[galaxy-dev] possible bug
Hey guys, we found a curios bug, but it is a little bit tricky to explain. Here is an example: - Click on Concatenate datasets tail-to-head - add a new data set - click on the first data field and select your data set of choice - press tab to get to the next data set an select the second data set by typing the number of the data set via the numpad (might only be possible if you have a long history with many files) = the first number is written as an character, e.g., 1=a, 2=b, and so on. This bug only shows up if you use the numpad to type in the numbers. We tested it with different tools in our local Galaxy instance and in the Galaxy Main instance. Can anybody confirm this behavior? Best regards, Thomas ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Possible bug in managing tool shed repositories
Hi all, Before posting on Trello, perhaps someone can confirm that it is a bug: 1. In the admin menu, go to 'Manage installed tool shed repositories' 2. click on a tool that you have installed with dependencies (!) 3. In the top right 'repository actions', choose 'Manage tool dependencies' 4. In the top right 'Actions', choose 'Manage repository'. 5. An error similar like this one appears: Error Traceback: View as: Interactive | Text | XML (full) â ValueError: invalid literal for int() with base 10: 'a9975dcda42e2b00' URL: http://localhost/admin_toolshed/manage_repository?id=3f428053038c8626b08a92869ee1362d132430354fe813e0 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:561 in manage_repository view repository = suc.get_installed_tool_shed_repository( trans, repository_id ) Module tool_shed.util.shed_util_common:513 in get_installed_tool_shed_repository view return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) Module galaxy.web.security:60 in decode_id view return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) ValueError: invalid literal for int() with base 10: 'a9975dcda42e2b00' All tools with dependencies seem to have this behaviour. Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Possible bug in managing tool shed repositories
Hi Joachim, confirmed, it seems like a bug. Cheers, Björn Hi all, Before posting on Trello, perhaps someone can confirm that it is a bug: 1. In the admin menu, go to 'Manage installed tool shed repositories' 2. click on a tool that you have installed with dependencies (!) 3. In the top right 'repository actions', choose 'Manage tool dependencies' 4. In the top right 'Actions', choose 'Manage repository'. 5. An error similar like this one appears: Error Traceback: View as: Interactive | Text | XML (full) â ValueError: invalid literal for int() with base 10: 'a9975dcda42e2b00' URL: http://localhost/admin_toolshed/manage_repository?id=3f428053038c8626b08a92869ee1362d132430354fe813e0 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:561 in manage_repository view repository = suc.get_installed_tool_shed_repository( trans, repository_id ) Module tool_shed.util.shed_util_common:513 in get_installed_tool_shed_repository view return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) Module galaxy.web.security:60 in decode_id view return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) ValueError: invalid literal for int() with base 10: 'a9975dcda42e2b00' All tools with dependencies seem to have this behaviour. Cheers, Joachim ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Possible bug in managing tool shed repositories
Hello Joachim and Björn, This issue should be resolved in change set 10103:d842d50a6ed3, which is currently running on the test tool shed. Thanks fro reporting this! Greg Von Kuster On Jun 19, 2013, at 6:16 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Joachim, confirmed, it seems like a bug. Cheers, Björn Hi all, Before posting on Trello, perhaps someone can confirm that it is a bug: 1. In the admin menu, go to 'Manage installed tool shed repositories' 2. click on a tool that you have installed with dependencies (!) 3. In the top right 'repository actions', choose 'Manage tool dependencies' 4. In the top right 'Actions', choose 'Manage repository'. 5. An error similar like this one appears: Error Traceback: View as: Interactive | Text | XML (full) â ValueError: invalid literal for int() with base 10: 'a9975dcda42e2b00' URL: http://localhost/admin_toolshed/manage_repository?id=3f428053038c8626b08a92869ee1362d132430354fe813e0 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:561 in manage_repository view repository = suc.get_installed_tool_shed_repository( trans, repository_id ) Module tool_shed.util.shed_util_common:513 in get_installed_tool_shed_repository view return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) Module galaxy.web.security:60 in decode_id view return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) ) ValueError: invalid literal for int() with base 10: 'a9975dcda42e2b00' All tools with dependencies seem to have this behaviour. Cheers, Joachim ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Possible bug in dynamic options
Thanks for the reply but no, I wasn't using any filters. The relevant XML sections are like this: code file=listFiles.py/ ... param name = url_paste label = Select a file to copy type=select multiple=false dynamic_options = listFiles()/ Mutlu On 24 August 2012 17:28, John Chilton chil...@msi.umn.edu wrote: I cannot speak to the code running twi, but are using a unique_value filter? The dynamic_options code use to completely lock up our galaxy server for minutes at a time before I applied this optimization: https://bitbucket.org/jmchilton/galaxy-central-dynamic-options-fix/changeset/e4856cc362d92f7857699c5be6cab1a75c29932f It is only relevant if you are using a unique_value filter though. -John On Fri, Aug 24, 2012 at 11:07 AM, Mutlu Dogruel mutludogr...@gmail.com wrote: Hi, I wrote a script for dynamically populating a user form. It works but it's slow. When I checked the Galaxy log, I saw that the method called by my custom tool's xml is being run twice (the same debugging lines appear twice in the log, and that happens consistently). Is there any explanation for this? The script returns a list of strings fetched from a remote server. It's running a bit slow, taking up to 6 seconds, so it would be great if I can half that! For testing purposes, I wrote a dummy method that returns a few characters in a list of tuples. Again, my print statement in the Python script is called twice. Has anyone noticed such behaviour? Could it be related to this Galaxy bug: https://bitbucket.org/galaxy/galaxy-central/issue/491/data_column-parameter-bug-cannot-select The Galaxy script shown on that page says: NOTE: This is wasteful since dynamic options and dataset collection happens twice (here and when generating HTML). Thanks. Best regards, -- Mutlu ___ 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/ -- Mutlu ___ 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] Possible bug in dynamic options
I cannot speak to the code running twi, but are using a unique_value filter? The dynamic_options code use to completely lock up our galaxy server for minutes at a time before I applied this optimization: https://bitbucket.org/jmchilton/galaxy-central-dynamic-options-fix/changeset/e4856cc362d92f7857699c5be6cab1a75c29932f It is only relevant if you are using a unique_value filter though. -John On Fri, Aug 24, 2012 at 11:07 AM, Mutlu Dogruel mutludogr...@gmail.com wrote: Hi, I wrote a script for dynamically populating a user form. It works but it's slow. When I checked the Galaxy log, I saw that the method called by my custom tool's xml is being run twice (the same debugging lines appear twice in the log, and that happens consistently). Is there any explanation for this? The script returns a list of strings fetched from a remote server. It's running a bit slow, taking up to 6 seconds, so it would be great if I can half that! For testing purposes, I wrote a dummy method that returns a few characters in a list of tuples. Again, my print statement in the Python script is called twice. Has anyone noticed such behaviour? Could it be related to this Galaxy bug: https://bitbucket.org/galaxy/galaxy-central/issue/491/data_column-parameter-bug-cannot-select The Galaxy script shown on that page says: NOTE: This is wasteful since dynamic options and dataset collection happens twice (here and when generating HTML). Thanks. Best regards, -- Mutlu ___ 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] Possible bug: Tags in a workflow gets duplicated hundreds of times
Thanks for addressing this...The workflows load MUCH faster now...ThonOn Mar 20, 2012, at 07:54 AM, Dannon Baker dannonba...@me.com wrote:Hi Thon, Thanks for reporting this. I see what the problem is here at least for the clone duplication, and I've committed a fix in 6833:e8e361707865 that will affect all workflows going forward. Unfortunately, there isn't a complete solution for fixing the extra tags. The problem was that any time you cloned a workflow, the mapping that retrieved the set of tags that should have been copied was actually returning *all* of the user's tags. That means that even if the source workflow had no tags, all workflow tags owned by the user would get copied to the newly created workflow. Because of this, just removing duplicate tags (while an obvious step in the right direction) won't be enough and you'll still have tags where they shouldn't be. I'll add the duplicate removal code as a migration, but in the short term if there are a few individual workflows that you need to fix (by simply removing all tags) the easiest thing to do on your end would be to manually remove the stored_workflow_tag_associations for those particular workflows, using something like this sql statement: delete from stored_workflow_tag_associations where stored_workflow_id = 'enter stored_workflow id to fix' -Dannon On Mar 19, 2012, at 1:47 PM, Anthonius deBoer wrote: Hi,I have run into an issue with a tag being duplicated hundreds of times each time I open, edit or clone a workflow. I have tried to manually remove them, but each time the tag gets inserted somehow and duplicated each time I edit the workflow. By now there are hundreds of copies of the tags at it makes loading and running the workflow very slow.Is there a way to remove a tag from the system somehow? I am willing to dig into the database with some SQL statement but not sure where to start... Thanks Thon ___ 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] Possible bug: Tags in a workflow gets duplicated hundreds of times
Hi Thon, Thanks for reporting this. I see what the problem is here at least for the clone duplication, and I've committed a fix in 6833:e8e361707865 that will affect all workflows going forward. Unfortunately, there isn't a complete solution for fixing the extra tags. The problem was that any time you cloned a workflow, the mapping that retrieved the set of tags that should have been copied was actually returning *all* of the user's tags. That means that even if the source workflow had no tags, all workflow tags owned by the user would get copied to the newly created workflow. Because of this, just removing duplicate tags (while an obvious step in the right direction) won't be enough and you'll still have tags where they shouldn't be. I'll add the duplicate removal code as a migration, but in the short term if there are a few individual workflows that you need to fix (by simply removing all tags) the easiest thing to do on your end would be to manually remove the stored_workflow_tag_associations for those particular workflows, using something like this sql statement: delete from stored_workflow_tag_associations where stored_workflow_id = 'enter stored_workflow id to fix' -Dannon On Mar 19, 2012, at 1:47 PM, Anthonius deBoer wrote: Hi, I have run into an issue with a tag being duplicated hundreds of times each time I open, edit or clone a workflow. I have tried to manually remove them, but each time the tag gets inserted somehow and duplicated each time I edit the workflow. By now there are hundreds of copies of the tags at it makes loading and running the workflow very slow. Is there a way to remove a tag from the system somehow? I am willing to dig into the database with some SQL statement but not sure where to start... Thanks Thon ___ 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/
[galaxy-dev] Possible bug: Tags in a workflow gets duplicated hundreds of times
Hi,I have run into an issue with a tag being duplicated hundreds of times each time I open, edit or clone a workflow.I have tried to manually remove them, but each time the tag gets inserted somehow and duplicated each time I edit the workflow.By now there are hundreds of copies of the tags at it makes loading and running the workflow very slow.Is there a way to remove a tag from the system somehow? I am willing to dig into the database with some SQL statement but not sure where to start...ThanksThon ___ 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] possible bug - user log in / browser cache
Ryan Golhar wrote: I have a local instance running. When I'm logged in as user1, log out, then try to log in as user2, I keep getting the You have been logged out message. Its as if the browser's cache is retaining some information. To get around this, after I log out as user1, I have to click on Analyze Data, then click on Log in to log in as user2. I'm running Safari on Mac, but have noticed this with Firefox as well. Hi Ryan, The login page will redirect you back to whatever page you to whatever page you were on before clicking log in. If this page is the logout page, the behavior you reported will be what happens. If you log in from any other page, this should go away. Please let us know if this is not the case. --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] possible bug - user log in / browser cache
On Mon, Mar 7, 2011 at 5:56 PM, Nate Coraor n...@bx.psu.edu wrote: Ryan Golhar wrote: I have a local instance running. When I'm logged in as user1, log out, then try to log in as user2, I keep getting the You have been logged out message. Its as if the browser's cache is retaining some information. To get around this, after I log out as user1, I have to click on Analyze Data, then click on Log in to log in as user2. I'm running Safari on Mac, but have noticed this with Firefox as well. Hi Ryan, The login page will redirect you back to whatever page you to whatever page you were on before clicking log in. If this page is the logout page, the behavior you reported will be what happens. If you log in from any other page, this should go away. Bug confirmed on Firefox on Mac, and Chrome on Windows using http://test.g2.bx.psu.edu/ I guess you just need to say if the previous page was the logout page, go to the main page instead, rather than a blind redirect. Issue filed: https://bitbucket.org/galaxy/galaxy-central/issue/486 I expect many people to be caught out by this (back when I was debugging a proxy problem I was probably hitting this bug too). Regards, Peter ___ 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] possible bug - user log in / browser cache
Peter Cock wrote: On Mon, Mar 7, 2011 at 5:56 PM, Nate Coraor n...@bx.psu.edu wrote: Ryan Golhar wrote: I have a local instance running. When I'm logged in as user1, log out, then try to log in as user2, I keep getting the You have been logged out message. Its as if the browser's cache is retaining some information. To get around this, after I log out as user1, I have to click on Analyze Data, then click on Log in to log in as user2. I'm running Safari on Mac, but have noticed this with Firefox as well. Hi Ryan, The login page will redirect you back to whatever page you to whatever page you were on before clicking log in. If this page is the logout page, the behavior you reported will be what happens. If you log in from any other page, this should go away. Bug confirmed on Firefox on Mac, and Chrome on Windows using http://test.g2.bx.psu.edu/ I guess you just need to say if the previous page was the logout page, go to the main page instead, rather than a blind redirect. Issue filed: https://bitbucket.org/galaxy/galaxy-central/issue/486 I expect many people to be caught out by this (back when I was debugging a proxy problem I was probably hitting this bug too). This is fixed in changeset 5188:52b59886df27, and will be available in our stable distribution the next time it's updated. --nate Regards, Peter ___ 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/
