James Taylor
c245b5b6ca
Changes to the 'list histories' interface. This incorporates the changes from Assaf Gordon to display datasets by state, as well as changing how switch / delete/ undelete work to make the interface less disruptive. Share and rename still work as before. There is now a history controller, and some fixes to tests to deal with that. New grid styles used here will eventually be propogated to other data grid tables.
2009-01-12 18:25:32 -05:00
Nate Coraor
760f024584
New styles from Anton
2009-01-05 10:05:36 -05:00
Greg Von Kuster
db1c1fb660
merging from central
2008-12-18 16:44:34 -05:00
Greg Von Kuster
42ca95a373
Enhance the tool panel, now supports following tags:
...
<toolbox>
<tool file="data_source/upload.xml"/> # tools outside sections
<label text="Basic Tools" id="basic_tools" /> # labels outside sections
<workflow id="529fd61ab1c6cc36" /> # workflows outside sections
<section name="Get Data" id="getext"> # sections
<tool file="data_source/biomart.xml" /> # tools inside sections
<label text="In Section" id="in_section" /> # labels inside sections
<workflow id="adb5f5c93f827949" /> # workflows inside sections
</section>
</toolbox>
2008-12-18 16:35:26 -05:00
Nate Coraor
b6d561fb42
Allow users to download a selection of datasets directly from the library in an archive format of their choosing.
2008-12-15 16:37:54 -05:00
Daniel Blankenberg
52e1d4686d
Merging heads
2008-11-24 11:20:18 -05:00
Daniel Blankenberg
7e0479473c
Update GMAJ to latest beta.
2008-11-24 11:19:48 -05:00
Nate Coraor
1369b8d199
You can now require that users log in to use Galaxy. The sample config is way different but it's only because I cleaned it up a bit. The only new options are require_login/allow_user_creation.
2008-11-20 15:14:47 -05:00
Anton Nekrutenko
bf540d2628
Unseq genomes for oct
2008-09-19 16:28:11 -04:00
Daniel Blankenberg
6d2e714820
merging heads
2008-09-18 16:02:48 -04:00
Daniel Blankenberg
0dff1b0662
Update to latest gmaj.
2008-09-18 15:24:51 -04:00
Nate Coraor
b1caa7431a
Admin side of the new file browser. It's late, I've been working all night,
...
and I'm not sure what my name is... so there are probably bugs. Please play
with this stuff and try to break it.
This commit also includes permissions editing that actually (finally!) lets you
create new group->dataset associations after the dataset already exists.
Currently the only entry point is from the Library, but the "display a group's
datasets" page can now be extended to contain useful information about
associated datasets (like whose history a dataset is part of and what folder a
dataset is in) to make it actually, like, useful and stuff.
2008-09-10 23:22:06 -04:00
Nate Coraor
4edc6d6626
Spiffy new library browser interface. Also, dim datasets in your
...
history on which you don't have permissions.
2008-09-10 10:10:13 -04:00
James Taylor
bd1a4e01cc
More cleanup for admin UI.
2008-09-08 13:41:55 -04:00
Daniel Blankenberg
8bdd875488
my message
2008-09-08 11:21:29 -04:00
James Taylor
a212c44899
Update packed version of workflow editor script (fix z-index problem again?)
2008-09-08 09:47:37 -04:00
James Taylor
dc049016d7
Add permission style to CSS template and regenerate.
2008-09-03 13:25:27 -04:00
James Taylor
48ae7803aa
First pass on improving admin ui. Just the top level interface and the pages for users and groups. Hopefully this at least gives an idea of the way these things should be encoded in HTML.
2008-09-03 12:45:29 -04:00
James Taylor
85d1203a5c
Tab-like top level navigation. This makes the "workflow" view separate from the "interactive analysis" view, which makes sense since tools and history are irrelevant when managing workflows. The "workflow" entry in the tool menu now only shows up if a user has workflows added to it, otherwise you get to the workflow management screen from the top. Adds infrastructure for a few things (including pages with 0, 1, or both panels, a compact message box).
2008-09-03 12:27:41 -04:00
Greg Von Kuster
745f1e6d07
my message
2008-09-02 09:21:33 -04:00
James Taylor
acb14a2b1b
Remove node from workflow before removing associated element
...
from canvas, make sure to actually set "active_node" to null
when clearing the active node.
2008-08-31 21:14:06 -04:00
James Taylor
e8ae9e040a
Another IE fix for stacking / deleting workflow editor nodes.
2008-08-28 13:57:23 -04:00
James Taylor
3b15ac9627
A better fix for bring-to-front stacking in workflow editor
2008-08-28 13:38:54 -04:00
James Taylor
d294f00821
Bugfix for workflow editor.
2008-08-27 15:51:59 -04:00
Nate Coraor
c02f382874
Merged changes from central.
2008-08-26 10:47:08 -04:00
James Taylor
42992455c2
Internet explorer fixes and support -- popup menus and dialogs work better on IE6+,
...
workflow editor works on IE7 (using excanvas). It actually *nearly* works on IE6 but
there are some layout problems that are probably not worth wasting time on. If any IE
users can test this that would be great!
2008-08-22 17:47:43 -04:00
James Taylor
a32ae71d33
Add excanvas javascript (emulates <canvas> in IE using silverlight)
2008-08-22 17:44:32 -04:00
Nate Coraor
3802816b69
User interface to permissions, and a bunch of changes to ensure that
...
both permitted_actions and groups are set appropriately on datasets.
Somewhat tested and mostly working, but needs more testing.
Greg: If a userless session has a history, if that user logs in,
the DefaultHistoryGroupAssociation for the current history as well
as the datasets in that history are supposed to be updated with the
permissions in DefaultUserGroupAssociation, but this isn't happening.
Possibly because the default permissions on userless histories create
datasets in the public group with only the DATASET_ACCESS permission
(or possibly for another reason). What are the implications of giving
public users DATASET_MANAGE_PERMISSIONS?
2008-08-20 18:11:04 -04:00
James Taylor
931a51c9cb
Updating packed versions of javascripts.
2008-08-07 19:28:42 -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
65bf65223f
Handle target = "_parent" in popup menu so that workflow editor doesn't load
...
in the middle frame.
2008-07-17 19:45:17 -04:00
James Taylor
c8d610fa63
Remove javascript log messages
2008-07-14 21:39:28 -04:00
James Taylor
c3a76ab7d5
Fix popup menu positioning
2008-07-14 21:39:08 -04:00
James Taylor
ab6c577e85
Javascript to support popup menus.
2008-07-14 19:47:32 -04:00
James Taylor
9c1474f810
Styles for buttons and popup menus.
2008-07-14 19:47:08 -04:00
James Taylor
538dacd45d
Icon for "add" buttons.
2008-07-14 19:39:19 -04:00
James Taylor
24fed10a05
Add appropriate padding for table headers.
2008-07-14 01:53:10 +00:00
James Taylor
e0eeef9e43
jquery-ui 1.5.2 (various upstream bug fixes).
2008-07-10 19:29:25 +00:00
Daniel Blankenberg
1e1a3e81bf
Update to latest version (June 30, 2008) of GMAJ.
2008-07-09 19:07:03 +00:00
James Taylor
69c4444de2
Workflow: create a new python module for 'WorkflowModules'. Tools are now another type of module, which removes a lot of special cases in the controller. Fixed some problems with validation and parameter groups.
2008-06-27 00:22:02 +00:00
James Taylor
3b39fb87f3
Upgrade jquery to 1.2.6 and jquery-ui to 1.5, drag and drop should be a bit
...
faster. Improvements to scrolling panel in workflow editor. Removed unused
and obsolete jquery plugins.
2008-06-21 03:04:28 +00:00
Anton Nekrutenko
ae1ef0bc59
Unseq genome for June
2008-06-04 01:13:33 +00:00
Daniel Blankenberg
86f0862aa4
Move ucsc and gbrowse data from static to tool-data/shared.
...
Cron scripts on test and main will need to be updated when the server is.
GOPS complement tool and annotation profiler will now correctly use chromosome lengths files if available.
2008-06-03 18:53:26 +00:00
Daniel Blankenberg
a52c890c4a
Enhance the displaying of Drill Down menu items.
2008-05-22 20:21:23 +00:00
Daniel Blankenberg
310911f861
Update GMAJ to the latest beta.
...
GMAJ can now export MAF blocks back into the user's history.
The Interface for defining annotations has been updated.
2008-05-16 18:39:41 +00:00
Greg Von Kuster
8f944ef045
Changed URL for communicating with elegans server.
2008-05-16 12:15:04 +00:00
Greg Von Kuster
3f9afc5281
Fixes for GBrowse communication.
2008-05-15 13:38:31 +00:00
Greg Von Kuster
c32f87624f
Added code for integration with C. Elegans / GBrowse test server.
2008-05-12 18:55:48 +00:00
James Taylor
8cfa45310e
"Input dataset" module now works for running. Many bug fixes to workflows
...
and tools. Moved some methods related to params out of the Tool class, sets
of inputs can also be used in other ways (e.g. for modules). More abstraction
needed here.
2008-05-09 16:18:38 +00:00
James Taylor
24a3ce01c6
Workflows can now have steps of other kinds (not just tools). The first one
...
is "InputDataset" which allows a workflow to have an input dataset which many
different tools can use (without needing to specify it repeatedly. Still need
to extract out a common interface (tools will become another type of "module")
which will clean this up a lot.
2008-05-05 02:08:32 +00:00
James Taylor