[hidden email]> wrote:

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:
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.pmand /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:
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
Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.
On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:
Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:
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!
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_______________________________________________
Gmod-webgbrowse mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
<error.log><uploadData><WebGB.pm>
<GFFData.pm><Exceptions.pm>
------------------------------------------------------------------------------
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
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https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse

Nicolae Herndon

Re: 500 Internal Server Error

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?

Yes, but is /usr/local/lib/... in Apache's @INC? I bet not. Look at mod_env:

http://httpd.apache.org/docs/2.2/mod/mod_env.html

So that you can use SetEnv in you apache config to set the PERL5LIB to include it.

Scott

On Wed, Apr 17, 2013 at 3:52 PM, Nic Herndon <[hidden email]> wrote:

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:
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.pmand /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:
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
Can't locate WebGB.pm in @INC
BEGIN failed--compilation aborted at /usr/lib/cgi-bin/webgbrowse/uploadData line 9.
On Apr 16, 2013, at 9:59 AM, Ram Podicheti <[hidden email]> wrote:
Hi Nic,
Can you provide me the message in apache error log?
Thanks,

Ram

On 04/15/2013 01:54 PM, Nic Herndon wrote:
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
<error.log><uploadData><WebGB.pm>
<GFFData.pm><Exceptions.pm>
------------------------------------------------------------------------------
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