Re: [galaxy-dev] Upload issue in local installation

2012-10-23 Thread Nate Coraor
On Oct 23, 2012, at 10:06 AM, Peter Briggs wrote:

> In case this is of use to someone else: I've been experiencing a 
> similar-sounding issue to that described below - the symptoms were that only 
> very small (e.g. 40kb) files could be uploaded successfully.
> 
> The problem seemed to be caused by the SecRequestBodyLimit directive in 
> Apache's mod_security.conf file putting a very low limit on the size of 
> files. The fix (for me) was simply to up the limit to something more 
> appropriate.

Hi Peter,

Thanks for finding this, I've added this information to our documentation.

--nate

> 
> Disabling the ajax uploads as described by Dan didn't fix the problem but it 
> did make the source more obvious, as Galaxy immediately reported the error 
> message "413 Request Entity Too Large" (with the clue about mod_security 
> turning up in the Apache log).
> 
> I don't think this is the same problem as previously reported but maybe this 
> info will help someone else.
> 
> Best wishes
> 
> Peter
> 
> On 03/08/12 14:58, David Roquis wrote:
>> Hi Dan,
>> 
>> It works like a charm! Thanks a lot! I have been looking for a
>> workaround for this issue for almost a month!
>> 
>> Once again, thanks you so much!
>> 
>> David
>> 
>> 
>> 
>> Subject: Re: [galaxy-dev] Upload issue in local installation
>> From: d...@bx.psu.edu
>> Date: Fri, 3 Aug 2012 09:24:43 -0400
>> CC: bat...@gmail.com; galaxy-dev@lists.bx.psu.edu
>> To: david_roq...@hotmail.com
>> 
>> Hi David and Bastal,
>> 
>> We have been able to reproduce this behavior under certain conditions
>> and are working on a fix. Until this fix is available, you can disable
>> ajax uploads, which should allow the upload tool to work properly.
>> In tools/data_source/upload.xml change
>> 
>> > ajax-upload="true" help="TIP: Due to browser limitations, uploading
>> files larger than 2GB is guaranteed to fail.  To upload large files, use
>> the URL method (below) or FTP (if enabled by the site administrator).">
>> 
>> to
>> 
>> > ajax-upload="False" help="TIP: Due to browser limitations, uploading
>> files larger than 2GB is guaranteed to fail.  To upload large files, use
>> the URL method (below) or FTP (if enabled by the site administrator).">
>> 
>> 
>> Please let us know if this workaround doesn't work for you.
>> 
>> 
>> Thanks for using Galaxy,
>> 
>> Dan
>> 
>> 
>> On Aug 3, 2012, at 4:20 AM, David Roquis wrote:
>> 
>>Hi Batsal,
>> 
>>I have the exact same problem, on 2 different instances of Galaxy,
>>on two different servers. I can replicate this problem on a cloned
>>instance with no modification, and one using multiple galaxay
>>server, nginx proxy and postgresql, both instances being on
>>different machines (one on fedora 13, the other one on fedora 17).
>> From what I have seen, it seems to be browser related. I can
>>sometimes (rarely) upload data with firefox, chrome or safary, but
>>for me it has worked ALL the time using internet explorer 8/9. The
>>thing is that when you start the upload, the browser shows you that
>>it is uploaded, but the upload.py script is never launched, and
>>hence, the upload seems to be running forever. Seems we are not the
>>only ones with this problem, but no real solution until now.
>> 
>>Two options for you at the moment
>>- try using IE 8/9 to upload the data
>>- upload your data using data libraries under the admin menu (this
>>works on any browser).
>> 
>>Keep me in touch if you find a solution
>> 
>>David
>> 
>> 
>> 
>>> From:bat...@gmail.com <mailto:bat...@gmail.com>
>>> Date: Thu, 2 Aug 2012 15:48:40 -0400
>>> To:galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
>>> Subject: [galaxy-dev] Upload issue in local installation
>>>
>>> I installed galaxy locally in a linux server. However, I cannot upload 
>> the files (no matter how small, I have tried few kb size fasta files). When 
>> I try to upload, the link to the file shows up in the History and gets a new 
>> number (purple box). When I click on the link I get 'Dataset is uploading' 
>> forever.
>>>
>>> In the terminal window where I start galaxy, I get the following error 
>>

Re: [galaxy-dev] Upload issue in local installation

2012-10-23 Thread Peter Briggs
In case this is of use to someone else: I've been experiencing a 
similar-sounding issue to that described below - the symptoms were that 
only very small (e.g. 40kb) files could be uploaded successfully.


The problem seemed to be caused by the SecRequestBodyLimit directive in 
Apache's mod_security.conf file putting a very low limit on the size of 
files. The fix (for me) was simply to up the limit to something more 
appropriate.


Disabling the ajax uploads as described by Dan didn't fix the problem 
but it did make the source more obvious, as Galaxy immediately reported 
the error message "413 Request Entity Too Large" (with the clue about 
mod_security turning up in the Apache log).


I don't think this is the same problem as previously reported but maybe 
this info will help someone else.


Best wishes

Peter

On 03/08/12 14:58, David Roquis wrote:

Hi Dan,

It works like a charm! Thanks a lot! I have been looking for a
workaround for this issue for almost a month!

Once again, thanks you so much!

David


------------
Subject: Re: [galaxy-dev] Upload issue in local installation
From: d...@bx.psu.edu
Date: Fri, 3 Aug 2012 09:24:43 -0400
CC: bat...@gmail.com; galaxy-dev@lists.bx.psu.edu
To: david_roq...@hotmail.com

Hi David and Bastal,

We have been able to reproduce this behavior under certain conditions
and are working on a fix. Until this fix is available, you can disable
ajax uploads, which should allow the upload tool to work properly.
In tools/data_source/upload.xml change



to




Please let us know if this workaround doesn't work for you.


Thanks for using Galaxy,

Dan


On Aug 3, 2012, at 4:20 AM, David Roquis wrote:

Hi Batsal,

I have the exact same problem, on 2 different instances of Galaxy,
on two different servers. I can replicate this problem on a cloned
instance with no modification, and one using multiple galaxay
server, nginx proxy and postgresql, both instances being on
different machines (one on fedora 13, the other one on fedora 17).
 From what I have seen, it seems to be browser related. I can
sometimes (rarely) upload data with firefox, chrome or safary, but
for me it has worked ALL the time using internet explorer 8/9. The
thing is that when you start the upload, the browser shows you that
it is uploaded, but the upload.py script is never launched, and
hence, the upload seems to be running forever. Seems we are not the
only ones with this problem, but no real solution until now.

Two options for you at the moment
- try using IE 8/9 to upload the data
- upload your data using data libraries under the admin menu (this
works on any browser).

Keep me in touch if you find a solution

David



> From:bat...@gmail.com <mailto:bat...@gmail.com>
> Date: Thu, 2 Aug 2012 15:48:40 -0400
> To:galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>
> Subject: [galaxy-dev] Upload issue in local installation
>
> I installed galaxy locally in a linux server. However, I cannot upload 
the files (no matter how small, I have tried few kb size fasta files). When I try 
to upload, the link to the file shows up in the History and gets a new number 
(purple box). When I click on the link I get 'Dataset is uploading' forever.
>
> In the terminal window where I start galaxy, I get the following error 
report:
>
> 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" 
"Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - 
"http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - 
"http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - 
"http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 
200 - "http://redhat:8080/root/tool_menu"; "Mozilla/5.0 (Windows NT 5.2;
rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create 
HTTP/1.1" 200 - "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0)
Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message 
HTTP/1.1" 200 - &quo

Re: [galaxy-dev] Upload issue in local installation

2012-08-03 Thread David Roquis

Hi Dan,

It works like a charm! Thanks a lot! I have been looking for a workaround for 
this issue for almost a month!

Once again, thanks you so much!

David


Subject: Re: [galaxy-dev] Upload issue in local installation
From: d...@bx.psu.edu
Date: Fri, 3 Aug 2012 09:24:43 -0400
CC: bat...@gmail.com; galaxy-dev@lists.bx.psu.edu
To: david_roq...@hotmail.com

Hi David and Bastal,
We have been able to reproduce this behavior under certain conditions and are 
working on a fix. Until this fix is available, you can disable ajax uploads, 
which should allow the upload tool to work properly.In 
tools/data_source/upload.xml change

to


Please let us know if this workaround doesn't work for you.

Thanks for using Galaxy,
Dan

On Aug 3, 2012, at 4:20 AM, David Roquis wrote:Hi Batsal,

I have the exact same problem, on 2 different instances of Galaxy, on two 
different servers. I can replicate this problem on a cloned instance with no 
modification, and one using multiple galaxay server, nginx proxy and 
postgresql, both instances being on different machines (one on fedora 13, the 
other one on fedora 17). From what I have seen, it seems to be browser related. 
I can sometimes (rarely) upload data with firefox, chrome or safary, but for me 
it has worked ALL the time using internet explorer 8/9. The thing is that when 
you start the upload, the browser shows you that it is uploaded, but the 
upload.py script is never launched, and hence, the upload seems to be running 
forever. Seems we are not the only ones with this problem, but no real solution 
until now.

Two options for you at the moment
- try using IE 8/9 to upload the data
- upload your data using data libraries under the admin menu (this works on any 
browser).

Keep me in touch if you find a solution

David



> From: bat...@gmail.com
> Date: Thu, 2 Aug 2012 15:48:40 -0400
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] Upload issue in local installation
> 
> I installed galaxy locally in a linux server. However, I cannot upload the 
> files (no matter how small, I have tried few kb size fasta files). When I try 
> to upload, the link to the file shows up in the History and gets a new number 
> (purple box). When I click on the link I get 'Dataset is uploading' forever. 
> 
> In the terminal window where I start galaxy, I get the following error report:
> 
> 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" 
> "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 
> 200 - "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) 
> Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - 
> "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 
> Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage 
> HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET 
> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - 
> "http://redhat:8080/root/tool_menu"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) 
> Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST 
> /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/"; 
> "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET 
> /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/"; 
> "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - 
> "http://redhat:8080/tool_runner/upload_async_message"; "Mozilla/5.0 (Windows 
> NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage 
> HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates 
> HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates 
> HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 
> 
> The last line

Re: [galaxy-dev] Upload issue in local installation

2012-08-03 Thread Daniel Blankenberg
Hi David and Bastal,

We have been able to reproduce this behavior under certain conditions and are 
working on a fix. Until this fix is available, you can disable ajax uploads, 
which should allow the upload tool to work properly.
In tools/data_source/upload.xml change



to




Please let us know if this workaround doesn't work for you.


Thanks for using Galaxy,

Dan


On Aug 3, 2012, at 4:20 AM, David Roquis wrote:

> Hi Batsal,
> 
> I have the exact same problem, on 2 different instances of Galaxy, on two 
> different servers. I can replicate this problem on a cloned instance with no 
> modification, and one using multiple galaxay server, nginx proxy and 
> postgresql, both instances being on different machines (one on fedora 13, the 
> other one on fedora 17). From what I have seen, it seems to be browser 
> related. I can sometimes (rarely) upload data with firefox, chrome or safary, 
> but for me it has worked ALL the time using internet explorer 8/9. The thing 
> is that when you start the upload, the browser shows you that it is uploaded, 
> but the upload.py script is never launched, and hence, the upload seems to be 
> running forever. Seems we are not the only ones with this problem, but no 
> real solution until now.
> 
> Two options for you at the moment
> - try using IE 8/9 to upload the data
> - upload your data using data libraries under the admin menu (this works on 
> any browser).
> 
> Keep me in touch if you find a solution
> 
> David
> 
> 
> 
> > From: bat...@gmail.com
> > Date: Thu, 2 Aug 2012 15:48:40 -0400
> > To: galaxy-dev@lists.bx.psu.edu
> > Subject: [galaxy-dev] Upload issue in local installation
> > 
> > I installed galaxy locally in a linux server. However, I cannot upload the 
> > files (no matter how small, I have tried few kb size fasta files). When I 
> > try to upload, the link to the file shows up in the History and gets a new 
> > number (purple box). When I click on the link I get 'Dataset is uploading' 
> > forever. 
> > 
> > In the terminal window where I start galaxy, I get the following error 
> > report:
> > 
> > 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" 
> > "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 
> > 200 - "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) 
> > Gecko/20100101 Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - 
> > "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 
> > Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage 
> > HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> > rv:13.0) Gecko/20100101 Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET 
> > /tool_runner?tool_id=upload1 HTTP/1.1" 200 - 
> > "http://redhat:8080/root/tool_menu"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) 
> > Gecko/20100101 Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST 
> > /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/"; 
> > "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET 
> > /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/"; 
> > "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - 
> > "http://redhat:8080/tool_runner/upload_async_message"; "Mozilla/5.0 (Windows 
> > NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage 
> > HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> > rv:13.0) Gecko/20100101 Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST 
> > /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history"; 
> > "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> > 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST 
> > /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history"; 
> > "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> > 
>

Re: [galaxy-dev] Upload issue in local installation

2012-08-03 Thread David Roquis

Hi Batsal,

I have the exact same problem, on 2 different instances of Galaxy, on two 
different servers. I can replicate this problem on a cloned instance with no 
modification, and one using multiple galaxay server, nginx proxy and 
postgresql, both instances being on different machines (one on fedora 13, the 
other one on fedora 17). From what I have seen, it seems to be browser related. 
I can sometimes (rarely) upload data with firefox, chrome or safary, but for me 
it has worked ALL the time using internet explorer 8/9. The thing is that when 
you start the upload, the browser shows you that it is uploaded, but the 
upload.py script is never launched, and hence, the upload seems to be running 
forever. Seems we are not the only ones with this problem, but no real solution 
until now.

Two options for you at the moment
- try using IE 8/9 to upload the data
- upload your data using data libraries under the admin menu (this works on any 
browser).

Keep me in touch if you find a solution

David



> From: bat...@gmail.com
> Date: Thu, 2 Aug 2012 15:48:40 -0400
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] Upload issue in local installation
> 
> I installed galaxy locally in a linux server. However, I cannot upload the 
> files (no matter how small, I have tried few kb size fasta files). When I try 
> to upload, the link to the file shows up in the History and gets a new number 
> (purple box). When I click on the link I get 'Dataset is uploading'  forever. 
> 
> In the terminal window where I start galaxy, I get the following error report:
> 
> 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" 
> "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 
> 200 - "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) 
> Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - 
> "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 
> Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage 
> HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET 
> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - 
> "http://redhat:8080/root/tool_menu"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) 
> Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST 
> /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/"; 
> "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET 
> /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/"; 
> "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - 
> "http://redhat:8080/tool_runner/upload_async_message"; "Mozilla/5.0 (Windows 
> NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage 
> HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates 
> HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates 
> HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
> rv:13.0) Gecko/20100101 Firefox/13.0.1"
> 
> 
> The last line keeps going for ever... writes new line every 4 secs.
> 
> I am stuck and don't know where to look. Please help.
> 
> Batsal.
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
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[galaxy-dev] Upload issue in local installation

2012-08-02 Thread Batsal Devkota
I installed galaxy locally in a linux server. However, I cannot upload the 
files (no matter how small, I have tried few kb size fasta files). When I try 
to upload, the link to the file shows up in the History and gets a new number 
(purple box). When I click on the link I get 'Dataset is uploading'  forever. 

In the terminal window where I start galaxy, I get the following error report:

92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" 
"Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 
- "http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 
Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - 
"http://redhat:8080/"; "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 
Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage 
HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 
HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu"; "Mozilla/5.0 (Windows NT 
5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST 
/tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/"; 
"Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET 
/tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/"; 
"Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - 
"http://redhat:8080/tool_runner/upload_async_message"; "Mozilla/5.0 (Windows NT 
5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage 
HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates 
HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
rv:13.0) Gecko/20100101 Firefox/13.0.1"
92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates 
HTTP/1.1" 200 - "http://redhat:8080/history"; "Mozilla/5.0 (Windows NT 5.2; 
rv:13.0) Gecko/20100101 Firefox/13.0.1"


The last line keeps going for ever... writes new line every 4 secs.

I am stuck and don't know where to look. Please help.

Batsal.


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