Re: [galaxy-dev] problems previewing certain files, downloading files and with login
Hi, I have found an old thread where Matthew Conte talks about problems previewing certain files, downloading them. Matthew Conte wrote: 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. 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. http://gmod.827538.n3.nabble.com/problems-previewing-certain-files-downloading-files-and-with-login-td2919895.html#a3087703 In my case all this happen without a proxy, (so) and I can login in correctly but I still having problem previewing and downloading files. hg summary parent: 6298:b258de1e6cea tip branch: default ___ 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/
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
Nate Coraor wrote: Matthew Conte wrote: Hi Nate, I was able to finally track down the login issue. It had to do with the following setting in my universe_wsgi.ini: * * *cookie_path = /galaxy* Removing this out fixed the problem and I should be fine leaving it out out since I don't need to run more than one instance of Galaxy. I probably shouldn't have had this setting in the first place, though I'm not exactly sure what this caused the problem. Anyways, thanks for all the help tracking these issues down. Hi Matt, I was about to get back to this now that the conference is over and I was also wondering if that option was related - weird though, I'm not sure why it should have an effect, but I'm glad you've figured out what's up. I guess there's a bug with the cookie path I'll need to check out. Okay, in testing I can only get this to happen if the browser has two cookies - one with the correct proxied path set and another set using just '/'. This arises from something like a bug in the library Galaxy uses to handle the request (WebOb) and the fact that the cookie headers don't include the cookie path along with the contents, so we'd have to choose one cookie or the other to use as your current session (probably the newer of the two?). Since this should really only happen in the case of a user getting a Galaxy cookie while running with cookie_path unset and then another once it's been set, it should be pretty rare and easily worked around by clearing cookies. If you're still interested in testing this and find that clearing cookies still doesn't fix the issue, please let me know. Thanks, --nate --nate -Matt On Mon, May 16, 2011 at 5:26 PM, Matthew Conte mco...@umd.edu wrote: Yep. On May 16, 2011 7:14 AM, Nate Coraor n...@bx.psu.edu wrote: Matthew Conte wrote: On Fri, May 13, 2011 at 11:18 AM, Nate Coraor n...@bx.psu.edu wrote: That's correct, although it should've been fixed. Can you remove the contents of galaxy-dist/database/compiled_templates, clear cache, reload, and see if you still get the same results? Thanks, --nate I've removed the contents of that folder, cleared the browser cache, reloaded and still get the same results (nothing different in the log either). I'm not sure if this will help, but maybe I should mention that when I try to log in I do get the following screen to flash for a brief second before automatically taking me back to the welcome screen: [image: Screen shot 2011-05-13 at 1.44.25 PM.png] I'm going to try to set up a test environment to replicate this shortly. Does this happen with both Apache and nginx? --nate ___ 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/
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
Matthew Conte wrote: Hi Nate, I was able to finally track down the login issue. It had to do with the following setting in my universe_wsgi.ini: * * *cookie_path = /galaxy* Removing this out fixed the problem and I should be fine leaving it out out since I don't need to run more than one instance of Galaxy. I probably shouldn't have had this setting in the first place, though I'm not exactly sure what this caused the problem. Anyways, thanks for all the help tracking these issues down. Hi Matt, I was about to get back to this now that the conference is over and I was also wondering if that option was related - weird though, I'm not sure why it should have an effect, but I'm glad you've figured out what's up. I guess there's a bug with the cookie path I'll need to check out. --nate -Matt On Mon, May 16, 2011 at 5:26 PM, Matthew Conte mco...@umd.edu wrote: Yep. On May 16, 2011 7:14 AM, Nate Coraor n...@bx.psu.edu wrote: Matthew Conte wrote: On Fri, May 13, 2011 at 11:18 AM, Nate Coraor n...@bx.psu.edu wrote: That's correct, although it should've been fixed. Can you remove the contents of galaxy-dist/database/compiled_templates, clear cache, reload, and see if you still get the same results? Thanks, --nate I've removed the contents of that folder, cleared the browser cache, reloaded and still get the same results (nothing different in the log either). I'm not sure if this will help, but maybe I should mention that when I try to log in I do get the following screen to flash for a brief second before automatically taking me back to the welcome screen: [image: Screen shot 2011-05-13 at 1.44.25 PM.png] I'm going to try to set up a test environment to replicate this shortly. Does this happen with both Apache and nginx? --nate ___ 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/
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
Hi Nate, I was able to finally track down the login issue. It had to do with the following setting in my universe_wsgi.ini: * * *cookie_path = /galaxy* Removing this out fixed the problem and I should be fine leaving it out out since I don't need to run more than one instance of Galaxy. I probably shouldn't have had this setting in the first place, though I'm not exactly sure what this caused the problem. Anyways, thanks for all the help tracking these issues down. -Matt On Mon, May 16, 2011 at 5:26 PM, Matthew Conte mco...@umd.edu wrote: Yep. On May 16, 2011 7:14 AM, Nate Coraor n...@bx.psu.edu wrote: Matthew Conte wrote: On Fri, May 13, 2011 at 11:18 AM, Nate Coraor n...@bx.psu.edu wrote: That's correct, although it should've been fixed. Can you remove the contents of galaxy-dist/database/compiled_templates, clear cache, reload, and see if you still get the same results? Thanks, --nate I've removed the contents of that folder, cleared the browser cache, reloaded and still get the same results (nothing different in the log either). I'm not sure if this will help, but maybe I should mention that when I try to log in I do get the following screen to flash for a brief second before automatically taking me back to the welcome screen: [image: Screen shot 2011-05-13 at 1.44.25 PM.png] I'm going to try to set up a test environment to replicate this shortly. Does this happen with both Apache and nginx? --nate ___ 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/
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
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/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@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: 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/
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
Hi Nate, On Mon, May 9, 2011 at 3:30 PM, Nate Coraor n...@bx.psu.edu wrote: 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? 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/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@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: 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/
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
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/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@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: 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/
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
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 n...@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/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@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: 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/
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
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 n...@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/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@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: 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/
