Frederick, The API is distributed along with galaxy. To enable it, set the following in your universe_wsgi.ini: enable_api = True Once that's enabled, each user can create an API key using the "API Keys" option in the user menu of the main masthead. For additional information, see /scripts/api/README in your galaxy directory, or email back and I'll do what I can to help. -Dannon On May 12, 2011, at 2:08 PM, Frederick van Staden wrote:
Anyone know where i can get the galaxy API?
Regards Fred ___________________________________________________________ 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:
Hello I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary. Is there a way to do that? I had a look at lib/galaxy/web/controller/admin.py and templates/grid_base.mako but I fail to see where the "query" variable (containing the items, therefore the users) come from in the mako template, so I didn't figure out what each column class in admin.py actually manipulates in the get_value() methods. Regards, L-A
Hello Louise, I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size diff -r 56be3f4871cd lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri May 13 21:24:03 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon May 16 14:15:23 2011 -0400 @@ -41,6 +41,13 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class DiskUseageColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + disk_used = 0 + for history in user.active_histories: + for hda in history.active_datasets: + disk_used += hda.get_size() + return disk_used # Grid definition webapp = "galaxy" @@ -65,6 +72,7 @@ ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), + DiskUseageColumn( "Disk Used", attach_popup=False ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote:
Hello
I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary.
Is there a way to do that?
I had a look at lib/galaxy/web/controller/admin.py and templates/grid_base.mako but I fail to see where the "query" variable (containing the items, therefore the users) come from in the mako template, so I didn't figure out what each column class in admin.py actually manipulates in the get_value() methods.
Regards, L-A ___________________________________________________________ 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
Thank you so much!!! It works really fine! I suspected something akin to that but I couldn't find the right attributes. But I still have a question: It comprises the datasets stored in libraries right? Is there a way to ignore them? Thanks again, L-A Greg Von Kuster wrote:
Hello Louise,
I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size
diff -r 56be3f4871cd lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri May 13 21:24:03 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon May 16 14:15:23 2011 -0400 @@ -41,6 +41,13 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class DiskUseageColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + disk_used = 0 + for history in user.active_histories: + for hda in history.active_datasets: + disk_used += hda.get_size() + return disk_used
# Grid definition webapp = "galaxy" @@ -65,6 +72,7 @@ ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), + DiskUseageColumn( "Disk Used", attach_popup=False ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ]
On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote:
Hello
I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary.
Is there a way to do that?
I had a look at lib/galaxy/web/controller/admin.py and templates/grid_base.mako but I fail to see where the "query" variable (containing the items, therefore the users) come from in the mako template, so I didn't figure out what each column class in admin.py actually manipulates in the get_value() methods.
Regards, L-A ___________________________________________________________ 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 <mailto:greg@bx.psu.edu>
Louise, The original code would not eliminate a dataset file that was pointed to by a LibraryDatasetDatasetAssociation, and then imported from the data library into the user's history, creating a HistoryDatasetAssociation that points to the same file. I've added a bit of code below that should eliminate datasets falling into this category - not tested at all though... On May 17, 2011, at 8:42 AM, Louise-Amelie Schmitt wrote:
But I still have a question: It comprises the datasets stored in libraries right? Is there a way to ignore them?
Greg Von Kuster wrote:
Hello Louise,
I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size
diff -r 56be3f4871cd lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri May 13 21:24:03 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon May 16 14:15:23 2011 -0400 @@ -41,6 +41,13 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class DiskUseageColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + disk_used = 0 + for history in user.active_histories: + for hda in history.active_datasets:
dataset = hda.dataset if not dataset.active_library_associations:
+ disk_used += hda.get_size()
+ return disk_used # Grid definition webapp = "galaxy" @@ -65,6 +72,7 @@ ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), + DiskUseageColumn( "Disk Used", attach_popup=False ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ]
On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote:
Hello
I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary.
Is there a way to do that?
I had a look at lib/galaxy/web/controller/admin.py and templates/grid_base.mako but I fail to see where the "query" variable (containing the items, therefore the users) come from in the mako template, so I didn't figure out what each column class in admin.py actually manipulates in the get_value() methods.
Regards, L-A ___________________________________________________________ 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 <mailto:greg@bx.psu.edu>
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Looks like it's working, a couple of values were reduced :) Thank you so much!!! L-A Greg Von Kuster wrote:
Louise,
The original code would not eliminate a dataset file that was pointed to by a LibraryDatasetDatasetAssociation, and then imported from the data library into the user's history, creating a HistoryDatasetAssociation that points to the same file. I've added a bit of code below that should eliminate datasets falling into this category - not tested at all though...
On May 17, 2011, at 8:42 AM, Louise-Amelie Schmitt wrote:
But I still have a question: It comprises the datasets stored in libraries right? Is there a way to ignore them?
Greg Von Kuster wrote:
Hello Louise,
I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size
diff -r 56be3f4871cd lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri May 13 21:24:03 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon May 16 14:15:23 2011 -0400 @@ -41,6 +41,13 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class DiskUseageColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + disk_used = 0 + for history in user.active_histories: + for hda in history.active_datasets:
dataset = hda.dataset if not dataset.active_library_associations:
+ disk_used += hda.get_size()
+ return disk_used # Grid definition webapp = "galaxy" @@ -65,6 +72,7 @@ ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), + DiskUseageColumn( "Disk Used", attach_popup=False ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ]
On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote:
Hello
I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary.
Is there a way to do that?
I had a look at lib/galaxy/web/controller/admin.py and templates/grid_base.mako but I fail to see where the "query" variable (containing the items, therefore the users) come from in the mako template, so I didn't figure out what each column class in admin.py actually manipulates in the get_value() methods.
Regards, L-A ___________________________________________________________ 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 <mailto:greg@bx.psu.edu>
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote:
Hello
I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary.
Is there a way to do that?
On Mon, May 16, 2011 at 7:18 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Louise, I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size
That sounds really useful - it is something that you plan on adding to Galaxy officially? Thanks, Peter
Possibly, but it would require an enable flag in the config since instances with hundreds of users could pose problems with rendering delays. If someone will proved the precise specs for what yo9u want, I'll add it to my list, but it will be awhile before I get to ti. For example, should dataset files that have both LibraryDatasetDatasetAssociations and HistoryDatasetAssociations be eliminated from the total? On May 17, 2011, at 9:10 AM, Peter Cock wrote:
On May 16, 2011, at 10:18 AM, Louise-Amelie Schmitt wrote:
Hello
I would like to add a column in the admin panel's user list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary.
Is there a way to do that?
On Mon, May 16, 2011 at 7:18 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Louise, I've pasted a diff below for the file ~/lib/galaxy/web/controller/admin.py that will provide what you want, I believe. I didn't have time to fully test, but it gives you the idea. You can make things prettier by wrapping the returned value in galaxy.datatypes.data.nice_size
That sounds really useful - it is something that you plan on adding to Galaxy officially?
Thanks,
Peter
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Peter Cock wrote:
That sounds really useful - it is something that you plan on adding to Galaxy officially?
Yes, I'm working on adding a lot of user- and admin- side access to various numbers about disk usage (used by histories, used by deleted data, etc. and disk quotas. I hope to have this done shortly after the GCC. Thanks, --nate
Thanks,
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:
On Tue, May 17, 2011 at 2:21 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Peter Cock wrote:
That sounds really useful - it is something that you plan on adding to Galaxy officially?
Yes, I'm working on adding a lot of user- and admin- side access to various numbers about disk usage (used by histories, used by deleted data, etc. and disk quotas. I hope to have this done shortly after the GCC.
Thanks, --nate
Hi Nate, Since you're looking at this kind of thing, would the "Saved Histories" page be worth updating to show the size on disk of each history? As a Galaxy user that seems moderately useful - although perhaps more of interest to Galaxy admins? Peter
Peter Cock wrote:
On Tue, May 17, 2011 at 2:21 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Peter Cock wrote:
That sounds really useful - it is something that you plan on adding to Galaxy officially?
Yes, I'm working on adding a lot of user- and admin- side access to various numbers about disk usage (used by histories, used by deleted data, etc. and disk quotas. I hope to have this done shortly after the GCC.
Thanks, --nate
Hi Nate,
Since you're looking at this kind of thing, would the "Saved Histories" page be worth updating to show the size on disk of each history? As a Galaxy user that seems moderately useful - although perhaps more of interest to Galaxy admins?
This is already done in development, I was going to finish up the code and commit it within the next couple of weeks. --nate
Peter
On Thu, Jun 9, 2011 at 4:20 PM, Nate Coraor <nate@bx.psu.edu> wrote:
Peter Cock wrote:
Hi Nate,
Since you're looking at this kind of thing, would the "Saved Histories" page be worth updating to show the size on disk of each history? As a Galaxy user that seems moderately useful - although perhaps more of interest to Galaxy admins?
This is already done in development, I was going to finish up the code and commit it within the next couple of weeks.
This has now been committed to galaxy-central, and looks very useful. I notice the "Saved Histories" page now has buttons "Rename", "Delete", "Delete and remove datasets from disk" (new) and "Undelete". That distinction between "hide it away" and "really delete" should make sense to users from the "Recycle Bin"/"Trash" idea for files on Windows/MacOSX. Thanks, Peter
participants (6)
-
Dannon Baker -
Frederick van Staden -
Greg Von Kuster -
Louise-Amelie Schmitt -
Nate Coraor -
Peter Cock