James Taylor
931a51c9cb
Updating packed versions of javascripts.
2008-08-07 19:28:42 -04:00
Daniel Blankenberg
00f2bc165e
Move moving around of security.
2008-08-07 13:47:20 -04:00
Nate Coraor
9553034811
Merged Dan's latest commit
2008-08-07 12:08:25 -04:00
Daniel Blankenberg
9b263ea4de
Fix for dynamic select lists generated from contents of input file when no valid datasets exist in the history.
2008-08-07 11:41:59 -04:00
Daniel Blankenberg
c546f50963
Properly set permissions on tools that create new datasets in their post job hooks (this is deprecated).
2008-08-06 15:41:38 -04:00
Daniel Blankenberg
32cb3c5341
Moved security code out of model and into its own directory.
2008-08-06 15:22:02 -04:00
Daniel Blankenberg
4a2efcffd1
Changes to access controls, mostly cosmetic.
2008-08-05 16:35:14 -04:00
Nate Coraor
375203a4e0
Merged head from central
2008-08-05 10:17:42 -04:00
Greg Von Kuster
223bb40e74
Better fix for gops command line parser, now properly handles no strand column.
2008-08-04 10:20:23 -04:00
Daniel Blankenberg
80e56db29d
RECOMMIT: Removing newly created history controller, and moving
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history_set_permissions into the root controller with the rest of the
history methods.
2008-08-01 15:47:57 -04:00
Daniel Blankenberg
250c5ae759
RECOMMIT: Allow users to specify the default permissions assigned to
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new histories.
2008-08-01 15:47:06 -04:00
Daniel Blankenberg
8fd301c2e6
RECOMMIT: Allow users to change the default permissions assigned to new
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datasets (not relying on input) for their current history.
2008-08-01 15:45:11 -04:00
Daniel Blankenberg
fddd3b572f
RECOMMIT: First pass with adding role based access controls. Added roles
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and groups. Users can be associated with groups. Roles can be associated
with roles, datasets, groups, and users.
Currently the creator of a dataset can mark the dataset as private,
preventing other users from viewing or utilizing this dataset, even if
it's containing history is shared. This is done via the edit attributes
page for a particular dataset.
This requires enable_beta_features to be set.
2008-08-01 15:44:10 -04:00
Nate Coraor
0492964745
Remove a couple templates that I missed in the rollback.
2008-08-01 15:26:02 -04:00
Daniel Blankenberg
ec3176905a
Fix for the creation of workflows from shared histories.
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Added a column 'copied_from_history_dataset_association' to history_dataset_association. This requires a db change.
2008-08-01 15:05:54 -04:00
Greg Von Kuster
693caa34fc
Fix for gops metadata param parser when strand column not included in input dataset, added new test for gops intersect. Fix for datatype converters - now use new approach to metadata params.
2008-08-01 14:34:16 -04:00
Greg Von Kuster
81bb5e4996
Fix for JobWrapper.finish, dataset state no longer flushed prior to other attributes ( e.g., metadata) being flushed.
2008-08-01 14:25:42 -04:00
James Taylor
61caa7ea18
Compensatory bug in conditional parameters that was revealed by previous
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commit.
2008-07-31 20:49:06 -04:00
James Taylor
3221a71df3
Fix for preserving values of parameters after a repeat/conditional in
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Tool.update_state. This should fix the problem reported by Dan with the
subject "Re: [galaxy-bugs] Galaxy tool error report from cathy@bx.psu.edu ".
2008-07-31 17:55:41 -04:00
Nate Coraor
497ff6e05d
Rolling back Dan's most recent commits, we'll be setting up a branch for this.
2008-07-30 17:15:40 -04:00
Daniel Blankenberg
fd6b8b9b9d
Bug fix for Concatenate FASTA alignment by species tool.
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Also added a warning stating that this tool will only work on Galaxy style FASTA headers.
2008-07-29 11:24:28 -04:00
Daniel Blankenberg
633a218fce
Removing newly created history controller, and moving history_set_permissions into the root controller with the rest of the history methods.
2008-07-28 13:01:18 -04:00
Daniel Blankenberg
1554a13287
Allow users to specify the default permissions assigned to new histories.
2008-07-28 12:48:15 -04:00
Daniel Blankenberg
9a010cc626
Allow users to change the default permissions assigned to new datasets (not relying on input) for their current history.
2008-07-28 12:32:09 -04:00
Daniel Blankenberg
404d86d2ea
First pass with adding role based access controls. Added roles and groups. Users can be associated with groups. Roles can be associated with roles, datasets, groups, and users.
...
Currently the creator of a dataset can mark the dataset as private, preventing other users from viewing or utilizing this dataset, even if it's containing history is shared. This is done via the edit attributes page for a particular dataset.
This requires enable_beta_features to be set.
2008-07-25 14:16:41 -04:00
Greg Von Kuster
8d679d6541
Change C Elegans server URL to wormbase using GBrowse version 1.69.
2008-07-24 13:59:23 -04:00
Greg Von Kuster
bfabec75a0
Fixes for column_maker and filtering tool to use new approach for handling metadata in the tool params - functional tests should now pass.
2008-07-23 17:12:01 -04:00
Greg Von Kuster
5dd014a91e
Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.
2008-07-23 15:27:39 -04:00
Greg Von Kuster
9dbf7c0385
Corrected some text in the compare tool config.
2008-07-23 09:35:34 -04:00
Greg Von Kuster
0ca286098f
Add use_remote_user to the reports config.
2008-07-23 09:24:13 -04:00
Greg Von Kuster
872c0d6c94
Make sure dataset peek is set before trying to display it.
2008-07-22 12:27:26 -04:00
James Taylor
b23200d5b8
Fix generation of links in tool_menu so that they point to the tool_runner
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controller even when called as /root/tool_menu.
2008-07-22 11:02:41 -04:00
James Taylor
958770640d
Fixes to tool parameter error handling in workflows. Workflows are now
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ordered by update_time desc in index pages. The menu frame refreshes
properly on changing the workflow menu.
2008-07-21 21:15:10 -04:00
James Taylor
64aea7a907
Move "Run Workflow" button to bottom for consistency with other forms.
2008-07-21 20:48:06 -04:00
James Taylor
1033fcf211
Allow result of file upload (and other datasets that don't have job records)
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to be used as "Input Datasets" when constructing a workflow from a history.
Fix problem with dynamic selects in histories (the values are now properly
wrapped with UnvalidatedValue).
2008-07-21 20:04:11 -04:00
James Taylor
d2c5e99b9e
Eager load HDAs. Must be careful with these joins, this was really slowing
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down /history on test. Run with "echo=True" for a while after making
substantial database changes.
2008-07-21 19:59:42 -04:00
James Taylor
e65294e0d5
Fix workflow menu configuration (submitting with not entries works,
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orphaned entry rows are deleted). Also prevent users from sharing a workflow
with themselves.
2008-07-21 18:39:18 -04:00
Greg Von Kuster
f8c00de9bc
Fix for displaying peek columns if a column contains no data.
2008-07-21 10:51:46 -04:00
Daniel Blankenberg
2c38721060
Typo in last commit.
2008-07-18 12:11:58 -04:00
Daniel Blankenberg
a19093d158
Fix bug in JobWrapper.get_input_fnames(), used by pbs runner, when an input dataset was optional and left empty.
2008-07-18 12:10:23 -04:00
James Taylor
70c4b8ee23
Workflows (owned and shared) can now be added to the tool menu.
2008-07-17 22:14:40 -04:00
James Taylor
a46def3c5c
Merge.
2008-07-17 20:42:00 -04:00
James Taylor
d6607906d4
Allow loading a specific controller/action in the root middle frame, and use
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this to allow the workflow editor to return to the workflow management page.
2008-07-17 20:40:20 -04:00
James Taylor
a633e8cd25
Fix for scroll panel when dropping while still overlapping the edge.
2008-07-17 20:16:13 -04:00
James Taylor
b1c4645b54
Some page titles
2008-07-17 19:46:28 -04:00
James Taylor
3fc7bb94ad
Eagerload stored -> current workflow and workflow -> steps.
2008-07-17 19:45:56 -04:00
James Taylor
65bf65223f
Handle target = "_parent" in popup menu so that workflow editor doesn't load
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in the middle frame.
2008-07-17 19:45:17 -04:00
Greg Von Kuster
8ce37ea721
Fix for Tabular.set_meta() - when column contains no values, default column type metadata to string.
2008-07-17 14:58:30 -04:00
Nate Coraor
8e8c1c9cf2
Basic $REMOTE_USER support.
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A database change is necessary:
ALTER TABLE galaxy_user ADD COLUMN external boolean;
To use:
http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy
I've tried to be as friendly as possible with respect to enabling and
disabling $REMOTE_USER support. If you have an existing server and
enable use_remote_user, users whose external login matches their Galaxy
username will have access to their existing history/session. If the
logins don't match, any existing credentials they had are destroyed.
Likewise, when disabled, users who weren't created automatically may
continue to access their histories/sessions. Automatically created
users are logged out, and can't log in unless enabled by an administrator.
2008-07-17 09:15:38 -04:00
James Taylor
8cb0cc1edd
Don't use redirects in workflow to avoid a really annoying safari
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history bug. Use programatically generated form in 'rename'.
2008-07-14 21:41:29 -04:00
James Taylor