Error getting to http://galaxy/user/create on local instance
We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given) Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade. Did something change, in configuration of the create user page? Any thoughts what might be causing this? Thanks, Dave
Hello Dave, The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ). However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored. Greg Von Kuster On May 24, 2011, at 4:02 PM, Dave Walton wrote:
We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error.
The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given)
Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade.
Did something change, in configuration of the create user page?
Any thoughts what might be causing this?
Thanks,
Dave
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg, We've tried just reloading the browser and that didn't do anything. As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you. The only cache related variable in my universe_wsgi files is "static_cache_time = 360". Thanks, Dave On 5/24/11 4:27 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hello Dave,
The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ).
However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored.
Greg Von Kuster
On May 24, 2011, at 4:02 PM, Dave Walton wrote:
We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error.
The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given)
Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade.
Did something change, in configuration of the create user page?
Any thoughts what might be causing this?
Thanks,
Dave
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi Dave, If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates. Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause. You mention your "development server" in your response. Are you running only 1 Galaxy instance, or more than 1? Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand? What version of Galaxy are your running? Thanks Dave, Greg Von Kuster On May 24, 2011, at 6:06 PM, Dave Walton wrote:
Greg,
We've tried just reloading the browser and that didn't do anything.
As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you.
The only cache related variable in my universe_wsgi files is "static_cache_time = 360".
Thanks,
Dave
On 5/24/11 4:27 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hello Dave,
The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ).
However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored.
Greg Von Kuster
On May 24, 2011, at 4:02 PM, Dave Walton wrote:
We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error.
The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given)
Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade.
Did something change, in configuration of the create user page?
Any thoughts what might be causing this?
Thanks,
Dave
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg. We do not use the "template_cache_path" in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71 We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the "galaxy process". 3 Web applications and 1 job runner. We get the error on both servers, but I'm doing all of this troubleshooting on our development server. This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help). I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help. We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade. Thanks, Dave On 5/24/11 11:29 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hi Dave,
If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates.
Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause.
You mention your "development server" in your response. Are you running only 1 Galaxy instance, or more than 1?
Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand?
What version of Galaxy are your running?
Thanks Dave,
Greg Von Kuster
On May 24, 2011, at 6:06 PM, Dave Walton wrote:
Greg,
We've tried just reloading the browser and that didn't do anything.
As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you.
The only cache related variable in my universe_wsgi files is "static_cache_time = 360".
Thanks,
Dave
On 5/24/11 4:27 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hello Dave,
The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ).
However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored.
Greg Von Kuster
On May 24, 2011, at 4:02 PM, Dave Walton wrote:
We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error.
The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given)
Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade.
Did something change, in configuration of the create user page?
Any thoughts what might be causing this?
Thanks,
Dave
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hello Dave, Can you clarify how your users are accessing the following URL
I originally assumed they were using the Galaxy UI to register by clicking the "Register" link on the "User" popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link? If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here:
Greg ~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote:
Greg.
We do not use the "template_cache_path" in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71
We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the "galaxy process". 3 Web applications and 1 job runner.
We get the error on both servers, but I'm doing all of this troubleshooting on our development server.
This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help).
I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help.
We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade.
Thanks,
Dave
On 5/24/11 11:29 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hi Dave,
If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates.
Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause.
You mention your "development server" in your response. Are you running only 1 Galaxy instance, or more than 1?
Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand?
What version of Galaxy are your running?
Thanks Dave,
Greg Von Kuster
On May 24, 2011, at 6:06 PM, Dave Walton wrote:
Greg,
We've tried just reloading the browser and that didn't do anything.
As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you.
The only cache related variable in my universe_wsgi files is "static_cache_time = 360".
Thanks,
Dave
On 5/24/11 4:27 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hello Dave,
The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ).
However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored.
Greg Von Kuster
On May 24, 2011, at 4:02 PM, Dave Walton wrote:
We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error.
The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given)
Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade.
Did something change, in configuration of the create user page?
Any thoughts what might be causing this?
Thanks,
Dave
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
I just checked, Using the User->Register menu works, however we require our users to log in so when they go to galaxy.jax.org<http://galaxy.jax.org> they are redirected to a login page if they are not already logged in. That page has the text "This installation of Galaxy has been configured such that only users who are logged in may use it. If you don't already have an account, you may create one<http://galaxy.jax.org/user/create>." , and "you may create one" links to http://galaxy.jax.org/user/create. clicking on the link results in the error. -glen On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote: Hello Dave, Can you clarify how your users are accessing the following URL http://galaxy.jax.org/user/create I originally assumed they were using the Galaxy UI to register by clicking the "Register" link on the "User" popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link? If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here: http://galaxy.jax.org/user/create?cntrller=user Greg ~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote: Greg. We do not use the "template_cache_path" in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71 We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the "galaxy process". 3 Web applications and 1 job runner. We get the error on both servers, but I'm doing all of this troubleshooting on our development server. This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help). I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help. We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade. Thanks, Dave On 5/24/11 11:29 PM, "Greg Von Kuster" <greg@bx.psu.edu<mailto:greg@bx.psu.edu>> wrote: Hi Dave, If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates. Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause. You mention your "development server" in your response. Are you running only 1 Galaxy instance, or more than 1? Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand? What version of Galaxy are your running? Thanks Dave, Greg Von Kuster On May 24, 2011, at 6:06 PM, Dave Walton wrote: Greg, We've tried just reloading the browser and that didn't do anything. As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you. The only cache related variable in my universe_wsgi files is "static_cache_time = 360". Thanks, Dave On 5/24/11 4:27 PM, "Greg Von Kuster" <greg@bx.psu.edu<mailto:greg@bx.psu.edu>> wrote: Hello Dave, The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ). However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored. Greg Von Kuster On May 24, 2011, at 4:02 PM, Dave Walton wrote: We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given) Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade. Did something change, in configuration of the create user page? Any thoughts what might be causing this? Thanks, Dave ___________________________________________________________ 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/ Greg Von Kuster Galaxy Development Team greg@bx.psu.edu<mailto:greg@bx.psu.edu> Greg Von Kuster Galaxy Development Team greg@bx.psu.edu<mailto:greg@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/ Greg Von Kuster Galaxy Development Team greg@bx.psu.edu<mailto:greg@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/ -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
Hi Glen, I've never seen this before, but perhaps your user controller is using an old version ( I'm just grasping here, because this is pretty obscure behavior ). Try deleting the following file - make sure it is the .pyc file. ~/lib/galaxy/web/controllers/user.pyc The user controller contains the code that generates the you may create one link, but the current versions of this controller is using the new method signature as well, so the only thing I can think of is that your compiled version ( user.pyc ) is old. Let us know if this doesn't resolve the issue. Thanks! On May 26, 2011, at 7:39 AM, Glen Beane wrote:
I just checked,
Using the User->Register menu works, however we require our users to log in so when they go to galaxy.jax.org they are redirected to a login page if they are not already logged in. That page has the text "This installation of Galaxy has been configured such that only users who are logged in may use it. If you don't already have an account, you may create one." , and "you may create one" links to http://galaxy.jax.org/user/create. clicking on the link results in the error.
-glen
On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote:
Hello Dave,
Can you clarify how your users are accessing the following URL
I originally assumed they were using the Galaxy UI to register by clicking the "Register" link on the "User" popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link?
If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here:
Greg
~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote:
Greg.
We do not use the "template_cache_path" in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71
We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the "galaxy process". 3 Web applications and 1 job runner.
We get the error on both servers, but I'm doing all of this troubleshooting on our development server.
This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help).
I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help.
We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade.
Thanks,
Dave
On 5/24/11 11:29 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hi Dave,
If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates.
Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause.
You mention your "development server" in your response. Are you running only 1 Galaxy instance, or more than 1?
Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand?
What version of Galaxy are your running?
Thanks Dave,
Greg Von Kuster
On May 24, 2011, at 6:06 PM, Dave Walton wrote:
Greg,
We've tried just reloading the browser and that didn't do anything.
As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you.
The only cache related variable in my universe_wsgi files is "static_cache_time = 360".
Thanks,
Dave
On 5/24/11 4:27 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hello Dave,
The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ).
However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored.
Greg Von Kuster
On May 24, 2011, at 4:02 PM, Dave Walton wrote:
> We upgraded our Galaxy instance to the current Dist build at the end of > last > week. Since then we've had a couple new users attempt to create accounts. > When they go to the create user page (http://galaxy.jax.org/user/create) > they get a 500 Server Error. > > The message in the error log is: > 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" > 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X > 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" > Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments > (2 given) > > > Glen is traveling to the Galaxy Community Conference, he's the one that did > the upgrade, but as far as I know, he did a pretty straight forward > upgrade. > > Did something change, in configuration of the create user page? > > Any thoughts what might be causing this? > > Thanks, > > Dave > > > ___________________________________________________________ > 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/
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@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:
Greg Von Kuster Galaxy Development Team greg@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:
-- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Just removed user.pyc and restarted the server. Did not resolve the problem. Dave On 5/26/11 8:09 AM, "Greg Von Kuster" <greg@bx.psu.edu> wrote: Hi Glen, I've never seen this before, but perhaps your user controller is using an old version ( I'm just grasping here, because this is pretty obscure behavior ). Try deleting the following file - make sure it is the .pyc file. ~/lib/galaxy/web/controllers/user.pyc The user controller contains the code that generates the you may create one <http://galaxy.jax.org/user/create> link, but the current versions of this controller is using the new method signature as well, so the only thing I can think of is that your compiled version ( user.pyc ) is old. Let us know if this doesn't resolve the issue. Thanks! On May 26, 2011, at 7:39 AM, Glen Beane wrote: I just checked, Using the User->Register menu works, however we require our users to log in so when they go to galaxy.jax.org <http://galaxy.jax.org/> they are redirected to a login page if they are not already logged in. That page has the text "This installation of Galaxy has been configured such that only users who are logged in may use it. If you don't already have an account, you may create one <http://galaxy.jax.org/user/create> ." , and "you may create one" links to http://galaxy.jax.org/user/create. clicking on the link results in the error. -glen On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote: Hello Dave, Can you clarify how your users are accessing the following URL http://galaxy.jax.org/user/create I originally assumed they were using the Galaxy UI to register by clicking the "Register" link on the "User" popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link? If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here: http://galaxy.jax.org/user/create?cntrller=user Greg ~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote: Greg. We do not use the "template_cache_path" in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71 We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the "galaxy process". 3 Web applications and 1 job runner. We get the error on both servers, but I'm doing all of this troubleshooting on our development server. This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help). I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help. We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade. Thanks, Dave On 5/24/11 11:29 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote: Hi Dave, If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates. Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause. You mention your "development server" in your response. Are you running only 1 Galaxy instance, or more than 1? Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand? What version of Galaxy are your running? Thanks Dave, Greg Von Kuster On May 24, 2011, at 6:06 PM, Dave Walton wrote: Greg, We've tried just reloading the browser and that didn't do anything. As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you. The only cache related variable in my universe_wsgi files is "static_cache_time = 360". Thanks, Dave On 5/24/11 4:27 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote: Hello Dave, The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ). However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored. Greg Von Kuster On May 24, 2011, at 4:02 PM, Dave Walton wrote: We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error. The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given) Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade. Did something change, in configuration of the create user page? Any thoughts what might be causing this? Thanks, Dave ___________________________________________________________ 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/ Greg Von Kuster Galaxy Development Team greg@bx.psu.edu Greg Von Kuster Galaxy Development Team greg@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/ Greg Von Kuster Galaxy Development Team greg@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/ -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153 ___________________________________________________________ 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/ Greg Von Kuster Galaxy Development Team greg@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/
Fixed on trunk by setting a default cntrller when there isn't one. -K On Thu, May 26, 2011 at 2:16 PM, Dave Walton <Dave.Walton@jax.org> wrote:
Just removed user.pyc and restarted the server. Did not resolve the problem.
Dave
On 5/26/11 8:09 AM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hi Glen,
I've never seen this before, but perhaps your user controller is using an old version ( I'm just grasping here, because this is pretty obscure behavior ). Try deleting the following file - make sure it is the .pyc file.
~/lib/galaxy/web/controllers/user.pyc
The user controller contains the code that generates the you may create one <http://galaxy.jax.org/user/create> link, but the current versions of this controller is using the new method signature as well, so the only thing I can think of is that your compiled version ( user.pyc ) is old.
Let us know if this doesn't resolve the issue.
Thanks!
On May 26, 2011, at 7:39 AM, Glen Beane wrote:
I just checked,
Using the User->Register menu works, however we require our users to log in so when they go to galaxy.jax.org <http://galaxy.jax.org/> they are redirected to a login page if they are not already logged in. That page has the text "This installation of Galaxy has been configured such that only users who are logged in may use it. If you don't already have an account, you may create one <http://galaxy.jax.org/user/create> ." , and "you may create one" links to http://galaxy.jax.org/user/create. clicking on the link results in the error.
-glen
On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote:
Hello Dave,
Can you clarify how your users are accessing the following URL
http://galaxy.jax.org/user/create
I originally assumed they were using the Galaxy UI to register by clicking the "Register" link on the "User" popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link?
If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here:
http://galaxy.jax.org/user/create?cntrller=user
Greg
~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote:
Greg.
We do not use the "template_cache_path" in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71
We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the "galaxy process". 3 Web applications and 1 job runner.
We get the error on both servers, but I'm doing all of this troubleshooting on our development server.
This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help).
I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help.
We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade.
Thanks,
Dave
On 5/24/11 11:29 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hi Dave,
If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates.
Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause.
You mention your "development server" in your response. Are you running only 1 Galaxy instance, or more than 1?
Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand?
What version of Galaxy are your running?
Thanks Dave,
Greg Von Kuster
On May 24, 2011, at 6:06 PM, Dave Walton wrote:
Greg,
We've tried just reloading the browser and that didn't do anything.
As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you.
The only cache related variable in my universe_wsgi files is "static_cache_time = 360".
Thanks,
Dave
On 5/24/11 4:27 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hello Dave,
The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ).
However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored.
Greg Von Kuster
On May 24, 2011, at 4:02 PM, Dave Walton wrote:
We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error.
The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given)
Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade.
Did something change, in configuration of the create user page?
Any thoughts what might be causing this?
Thanks,
Dave
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@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:
Greg Von Kuster Galaxy Development Team greg@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:
-- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@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:
___________________________________________________________ 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:
It's also fixed in stable - the release right before the community conference includes a bug fix for that fixes the URL generated for that link. --nate Kanwei Li wrote:
Fixed on trunk by setting a default cntrller when there isn't one.
-K
On Thu, May 26, 2011 at 2:16 PM, Dave Walton <Dave.Walton@jax.org> wrote:
Just removed user.pyc and restarted the server. Did not resolve the problem.
Dave
On 5/26/11 8:09 AM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hi Glen,
I've never seen this before, but perhaps your user controller is using an old version ( I'm just grasping here, because this is pretty obscure behavior ). Try deleting the following file - make sure it is the .pyc file.
~/lib/galaxy/web/controllers/user.pyc
The user controller contains the code that generates the you may create one <http://galaxy.jax.org/user/create> link, but the current versions of this controller is using the new method signature as well, so the only thing I can think of is that your compiled version ( user.pyc ) is old.
Let us know if this doesn't resolve the issue.
Thanks!
On May 26, 2011, at 7:39 AM, Glen Beane wrote:
I just checked,
Using the User->Register menu works, however we require our users to log in so when they go to galaxy.jax.org <http://galaxy.jax.org/> they are redirected to a login page if they are not already logged in. That page has the text "This installation of Galaxy has been configured such that only users who are logged in may use it. If you don't already have an account, you may create one <http://galaxy.jax.org/user/create> ." , and "you may create one" links to http://galaxy.jax.org/user/create. clicking on the link results in the error.
-glen
On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote:
Hello Dave,
Can you clarify how your users are accessing the following URL
http://galaxy.jax.org/user/create
I originally assumed they were using the Galaxy UI to register by clicking the "Register" link on the "User" popup menu. However, perhaps they are just pointing their browser to the URL. Is this the case? If so, why are you not clicking on the menu link?
If it is the case that your users are entering the address in their browsers rather than using the normal Galaxy UI, then the address should include an additional request param as is shown here:
http://galaxy.jax.org/user/create?cntrller=user
Greg
~/ On May 25, 2011, at 1:46 PM, Dave Walton wrote:
Greg.
We do not use the "template_cache_path" in our config. I deleted all the files in ~/database/compiled_templates and restarted my server. I still get the error (even with a shift reload of my browser). I've tried it (on the Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71
We run two totally separate instances of Galaxy, on different virtual machines. One for testing, development of tools and deploying new versions of galaxy, and one for production, where our scientists do their analysis. Each of these servers run 4 instances of the "galaxy process". 3 Web applications and 1 job runner.
We get the error on both servers, but I'm doing all of this troubleshooting on our development server.
This behavior is occuring for any user who tries to create a new galaxy account (so the original user who reported the problem, and myself as I test it. I can ask others to try if you think that will help).
I mentioned the browsers I've tried it with above. I've not tried it from a windows box, but can, again, if you think that will help.
We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade.
Thanks,
Dave
On 5/24/11 11:29 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hi Dave,
If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached templates are stored in the default directory of ~/database/compiled_templates.
Deleting your cached templates in ~/database/compiled_templates should have corrected the problem, assuming there are no other issues within your Galaxy environment, so let's begin down the path of determining the cause.
You mention your "development server" in your response. Are you running only 1 Galaxy instance, or more than 1?
Is the behavior occurring for all of your users or just a few? Does it occur with different browsers, or is it related to a certain browser brand?
What version of Galaxy are your running?
Thanks Dave,
Greg Von Kuster
On May 24, 2011, at 6:06 PM, Dave Walton wrote:
Greg,
We've tried just reloading the browser and that didn't do anything.
As for deleting the cached templates, on our development server I tried deleting everything under the database/compiled_templates directory (I even restarted my server) and it appeared to have no affect. We still get the error message. Maybe I misunderstood you.
The only cache related variable in my universe_wsgi files is "static_cache_time = 360".
Thanks,
Dave
On 5/24/11 4:27 PM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
Hello Dave,
The index method signature of the user controller changed, so this is a template cache issue. It may work to simply have your users refresh their Galaxy masthead ( the top menu banner that includes the login in the User pop-up ).
However, sometimes this isn't enough to clear the cache, so you can fix things for sure by deleting the cached templates in ~//database/compiled_templates/user assuming you have not changed the setting for the template cache in your universe_wsgi.ini file. If you have, delete the files in the user directory where you have them stored.
Greg Von Kuster
On May 24, 2011, at 4:02 PM, Dave Walton wrote:
We upgraded our Galaxy instance to the current Dist build at the end of last week. Since then we've had a couple new users attempt to create accounts. When they go to the create user page (http://galaxy.jax.org/user/create) they get a 500 Server Error.
The message in the error log is: 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0" 500 - "http://galaxy/user/login" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2" Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given)
Glen is traveling to the Galaxy Community Conference, he's the one that did the upgrade, but as far as I know, he did a pretty straight forward upgrade.
Did something change, in configuration of the create user page?
Any thoughts what might be causing this?
Thanks,
Dave
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Greg Von Kuster Galaxy Development Team greg@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:
Greg Von Kuster Galaxy Development Team greg@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:
-- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@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:
___________________________________________________________ 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:
___________________________________________________________ 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 (5)
-
Dave Walton -
Glen Beane -
Greg Von Kuster -
Kanwei Li -
Nate Coraor