7:48 p.m.
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.
8:20 a.m.
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: batsal(a)gmail.com
Date: Thu, 2 Aug 2012 15:48:40 -0400
To: galaxy-dev(a)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
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
1:24 p.m.
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
<param name="file_data" type="file" size="30"
label="File" 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
<param name="file_data" type="file" size="30"
label="File" 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: batsal(a)gmail.com
> Date: Thu, 2 Aug 2012 15:48:40 -0400
> To: galaxy-dev(a)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
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
1:58 p.m.
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: dan(a)bx.psu.edu
Date: Fri, 3 Aug 2012 09:24:43 -0400
CC: batsal(a)gmail.com; galaxy-dev(a)lists.bx.psu.edu
To: david_roquis(a)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
<param name="file_data" type="file" size="30"
label="File" 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
<param name="file_data" type="file" size="30"
label="File" 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: batsal(a)gmail.com
Date: Thu, 2 Aug 2012 15:48:40 -0400
To: galaxy-dev(a)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
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
2:06 p.m.
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: dan(a)bx.psu.edu
Date: Fri, 3 Aug 2012 09:24:43 -0400
CC: batsal(a)gmail.com; galaxy-dev(a)lists.bx.psu.edu
To: david_roquis(a)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
<param name="file_data" type="file" size="30"
label="File"
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
<param name="file_data" type="file" size="30"
label="File"
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:batsal@gmail.com <mailto:batsal@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 - "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
> and other Galaxy lists, please use the interface at:
>
>http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
--
Peter Briggs peter.briggs(a)manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
2:23 p.m.
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: dan(a)bx.psu.edu
> Date: Fri, 3 Aug 2012 09:24:43 -0400
> CC: batsal(a)gmail.com; galaxy-dev(a)lists.bx.psu.edu
> To: david_roquis(a)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
>
> <param name="file_data" type="file" size="30"
label="File"
> 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
>
> <param name="file_data" type="file" size="30"
label="File"
> 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:batsal@gmail.com <mailto:batsal@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 - "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
> > and other Galaxy lists, please use the interface at:
> >
> >http://lists.bx.psu.edu/
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
>
--
Peter Briggs peter.briggs(a)manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
9:28 a.m.
Hi,
Sorry about that but we get that error too "Failed: Request Entity Too
Large (413)" on Firefox (43.0) but not on chrome (47.0.2526.106 (64-bit)).
The trick to disable "ajax-upload" parameter (set it to false) does not
seem to work (the window is still open and nothing changed).
Any iadea would be greatful
Best,
Remy
2012-10-23 16:23 GMT+02:00 Nate Coraor <nate(a)bx.psu.edu>:
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: dan(a)bx.psu.edu
>> Date: Fri, 3 Aug 2012 09:24:43 -0400
>> CC: batsal(a)gmail.com; galaxy-dev(a)lists.bx.psu.edu
>> To: david_roquis(a)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
>>
>> <param name="file_data" type="file" size="30"
label="File"
>> 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
>>
>> <param name="file_data" type="file" size="30"
label="File"
>> 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:batsal@gmail.com <mailto:batsal@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 - "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
>> > and other Galaxy lists, please use the interface at:
>> >
>> >http://lists.bx.psu.edu/
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>>
>
> --
> Peter Briggs peter.briggs(a)manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
3:07 p.m.
Ok, I answer to myself:
It works with nginx last stable version (1.8.1) whereas it did not work on
nginx 1.7.4 (same configuration).
Best,
Remy
2016-01-05 10:28 GMT+01:00 Rémy Dernat <remy.d1(a)gmail.com>:
Hi,
Sorry about that but we get that error too "Failed: Request Entity Too
Large (413)" on Firefox (43.0) but not on chrome (47.0.2526.106 (64-bit)).
The trick to disable "ajax-upload" parameter (set it to false) does not
seem to work (the window is still open and nothing changed).
Any iadea would be greatful
Best,
Remy
2012-10-23 16:23 GMT+02:00 Nate Coraor <nate(a)bx.psu.edu>:
> 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: dan(a)bx.psu.edu
> >> Date: Fri, 3 Aug 2012 09:24:43 -0400
> >> CC: batsal(a)gmail.com; galaxy-dev(a)lists.bx.psu.edu
> >> To: david_roquis(a)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
> >>
> >> <param name="file_data" type="file"
size="30" label="File"
> >> 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
> >>
> >> <param name="file_data" type="file"
size="30" label="File"
> >> 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:batsal@gmail.com <mailto:batsal@gmail.com>
> >> > Date: Thu, 2 Aug 2012 15:48:40 -0400
> >> > To:galaxy-dev@lists.bx.psu.edu <mailto:
> galaxy-dev(a)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
> >> > and other Galaxy lists, please use the interface at:
> >> >
> >> >http://lists.bx.psu.edu/
> >> ___________________________________________________________
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client. To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>
> >> http://lists.bx.psu.edu/
> >>
> >>
> >>
> >>
> >> ___________________________________________________________
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client. To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>
> >> http://lists.bx.psu.edu/
> >>
> >
> > --
> > Peter Briggs peter.briggs(a)manchester.ac.uk
> > Bioinformatics Core Facility University of Manchester
> > B.1083 Michael Smith Bldg Tel: (0161) 2751482
> >
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client. To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> > http://lists.bx.psu.edu/
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
>
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galaxy-dev@lists.galaxyproject.org
7 comments
6 participants
participants (6)
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Batsal Devkota -
Daniel Blankenberg -
David Roquis -
Nate Coraor -
Peter Briggs -
Rémy Dernat