Jeremy Goecks
b43ff3d153
Fix more unicode issues when listing and running workflows.
2010-10-20 16:10:37 -04:00
Jeremy Goecks
760785bd95
Enable display of unicode characters in history and workflow annotations.
2010-10-20 15:52:36 -04:00
Kanwei Li
43028dbcc0
trackster: Add proper CIGAR support to BAM display (properly displays matches, deletions, skipped bases, and clipping. Padding and insertions are skipped as of now as there is no good way to insert new space into the view.)
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- Don't re-add new datasets when refreshing after using "Add into current viz" link
- To prevent browser lockup, only display up to 50 lines of features by default (user-editable in future). TODO: add warning message when this occurs
2010-10-19 18:58:57 -04:00
Jeremy Goecks
3caf212cab
Add dynamic attribute filtering framework for trackster and enable dynamic filtering of VCF quality values and BED score values. Framework enables users to interactively filter a visualized dataset within trackster; for example, a BED file of peaks can be filtering so that only peaks with a score greater than 100 are shown.
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Individual changes include: (a) improvements to datatypes and data providers to support BED score filtering and VCF quality filtering; (b) addition of jQueryUI theme for slider; (c) modifications to trackster to show, update, and apply filters.
2010-10-19 16:25:51 -04:00
Ramkrishna Chakrabarty
83b1fba835
sample tracking
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- create request search+select box bug fixed.
- sample datasets grid operations fixed
2010-10-15 08:51:30 -04:00
Greg Von Kuster
bed3d3987c
A bit of code cleanup / optimization in sample tracking.
2010-10-14 11:23:33 -04:00
Ramkrishna Chakrabarty
4631710431
sample_tracking fixes
2010-10-14 00:24:56 -04:00
Ramkrishna Chakrabarty
ed6b6664e3
sample tracking UI fixes
2010-10-13 16:35:39 -04:00
Ramkrishna Chakrabarty
381b72258a
sample tracking bug fixes
2010-10-13 16:07:06 -04:00
Greg Von Kuster
2942a66c90
Clean up the code in the request_admin controller.
2010-10-12 15:36:22 -04:00
Kanwei Li
51da44adf9
trackster: Fix refactor breaking bam tracks. Only show draggable handle in editor mode. Update jQuery UI to 1.8.5 and add slider widget
2010-10-12 15:24:41 -04:00
Ramkrishna Chakrabarty
fe791cbdc7
sample_tracking:
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- bug fix in method to set library permissions for the data transfer user
- code cleanup
2010-10-12 15:06:00 -04:00
Ramkrishna Chakrabarty
aeb08431cb
sample_tracking bug fixes:
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- samples search now working for new unsubmitted requests
- sample state auto update using ajax now working
2010-10-12 14:23:44 -04:00
Ramkrishna Chakrabarty
d4610fa444
sample tracking bug fixes:
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- dataset select page now fixed
- find samples page now fixed for regular user
2010-10-12 09:17:04 -04:00
Ramkrishna Chakrabarty
6d9f1bf0a3
sample_tracking bug fixes:
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- when adding new sample, sample index now starts from 1 instead of 0
- removed searching on user email on the request grid
- replaced username with user email in request info page
2010-10-12 08:37:39 -04:00
Jeremy Goecks
2290fe1e85
Re-fix issue from 384c809db93e: show items in user menu when user is remote. Contributed by JJ and Ry4an Brase.
2010-10-11 17:07:59 -04:00
Greg Von Kuster
81c76fdb96
First pass at Galaxy sample tracking re-write. Highlights: lots of code cleanup with several not-needed methods removed, many mthods and mako templates have been renamed clarify what they do, all object ids are now encoded, methods in the requests_common controller that include features requiring an admin user are now secured. More work is needed in the requests_admin controller which will be in the next commit.
2010-10-11 16:35:57 -04:00
Ramkrishna Chakrabarty
37e41277e7
Making the 'Lab' tab visible to users own at least one sequencing request
2010-10-08 14:33:49 -04:00
Kanwei Li
e3979f52f5
Make published items set the "Shared Data" tab as the active tab
2010-10-07 15:33:54 -04:00
Kanwei Li
31b9198376
Data libraries: Use jStore to save folder expansion state
2010-10-07 14:02:18 -04:00
Kanwei Li
a889f76076
trackster: Can now reorder tracks inline. Put cancel button in modal dialogs to the left instead of right
2010-10-06 13:07:45 -04:00
Jeremy Goecks
3cfde269e5
Fix grid link/label bug introduced in 4372:269c46003857
2010-10-06 10:42:57 -04:00
Kanwei Li
aa7065d6b4
Visual tweaks to new search UI
2010-10-05 22:39:44 -04:00
Kanwei Li
6ba7f2811f
New style for search boxes in grids. Grid items will no longer show outline when hovered upon if there are no actions to be performed.
2010-10-05 18:21:31 -04:00
Kanwei Li
03c741cf19
Fix functional tests as they think dynamically created jQuery elements are real
2010-10-04 17:22:58 -04:00
Kanwei Li
06b9b59b96
Make links in split menubuttons take the link instead of popping up the menu options. Use new menubutton style in data libraries and sharing_base.
2010-10-03 19:12:40 -04:00
Kanwei Li
52459bceb0
Refactored refresh_on_change javascript code to run in galaxy.base when the page is loaded. Fixed bug with autocomplete_select: when switching from a value within refresh_on_change_values to a value outside of it, the page did not refresh. Removed duplicate code from templates.
2010-10-01 16:20:34 -04:00
Jeremy Goecks
0b5c59de0b
Remove unneeded grid initialization code.
2010-09-29 18:06:22 -04:00
Kanwei Li
65a474b9a0
trackster: Move "Add Tracks" button to main pane, UI tweaks for overview
2010-09-29 13:56:09 -04:00
Jeremy Goecks
f9719a7540
Fix bug that was causing Page item selection grids to be initialized twice and hence causing grid paging to fail.
2010-09-29 13:46:06 -04:00
Greg Von Kuster
0b97c298c1
Fix for rendering hidden widget field values associated with library templates whose fields are displayed on the upload form when importing a dataset from the current history. Added new functional test to cover behavior.
2010-09-29 12:39:39 -04:00
Greg Von Kuster
d3e5f3eda9
Fixes for column filtering and sorting problems introduced in change set 4275:
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eea6144270bf. Queries that include table joins cannot guarantee unique column names, so add support to the grid framework for <column>.key values like <TableName>.<ColumnName>. Enhance the tool shed grids to take advantage of this so that sorting snd filtering on columns is functionally correct.
2010-09-28 13:11:10 -04:00
Jeremy Goecks
e1876ef767
Use a job to export a history to an archive file. Exporting a history is now enabled in the history options panel, but importing a history is not yet a job and remains disabled. When a user exports a history, a link is provided that can be used to retrieve the archive or, in the future, moved to another Galaxy instance.
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The job that exports a history creates (a) a dataset for storing the archive and (b) multiple temporary attribute files to store the necessary data for exporting a history's datasets, jobs, etc. The temporary files are cleaned up when the job ends. Currently, there is no cleanup for history archive files.
2010-09-28 11:40:19 -04:00
Kanwei Li
0fbab45d14
trackster: Inline editing of configuration and removing of tracks, obsoleting the right editing panel. Improved appearance of overview box by adding a background for the scroll bar, and having a sliding window to indicate region shown. Added id numbers in front of API results for upcoming interactive script.
2010-09-23 20:00:58 -04:00
Greg Von Kuster
858349cb63
Rewrite the functional tests that cover all Galaxy forms related behavior. Clean up / fix bugs in several sample run request templates. Fix a bug introduced in change set a8cdece11998 which incorrectly generated selected options in a select list in the data library framework.
2010-09-22 16:38:49 -04:00
Ramkrishna Chakrabarty
0c1f60ce78
lims: ui improvements
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removed dbg stmt
2010-09-20 15:08:30 -04:00
Jeremy Goecks
6bfaa14643
Add tool search to workflow editor. Also standardize tool panel structure and style so that it is the same in both the main interface and in the workflow editor; workflow editor now uses styles in tool_menu.css as well.
2010-09-20 13:28:16 -04:00
Kanwei Li
a5ef9b53e2
- Refactored tagging/autocomplete JS, fixing bugs regarding leaving the tagging box
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- Better packing for trackster when zoomed in as packing will be done on a w_scale basis instead of rounding to levels
- Move folder icon in data libraries to next to the text, rephrase suggestion on compression schemes
2010-09-17 17:51:11 -04:00
Greg Von Kuster
f7334104a0
Move the upload_option (ie., file, directory, filesystem paths, import from history) into a select list on the data library upload form. Selecting an upload_option now performs a refresh_on_change on the upload form so that any form contents entered before selecting the option are now retained. Improvements and bug fixes were made throughout the pieces of the framework that support this.
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Major improvements and very significant code cleanup to the entire functional test framework was done in this change set as well.
2010-09-17 15:23:58 -04:00
Dannon Baker
fe4e70de03
Typos 'succesfully' -> 'successfully' fixed in tool_executed.mako
2010-09-15 17:11:10 -04:00
Jeremy Goecks
2fddd521fe
(1) Added templates for downloading/exporting objects and (2) created 'Download or Export' option for workflows that enables users to download a workflow to a file or export a workflow to myExperiment.
2010-09-10 17:37:13 -04:00
Greg Von Kuster
083e9fa547
(no commit message)(1) Add the ability to make any library item public ( and it's contents if it has any ).  There are now options on library item pop-up menus to make a library dataset public, make all contents of a folder public, or make an entire data library public.
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(2) Enhance and cleanup the test_library_security.py functional test script to cover new features.
(3) Clean up security checking code recently added to the library-common controller by creating methods for checking permissions and calling the methods when necessary.
(4) Add checks to the security controller methods to only flush to the db when necessary.
(5) Add a pop-up menu for folders in the Data Libraries perspective to enable users to view folder information since it may include template information.
(6) Fix all currently broken library-related functional test - should now all be green.
2010-09-10 12:06:54 -04:00
Jeremy Goecks
9e44caf592
UI improvements for annotating items: more descriptive messages and larger targets.
2010-09-08 17:52:01 -04:00
Kanwei Li
dae04b0dae
Clicking on a folder name in data libraries now expands the folder instead of displaying information/description, which is already in the name. Move fold icon next to folder name. Fix whitespace off by one
2010-09-08 17:20:16 -04:00
Jeremy Goecks
1ff003ba37
UI improvements to published items grids: (a) default sorting for community ratings is now correct (highest rated to lowest rated); (b) 'last updated' sorting arrow now consistent with other sorting; and (c) only first 150 characters of annotation are shown. Also added column 'ReverseSortColumn' to grid framework; this column is useful for when a column's natural sort is descending rather than ascending.
2010-09-08 15:59:43 -04:00
Kanwei Li
4e63b24869
Fix small html/js issues with data libraries
2010-09-08 15:22:47 -04:00
Jeremy Goecks
01ea051eee
Add CommunityRatingColumn to grid infrastructure and add 'Community Rating' columns to published item grids. Community ratings are computed on demand for now, but this may need to change in the future.
2010-09-08 11:43:25 -04:00
Greg Von Kuster
b15ed6a67a
Render disabled html fields instead of value strings when rendering un-editable data library template field information.
2010-09-07 16:07:11 -04:00
Ramkrishna Chakrabarty
4f5f59e7d8
lims: added support for bulk selection of library & folder for multiple samples
2010-09-07 11:07:50 -04:00
Nate Coraor
5127fe1456
Add a disk path field to the admin side of the library dataset info page.
2010-09-07 09:45:04 -04:00
Jeremy Goecks