Dear Ram,
Thanks that worked, but still some more errors.
That Internal Server error is still there.
But the error log shows, these new errors,
-----
[Mon Jun 04 23:29:35 2012] [error] [client 127.0.0.1] Could not open database: , referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=30e3662bc0feae4a46b362acc815ee95
[Mon Jun 04 23:29:35 2012] [error] [client 127.0.0.1] ------------- EXCEPTION: Bio::Root::Exception -------------, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=30e3662bc0feae4a46b362acc815ee95
[Mon Jun 04 23:29:35 2012] [error] [client 127.0.0.1] MSG: Couldn't open /var/www/html/webgbrowse/gbrowse2/databases/30e3662bc0feae4a46b362acc815ee95: No such file or directory, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=30e3662bc0feae4a46b362acc815ee95
[Mon Jun 04 23:29:35 2012] [error] [client 127.0.0.1] STACK: Error::throw, referer: http://localhost/cgi-bin/webgbrowse/configureTracks?tsd=30e3662bc0feae4a46b362acc815ee95
Thanking you,
--
Prakhar Gaur
Sent on my BlackBerry® from Vodafone
-----Original Message-----
From: Ram Podicheti <mnrusimh@...>
Date: Mon, 4 Jun 2012 14:01:24
To: Prakhar Gaur<prakhar@...>
Cc: <gmod-webgbrowse@...>
Subject: Re: Local Installation of Webgbrowse: Internal Server Error on "Display in Gbrowse 2.0"
I think you set the value for $CONF2 to "/etc/gbrowse2/GBrowse.conf".
Try setting it to "/etc/gbrowse2"
Starting from GBrowse 2.0, GBrowse.conf is no longer a folder, but is a
file that has all the conf file mappings. Your conf folder needs to be
the gbrowse2 folder.
Prakhar Gaur wrote:
> Hello,
>
> I checked and double checked.
> The folder group is set to 'root' and I have set all permissions to full
> access.
> $ls -lh
> drwxrwxrwx. 7 ganit root 4.0K Jun 4 22:08 gbrowse2
>
> I have also added user "apache" to group "root".
> If this is not the way, then how to give apache access ?
>
> --
> Prakhar Gaur
>
>
> On Mon, 2012-06-04 at 12:32 -0400, Ram Podicheti wrote:
>
>> This looks to me like another permission issue. Can you please check if
>> apache has permissions to write to the folder
>>
>> /etc/gbrowse2/GBrowse.conf/
>>
>>
>> The program is trying to create a file
>> /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
>> not able to do so.
>>
>> Ram
>>
>>
>> Prakhar Gaur wrote:
>>
>>> Hello,
>>>
>>> On repeating the process, its still not working, getting the same
>>> Internal Server Error.
>>> The relevant line from the error log is below.
>>>
>>> [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
>>> exist: /var/www/html/favicon.ico
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
>>> conf
>>> file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
>>> at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
>>> referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
>>> of script headers: generateConfigurationData2.0, referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>>
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
>>>
>>>
>>>> Prakhar,
>>>> I am sorry for all these errors. Can you open your script
>>>>
>>>> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>
>>>> and go to line 160 and change it from
>>>>
>>>> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
>>>> $timeStampDigest
>>>>
>>>> to
>>>>
>>>> -location =>
>>>> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>>>>
>>>> I don't know how it is working on our server in the first place, but
>>>> using single quotes was obviously a bug. I will be fixing it in the
>>>> repository. Thanks for reporting these issues, they shouldn't have been
>>>> there but at least I am fixing them now. Do let me know if you run into
>>>> more issues.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> Prakhar Gaur wrote:
>>>>
>>>>
>>>>> Hello Ram,
>>>>>
>>>>> I just repeated the steps and then shecked the apache error and access
>>>>> log file.
>>>>> The error log file has 3 lines, pertaining to that period of time,
>>>>>
>>>>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
>>>>> exist: /var/www/html/favicon.ico
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
>>>>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>> line 160., referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
>>>>> of script headers: generateConfigurationData2.0, referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>>
>>>>>
>>>>> Thanking you,
>>>>> --
>>>>> Prakhar Gaur
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hi Prakhar,
>>>>>> I am not sure why you are getting the internal server error. There must
>>>>>> be a more useful error message apache must be spitting in the error.log
>>>>>> file. Can you verify that?
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>> Prakhar Gaur wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hello Ram,
>>>>>>>
>>>>>>> Thank you for the help.
>>>>>>> We have another issue now,
>>>>>>> Now I am getting the Configure Track web-page and am able to configure
>>>>>>> tracks.
>>>>>>>
>>>>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>>>>>> error" page.
>>>>>>> Please find the screen shot attached.
>>>>>>>
>>>>>>>
>>>>>>> The previous issue was due to the permissions on the tmp folder.
>>>>>>> I changed folder owner to "apache" and group to "root".
>>>>>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>>>>>
>>>>>>>
>>>>>>> Thanking you,
>>>>>>> --
>>>>>>> Prakhar Gaur
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>>>>>
>>>>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Podicheti, Ram [mailto:mnrusimh@...]
>>>>>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>>>>>> To: Prakhar Gaur; gmod-webgbrowse@...
>>>>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> There are two things that might be going wrong.
>>>>>>>>
>>>>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>>>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>>>>>> Fixing this should let your program run without any issues.
>>>>>>>>
>>>>>>>> 2. The file errorpage is not in the location specified.
>>>>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Prakhar Gaur [mailto:prakhar@...]
>>>>>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>>>>>> To: gmod-webgbrowse@...
>>>>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I have a local installation of WebGbrowse.
>>>>>>>>
>>>>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>>>>>> "
>>>>>>>> Not Found
>>>>>>>>
>>>>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>>>>>
>>>>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>>>>>> See the attached screenshot.
>>>>>>>>
>>>>>>>> Also the url bar has unusual content.
>>>>>>>> "http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>>>>>> 20denied"
>>>>>>>>
>>>>>>>> Is this the problem? Permission denied for what?
>>>>>>>>
>>>>>>>> Thanking you,
>>>>>>>> --
>>>>>>>> Prakhar Gaur
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Live Security Virtual Conference
>>>>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-webgbrowse mailing list
>>>>>>>> Gmod-webgbrowse@...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>>
>>>
>
>
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> Jun 2012 21:59:21 +0530
> Message-ID: <1338828748.23288.95.camel@...>
> Subject: Re: Local Installation of Webgbrowse: Internal Server Error on
> "Display in Gbrowse 2.0"
> From: Prakhar Gaur <prakhar@...>
> To: Ram Podicheti <mnrusimh@...>
> CC: <gmod-webgbrowse@...>
> Date: Mon, 4 Jun 2012 22:22:28 +0530
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>
> Hello,
>
> I checked and double checked.
> The folder group is set to 'root' and I have set all permissions to full
> access.
> $ls -lh
> drwxrwxrwx. 7 ganit root 4.0K Jun 4 22:08 gbrowse2
>
> I have also added user "apache" to group "root".
> If this is not the way, then how to give apache access ?
>
> --
> Prakhar Gaur
>
>
> On Mon, 2012-06-04 at 12:32 -0400, Ram Podicheti wrote:
>
>> This looks to me like another permission issue. Can you please check if
>> apache has permissions to write to the folder
>>
>> /etc/gbrowse2/GBrowse.conf/
>>
>>
>> The program is trying to create a file
>> /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf, but is
>> not able to do so.
>>
>> Ram
>>
>>
>> Prakhar Gaur wrote:
>>
>>> Hello,
>>>
>>> On repeating the process, its still not working, getting the same
>>> Internal Server Error.
>>> The relevant line from the error log is below.
>>>
>>> [Mon Jun 04 21:31:37 2012] [error] [client 192.168.1.18] File does not
>>> exist: /var/www/html/favicon.ico
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Unable to open
>>> conf
>>> file /etc/gbrowse2/GBrowse.conf/4a18d1e85e6e4d6d27537e91d56063a0.conf
>>> at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0 line 50.,
>>> referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>> [Mon Jun 04 21:33:00 2012] [error] [client 192.168.1.18] Premature end
>>> of script headers: generateConfigurationData2.0, referer:
>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=4a18d1e85e6e4d6d27537e91d56063a0
>>>
>>>
>>>
>>> Thanking you,
>>> --
>>> Prakhar Gaur
>>>
>>>
>>>
>>> On Mon, 2012-06-04 at 11:57 -0400, Ram Podicheti wrote:
>>>
>>>
>>>> Prakhar,
>>>> I am sorry for all these errors. Can you open your script
>>>>
>>>> /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>
>>>> and go to line 160 and change it from
>>>>
>>>> -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
>>>> $timeStampDigest
>>>>
>>>> to
>>>>
>>>> -location =>
>>>> "http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/$timeStampDigest"
>>>>
>>>> I don't know how it is working on our server in the first place, but
>>>> using single quotes was obviously a bug. I will be fixing it in the
>>>> repository. Thanks for reporting these issues, they shouldn't have been
>>>> there but at least I am fixing them now. Do let me know if you run into
>>>> more issues.
>>>>
>>>> Thanks,
>>>>
>>>> Ram
>>>>
>>>> Prakhar Gaur wrote:
>>>>
>>>>
>>>>> Hello Ram,
>>>>>
>>>>> I just repeated the steps and then shecked the apache error and access
>>>>> log file.
>>>>> The error log file has 3 lines, pertaining to that period of time,
>>>>>
>>>>> [Mon Jun 04 20:50:45 2012] [error] [client 192.168.1.18] File does not
>>>>> exist: /var/www/html/favicon.ico
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Bad name after
>>>>> SERVER_NAME' at /var/www/cgi-bin/webgbrowse/generateConfigurationData2.0
>>>>> line 160., referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>> [Mon Jun 04 20:52:59 2012] [error] [client 192.168.1.18] Premature end
>>>>> of script headers: generateConfigurationData2.0, referer:
>>>>> http://192.168.1.177/cgi-bin/webgbrowse/configureTracks?tsd=d541239166a7a53a5d7d67ffeddfff2b
>>>>>
>>>>>
>>>>> Thanking you,
>>>>> --
>>>>> Prakhar Gaur
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 2012-06-04 at 11:17 -0400, Ram Podicheti wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hi Prakhar,
>>>>>> I am not sure why you are getting the internal server error. There must
>>>>>> be a more useful error message apache must be spitting in the error.log
>>>>>> file. Can you verify that?
>>>>>> Thanks,
>>>>>>
>>>>>> Ram
>>>>>>
>>>>>> Prakhar Gaur wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hello Ram,
>>>>>>>
>>>>>>> Thank you for the help.
>>>>>>> We have another issue now,
>>>>>>> Now I am getting the Configure Track web-page and am able to configure
>>>>>>> tracks.
>>>>>>>
>>>>>>> But when I click "Display In Gbrowse2.0", I get an "internal server
>>>>>>> error" page.
>>>>>>> Please find the screen shot attached.
>>>>>>>
>>>>>>>
>>>>>>> The previous issue was due to the permissions on the tmp folder.
>>>>>>> I changed folder owner to "apache" and group to "root".
>>>>>>> The tarball was downloaded from the Webgbrowse website, last week.
>>>>>>>
>>>>>>>
>>>>>>> Thanking you,
>>>>>>> --
>>>>>>> Prakhar Gaur
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Mon, 2012-06-04 at 12:50 +0000, Podicheti, Ram wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> It was in the svn repository. I am updating it now. However, you can handle it by making a small change in the scripts you already downloaded.
>>>>>>>>
>>>>>>>> Go to line number 167 in the file WebGB.pm. Change the line:
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/ errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> to
>>>>>>>>
>>>>>>>> return $q->redirect("/cgi-bin/webgbrowse/errorpage?status=$status&msg=$msg");
>>>>>>>>
>>>>>>>> That should fix the "page not found" part. However, you still need to check the permissions for your TMP folder.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Podicheti, Ram [mailto:mnrusimh@...]
>>>>>>>> Sent: Monday, June 04, 2012 8:39 AM
>>>>>>>> To: Prakhar Gaur; gmod-webgbrowse@...
>>>>>>>> Subject: Re: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hi Prakhar,
>>>>>>>> There are two things that might be going wrong.
>>>>>>>>
>>>>>>>> 1. The directory you indicated as $TMP in the WebGB.pm should allow WebGBrowse to create a tmp folder in it.
>>>>>>>> Open the file WebGB.pm and check the path listed for $TMP under "Server Settings" section.
>>>>>>>> Ensure that this folder exists and it has write permissions for Apache.
>>>>>>>> Fixing this should let your program run without any issues.
>>>>>>>>
>>>>>>>> 2. The file errorpage is not in the location specified.
>>>>>>>> This is a known error and it was fixed. Can you tell me where from did you download WebGBrowse? Is it the tar ball or the sourceforge svn? I think, the fix wasn't updated on one of these.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Ram
>>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>> From: Prakhar Gaur [mailto:prakhar@...]
>>>>>>>> Sent: Monday, June 04, 2012 5:18 AM
>>>>>>>> To: gmod-webgbrowse@...
>>>>>>>> Subject: [Gmod-webgbrowse] Local Installation of Webgbrowse: Error with configureTracks: Permission Denied
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I have a local installation of WebGbrowse.
>>>>>>>>
>>>>>>>> The upload data page is working, but when I select the test gff3 file and click submit button, this msg is displayed.
>>>>>>>> "
>>>>>>>> Not Found
>>>>>>>>
>>>>>>>> The requested URL /cgi-bin/errorpage was not found on this server.
>>>>>>>>
>>>>>>>> Apache/2.2.22 (Fedora) Server at 192.168.1.177 Port 80 "
>>>>>>>> See the attached screenshot.
>>>>>>>>
>>>>>>>> Also the url bar has unusual content.
>>>>>>>> "http://192.168.1.177/cgi-bin/errorpage?status=2&msg=Permission%
>>>>>>>> 20denied"
>>>>>>>>
>>>>>>>> Is this the problem? Permission denied for what?
>>>>>>>>
>>>>>>>> Thanking you,
>>>>>>>> --
>>>>>>>> Prakhar Gaur
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Live Security Virtual Conference
>>>>>>>> Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-webgbrowse mailing list
>>>>>>>> Gmod-webgbrowse@...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>>
>>>
>
>
>
|