problems previewing certain files, downloading files and with login
Good afternoon, I'm having several problems with my local galaxy install which may or may not be related to one another. The first problem I'm having is with the "Display data in browser" feature. Some files type formats (fastqsanger, fasta) display fine. However, other file type formats (png, svg, txt) simply do not display at all. I have debugging turned on, but do not see any error within the browser or within the galaxy log or web server log after clicking the "Display data in browser" eyeball icon. It is simply a blank middle panel. The next problem I'm having has to do with downloading files. Firefox and Safari will download any file from a history, but will just create an empty file on the client. Again, neither log file show an error with a clue to the problem. Chrome will download some files, but other files give me an error and won't download: *This webpage is not available* * * *error 100 (net::ERR_CONNECTION_CLOSED): The server unexpectedly closed the connection.* In this case, I don't see anything in the log files either. Finally, I'm also having a problem logging in from the main welcome page. It seems to authenticate fine (I get an error when I put in the wrong password and don't when I put in the correct password), but it doesn't actually log me in and just takes me back to the main welcome page. For this problem, I do get an error in the galaxy log: *Exception happened during processing of request from---------------------------------------- * *('myip', 50593)Exception happened during processing of request from * *('myip', 50594)* *Traceback (most recent call last):* *Traceback (most recent call last):* * File "/raid/galaxy_user/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread* * File "/raid/galaxy_user/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread* * self.finish_request(request, client_address)* * self.finish_request(request, client_address)* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 322, in finish_request* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 322, in finish_request* * self.RequestHandlerClass(request, client_address, self)* * self.RequestHandlerClass(request, client_address, self)* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 618, in __init__* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 618, in __init__* * self.finish()* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 661, in finish* * self.finish()* * self.wfile.flush()* * File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush* * self._sock.sendall(buffer(data, write_offset, buffer_size))* * File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 661, in finish* *error: [Errno 32] Broken pipe* *----------------------------------------* * self.wfile.flush()* * File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush* * self._sock.sendall(buffer(data, write_offset, buffer_size))* *error: [Errno 32] Broken pipe* I am able to log in via other routes, such as going to "Options->Saved Histories" which brings up an error "You must be logged in" to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same. I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScalin... Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mconte@umd.edu
Matthew Conte wrote:
Good afternoon,
I'm having several problems with my local galaxy install which may or may not be related to one another.
The first problem I'm having is with the "Display data in browser" feature. Some files type formats (fastqsanger, fasta) display fine. However, other file type formats (png, svg, txt) simply do not display at all. I have debugging turned on, but do not see any error within the browser or within the galaxy log or web server log after clicking the "Display data in browser" eyeball icon. It is simply a blank middle panel.
The next problem I'm having has to do with downloading files. Firefox and Safari will download any file from a history, but will just create an empty file on the client. Again, neither log file show an error with a clue to the problem. Chrome will download some files, but other files give me an error and won't download:
*This webpage is not available* * * *error 100 (net::ERR_CONNECTION_CLOSED): The server unexpectedly closed the connection.*
In this case, I don't see anything in the log files either.
Hi Matt, Are you using the sendfile/x-accel-redirect configurations of Apache/nginx? Are all of these issues the same if you connect directly to Galaxy's built-in webserver instead of through a proxy server?
Finally, I'm also having a problem logging in from the main welcome page. It seems to authenticate fine (I get an error when I put in the wrong password and don't when I put in the correct password), but it doesn't actually log me in and just takes me back to the main welcome page.
For this problem, I do get an error in the galaxy log:
*Exception happened during processing of request from---------------------------------------- * * self.wfile.flush()* * File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush* * self._sock.sendall(buffer(data, write_offset, buffer_size))* *error: [Errno 32] Broken pipe*
I see this occasionally on python 2.6, and it's usually just a harmless intentional interrupted connection. As above, can you test login via the welcome page without the use of the proxy server and report back whether there's any difference? Thanks, --nate
I am able to log in via other routes, such as going to "Options->Saved Histories" which brings up an error "You must be logged in" to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same.
I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScalin...
Thanks, Matt
-- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mconte@umd.edu
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Hi Nate, On Mon, May 9, 2011 at 3:30 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Good afternoon,
I'm having several problems with my local galaxy install which may or may not be related to one another.
The first problem I'm having is with the "Display data in browser" feature. Some files type formats (fastqsanger, fasta) display fine. However, other file type formats (png, svg, txt) simply do not display at all. I have debugging turned on, but do not see any error within the browser or within the galaxy log or web server log after clicking the "Display data in browser" eyeball icon. It is simply a blank middle panel.
The next problem I'm having has to do with downloading files. Firefox and Safari will download any file from a history, but will just create an empty file on the client. Again, neither log file show an error with a clue to the problem. Chrome will download some files, but other files give me an error and won't download:
*This webpage is not available* * * *error 100 (net::ERR_CONNECTION_CLOSED): The server unexpectedly closed
Matthew Conte wrote: the
connection.*
In this case, I don't see anything in the log files either.
Hi Matt,
Are you using the sendfile/x-accel-redirect configurations of Apache/nginx? Are all of these issues the same if you connect directly to Galaxy's built-in webserver instead of through a proxy server?
Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for nginx, but both webservers are showing the same problems. If I use Galaxy's built-in webserver, I don't have the above problems, so the problem is probably related to the proxy server. I just can't seem to pinpoint the problem.
Finally, I'm also having a problem logging in from the main welcome page. It seems to authenticate fine (I get an error when I put in the wrong password and don't when I put in the correct password), but it doesn't actually log me in and just takes me back to the main welcome page.
For this problem, I do get an error in the galaxy log:
*Exception happened during processing of request from---------------------------------------- * * self.wfile.flush()* * File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush* * self._sock.sendall(buffer(data, write_offset, buffer_size))* *error: [Errno 32] Broken pipe*
I see this occasionally on python 2.6, and it's usually just a harmless intentional interrupted connection. As above, can you test login via the welcome page without the use of the proxy server and report back whether there's any difference?
Thanks, --nate
This also works normal with the built-in webserver but not as a proxy server. Thanks, Matt
I am able to log in via other routes, such as going to "Options->Saved Histories" which brings up an error "You must be logged in" to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users.
It
is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same.
I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScalin...
Thanks, Matt
-- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mconte@umd.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:
Matthew Conte wrote:
Hi Nate,
Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for nginx, but both webservers are showing the same problems. If I use Galaxy's built-in webserver, I don't have the above problems, so the problem is probably related to the proxy server. I just can't seem to pinpoint the problem.
Okay, thanks for the info. Have you enabled debug logging in the proxy and checked the error logs for anything telling? Same for the login issue. --nate
This also works normal with the built-in webserver but not as a proxy server.
Thanks, Matt
I am able to log in via other routes, such as going to "Options->Saved Histories" which brings up an error "You must be logged in" to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users.
It
is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same.
I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScalin...
Thanks, Matt
-- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mconte@umd.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:
Hi Nate, I've turned both apache and nginx logging up to debug and still don't see anything of relevance in the error logs for each of the problems I listed. Should I send you my universe_wsgi.ini? Thanks, Matt On Mon, May 9, 2011 at 4:15 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Matthew Conte wrote:
Hi Nate,
Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for nginx, but both webservers are showing the same problems. If I use Galaxy's built-in webserver, I don't have the above problems, so the problem is probably related to the proxy server. I just can't seem to pinpoint the problem.
Okay, thanks for the info. Have you enabled debug logging in the proxy and checked the error logs for anything telling? Same for the login issue.
--nate
This also works normal with the built-in webserver but not as a proxy server.
Thanks, Matt
I am able to log in via other routes, such as going to
"Options->Saved
Histories" which brings up an error "You must be logged in" to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same.
I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScalin...
Thanks, Matt
-- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mconte@umd.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:
Matthew Conte wrote:
Hi Nate,
I've turned both apache and nginx logging up to debug and still don't see anything of relevance in the error logs for each of the problems I listed. Should I send you my universe_wsgi.ini?
That'd help, and the relevant sections of your Apache and/or nginx configurations, off-list please. Thanks, --nate
Thanks, Matt
On Mon, May 9, 2011 at 4:15 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Matthew Conte wrote:
Hi Nate,
Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for nginx, but both webservers are showing the same problems. If I use Galaxy's built-in webserver, I don't have the above problems, so the problem is probably related to the proxy server. I just can't seem to pinpoint the problem.
Okay, thanks for the info. Have you enabled debug logging in the proxy and checked the error logs for anything telling? Same for the login issue.
--nate
This also works normal with the built-in webserver but not as a proxy server.
Thanks, Matt
I am able to log in via other routes, such as going to
"Options->Saved
Histories" which brings up an error "You must be logged in" to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same.
I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScalin...
Thanks, Matt
-- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mconte@umd.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:
participants (2)
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Matthew Conte -
Nate Coraor