James Taylor
74db2397c5
Fixing up track browser UI. No longer uses session, cleaned up a bunch of unceccesary stuff. Still pretty limited -- coverage indexing doesn't seem to work right
2009-06-11 15:37:19 -04:00
James Taylor
537f8952ef
Merging Ian's trackster update with current head
2009-06-11 12:20:03 -04:00
James Taylor
8cfc65bb0f
Updating packed script for workflow editor
2009-05-01 12:24:07 -04:00
James Taylor
139a30e964
Handle the addition of new tool parameters better in the workflow editor. Default values will be filled in and a message displayed to the user
2009-04-29 13:46:02 -04:00
James Taylor
8f19b878dc
Fix for issubtype in workflow editor, would cause problems drawing connections for types with no inheritence relationships
2009-04-29 10:27:57 -04:00
Ian Schenck
feda672ffa
- Performance of indexers much improved.
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- Indexing for tracks done in background with a visual treatment done to Trackster
- DB builds can be uploaded by a user (chromInfo/len extension).
- TODO: Add ability to change the dbkey of a dataset to any arbitrary string value.
2009-04-23 13:46:52 -04:00
James Taylor
9a979abb36
Fix workflow auto-layout to properly handle nodes with no connections
2009-04-09 14:57:08 -04:00
James Taylor
74046a48e5
Reworking of workflow canvas. It is now infinite (grows to fit nodes as added). An overview map has been added, which can be dragged to quickly move around large workflows
2009-04-09 14:50:13 -04:00
James Taylor
8dbf032b0a
Cleaning up auto-scrolling in workflow editor a bit
2009-04-07 17:20:01 -04:00
James Taylor
cff3a62b8d
Auto-layout in workflow editor (much room to improve)
2009-04-07 16:56:00 -04:00
James Taylor
6b1caa0880
Redo of iphone UI using jqtouch. All ajax now so it works as an app from the home screen without needing to load safari
2009-03-29 18:14:24 -04:00
James Taylor
13c372529d
Improving the overlay support, and using it to display quickies on the welcome page
2009-03-31 15:03:36 -04:00
James Taylor
ee0e6b298f
Add some packed scripts that were missing, repack a few that had changed, and remove a few that are no longer used.
2009-03-31 12:07:22 -04:00
James Taylor
761500c9d1
Fix a bug in workflow UI that was messing up the detection of compatible datatypes (another missing 'var' problem).
2009-03-30 17:41:19 -04:00
James Taylor
14f1618dec
jquery 1.3.2 -- tested this time. Bad / deprecated selector syntax fixed in various templates and scripts
2009-03-28 23:35:08 -04:00
James Taylor
e8936b5f27
Add id attributes in many place to make it easier to locate elements in tests. Also,
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some changes to popups so they appear in the document near their anchor, rather than
at the top level.
2009-03-27 18:48:39 -04:00
Greg Von Kuster
2b818b3f91
jquery bug fix to make drop-down popup menus functional
2009-03-26 11:16:55 -04:00
James Taylor
4dce57dc04
Workflow parameterization!
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- When building a workflow, most parameters can be switched to
be set later ("at runtime"). The main (only?) exception is
parameters which are used as the test for conditionals
- When running a workflow, the user fills in the runtime parameters
just like in any other tool form.
- As a consequence, the run workflow form behaves more like a full
tool form (automatic refreshes, validation, et cetera).
- There is still a problem when paramters depend on a data input
that is not created until later. These should probably fall back
on late validation, but that requires a bit of cleanup to param
depedencies.
2009-03-22 10:33:07 -04:00
James Taylor
0507fb4b3d
Fix some javascript problems where code was assuming 'jQuery' would be available as 'q'
2009-03-19 21:23:50 -04:00
James Taylor
d7d01b53a5
Completely purge jquery-ui. Panels and workflow editor now use jquery.event.[drag/drop]
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As a consequence, the workflow editor now functions again.
2009-03-17 00:44:41 -04:00
Nate Coraor
86eb5e62b2
Asynchronous uploads. Currently disabled in IE, since IE throws
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occasional 'permission denied' errors when jquery attempts to set the
form target. Compatible with the nginx upload module, but interrupted
uploads will remain in the 'upload' state indefinitely.
2009-03-13 13:48:59 -04:00
Ian Schenck
985f7c63fa
Collapsed changeset: Trackster plugged into galaxy with behind-the-scenes indexing of Wiggle, coverage and interval datasets.
2009-03-11 00:29:01 +00:00
Nate Coraor
3058943a20
Backed out changeset 54276449337f
2009-03-05 20:31:52 -05:00
Ian Schenck
62fa85d78f
Backed out changeset 43786ade15d4
2009-03-05 19:36:52 +00:00
Nate Coraor
7da7368e55
Backed out changeset 71e66174dca2
2009-03-05 10:15:31 -05:00
Ian Schenck
c2281732e6
Merged conflicts with main branch.
2009-03-05 00:13:38 +00:00
Ian Schenck
b5f93ebc12
Combining changesets for tracks (lots of noise and not a lot of signal). This is a rough prototype of the tracks extension to Galaxy.
2009-03-04 23:55:51 +00:00
James Taylor
cb592fa20b
Updating the packed versions of all javascripts.
2009-02-25 14:24:46 -05:00
James Taylor
006b70e2a0
Move javascript for tabs up to galaxy.panels.js so it works in the workflow editor
2009-02-25 14:19:35 -05:00
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
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
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
acb14a2b1b
Remove node from workflow before removing associated element
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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
James Taylor
42992455c2
Internet explorer fixes and support -- popup menus and dialogs work better on IE6+,
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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
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
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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
ab6c577e85
Javascript to support popup menus.
2008-07-14 19:47:32 -04:00
James Taylor
e0eeef9e43
jquery-ui 1.5.2 (various upstream bug fixes).
2008-07-10 19:29:25 +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
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faster. Improvements to scrolling panel in workflow editor. Removed unused
and obsolete jquery plugins.
2008-06-21 03:04:28 +00:00
James Taylor
8cfa45310e
"Input dataset" module now works for running. Many bug fixes to workflows
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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
95ca08bb99
Workflow: Repeat/Conditional now work in workflows, adding/removing/refreshing
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properly update the 'terminals' for the nodes in the editor. Many other fixes
to saving and loading of workflows (error tracking should now be working
properly).
2008-05-04 20:10:57 +00:00
James Taylor
248797ce5f
Workflow editor now has a drag-to-scroll canvas and auto scrolling for
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contained elements.
2008-05-02 19:03:08 +00:00
James Taylor