Kanwei Li
1898e7712b
trackster: Add new dbkey column to viz tables, finish "Visualize in Trackster" button functionality
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- Dbkey now shown in "Saved Visualizations" grid
- "Visualize in Trackster" icon in history pane for supported dataset now works, letting you add that dataset to an existing browser or to a new browser. Dbkey for existing browsers is also shown.
2010-08-03 15:10:30 -04:00
Jeremy Goecks
1e12562272
Add a ratings framework so that users can rate shared items. All sharable items--histories, workflows, datasets, visualizations, and pages--can be rated. Main framework components are (1) database tables for storing ratings; (2) UsesItemRatings mixin that supports rating items and obtaining an item's average rating; (3) controller methods to handle rating asynchronously; and (4) jQuery star rating plugin and supporting code that enables interactive item rating. (2) and (4) can be reused in the community space.
2010-08-03 11:45:25 -04:00
Kanwei Li
c11b2ce4bc
trackster:
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- Fix Reference track incorrect display offset
- When no tracks exist in editor, show suggestion to add tracks
- Clicking "Visualize in Trackster" in history now shows a grid of current browsers, but actual adding is still work in progress
2010-07-28 18:51:32 -04:00
Kanwei Li
c44e91819e
trackster:
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- Fix vertical scrolling with mouse quirkiness
- Intro screen asking to select a chrom when no chrom is selected
- Fix Reference tracks not hiding when there is no longer sequence to display
- Make embedded vis not overflow
- Fix drag-selecting region not working in embedded viz
make_style.py can now be run without parameters, which will default to the blue theme
2010-07-26 12:26:39 -04:00
Kanwei Li
abf2404f02
trackster: remove mousewheel zoom (since scrolling window is more important), fix overview drag bug
2010-07-20 14:47:36 -04:00
Kanwei Li
8e2331d652
Add image_path global variable to base_panels so that images can always have the right path. Fix image issues with trackster
2010-07-13 16:22:27 -04:00
Kanwei Li
7bc37cfcf7
Fixed creation of new tracks, missing template-generated css for trackster, add .DS_Store, *.rej and *.orig to hgignore
2010-07-12 14:59:11 -04:00
Jeremy Goecks
f9911cae38
Pack scripts and update JS version.
2010-07-12 11:10:49 -04:00
Jeremy Goecks
b3e1228cdc
Make URLs for viz zoom in/out images relative.
2010-07-12 11:07:02 -04:00
Kanwei Li
ca09f826eb
trackster: Track browsers can now be embedded in Galaxy Pages as multiple browsers can now exist at the same time after refactoring. Display code is now separated from editor code. Some scrolling bugs have been fixed as well.
2010-07-01 20:04:29 -04:00
Jeremy Goecks
fc5110f08d
Fix bug that prevented correct toggling of recently used menu.
2010-06-21 15:07:38 -04:00
Jeremy Goecks
0a473b66f9
Smooth out the interactions b/t searching and recently used tools menu and add user preferences and logging to these features. In particular: (a) added code to manage hiding/showing of recently used items when search is active; (b) added simple Javascript framework for logging actions and setting user preferences asynchronously; and (c) enabled user preferences and logging for tool search and recently used tools menu.
2010-06-21 10:15:10 -04:00
Daniel Blankenberg
b243311c92
Enhance workflow editor to work with a list of output formats instead of only one. This fixes the bug were outputs utilizing a change_format tag could not be connected to an input that was of the changed-to type.
2010-06-18 14:26:18 -04:00
Jeremy Goecks
8d04bfe82b
Add tool searching functionality using Whoosh and lots of jQuery. Search is currently hidden by default but will soon be a user preference.
2010-06-17 17:22:55 -04:00
Kanwei Li
ce75edfa5f
trackster: Supports display of reference sequence in twobit format. Mapping of dbkey to twobit file is done in tool-data/twobit.loc. Reference track will automatically be shown when zoomed in if the twobit file exists for that dbkey. Also fixes a drawing issue with Reference/Read tracks.
2010-06-15 17:51:12 -04:00
Jeremy Goecks
d3f60664a9
Fix grid initialization bug that was preventing visualization grids from working properly.
2010-06-15 10:04:30 -04:00
Dannon Baker
e6fbb81168
Added annotations to run workflow display.
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New feature- actions in workflow steps. Change name, hide dataset, change datatype enabled.
2010-06-11 10:16:27 -04:00
Kanwei Li
dcfeb36f7c
Fix creating new trackster viz, fix autocomplete grouping by first character
2010-06-09 15:51:01 -04:00
Jeremy Goecks
a84c85004e
Set 3000 as the theoretical maximum and 1500 as the current maximum for the number of items that a search+select box can accept. These numbers balance capacity and performance.
2010-06-07 17:03:24 -04:00
Kanwei Li
47407f39ad
Fix autocomplete select not closing after dragging text inside, and holding arrow keys not triggering multiple times in firefox. Cleanup JS
2010-06-06 18:55:09 -04:00
Jeremy Goecks
af04947287
Better handling of return key in search+select.
2010-06-05 12:00:10 -04:00
Kanwei Li
0bcd4656bd
trackster: Implemented drag-zooming by letting you drag a region in the top label track (where chrom position is shown). Refactored to not use zoom levels anymore.
2010-06-03 17:58:58 -04:00
Jeremy Goecks
89aa0dd8bf
Search/select sorts only dbkey selects; others are unsorted.
2010-05-31 15:18:32 -04:00
Kanwei Li
64baf696f5
trackster: Can manually set display modes for tracks. Move buttons to the headers.
2010-05-28 21:13:25 -04:00
Jeremy Goecks
8d1b842279
Fix selector bug in search+select.
2010-05-26 15:27:06 -04:00
Jeremy Goecks
32acc918a8
Do not use search/select for multi-select inputs and pack scripts.
2010-05-25 14:42:52 -04:00
Kanwei Li
16bcc65b6f
trackster: respect block color for bam
2010-05-24 17:41:59 -04:00
Jeremy Goecks
dc0e679767
Another pass on search+select for autocomplete that handles user input much better.
2010-05-21 15:50:49 -04:00
Jeremy Goecks
c81b275d1c
Replace big selects that refresh on change with search+select.
2010-05-17 10:58:16 -04:00
Jeremy Goecks
08e6cee1fc
Only use search+select when jquery autocomplete plugin is defined.
2010-05-13 12:14:52 -04:00
Dannon Baker
bfcb63b35e
Fix for issue where connecting to a Workflow Step that had been changed wasn't being saved
2010-05-13 12:03:17 -04:00
Kanwei Li
d815c09491
trackster:
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- Prompt when leaving a viz with unsaved changes
- Can only add datatypes of the same dbkey
2010-05-12 17:43:29 -04:00
Kanwei Li
b83afd1dfb
trackster: fix track saving
2010-05-07 18:25:29 -04:00
Jeremy Goecks
815fd36e51
Another update to search+select: pack script and replace icon.
2010-05-07 10:28:28 -04:00
Jeremy Goecks
7f86345e99
Replace large selects w/o refresh_on_change with search+select.
2010-05-07 09:16:51 -04:00
Kanwei Li
25b041ef16
trackster:
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- Custom dbkeys now create new HDA and copies info in
- Fix track reordering for all browsers
- Fix track deletion
- Fix BAM display
2010-05-06 12:30:54 -04:00
Kanwei Li
0a7d97952c
trackster: fix BAM data error; display tweaks
2010-05-04 15:43:34 -04:00
Kanwei Li
7ce4296230
trackster: add filled line display
2010-05-04 12:50:48 -04:00
Jeremy Goecks
1b3280da58
Pack scripts.
2010-05-03 14:03:01 -04:00
Jeremy Goecks
2b94fd683b
Enable viewing of shared/accessible/published visualizations.
2010-05-03 14:02:08 -04:00
Kanwei Li
6a0147ec57
trackster: BAM display supports paired-end reads, displays sequence when possible
2010-04-28 17:35:02 -04:00
Kanwei Li
fbf74c9d0d
Fix various trackster issues
2010-04-21 18:35:59 -04:00
Kanwei Li
9ec4d4c82a
User-custom dbkeys can now be set for datasets in Edit Attributes and upload
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Always use autocomplete for dbkey entry (used to be >20)
2010-04-19 16:03:24 -04:00
Kanwei Li
4774cb4456
Fix issue where you cannot expand datasets in history pane after uploading a new dataset
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Alphanumeric sort when generating select field for dbkeys
trackster now supports custom dbkeys (but datasets don't yet)
2010-04-16 18:46:35 -04:00
Jeremy Goecks
f322c538fc
Pack scripts.
2010-04-13 13:14:59 -04:00
Ross Lazarus
855e2923a2
Add the raw uncompressed .js files needed for rgGRR svg display - the packed ones were already there
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Fix rgManQQ so the manhattan plot is not called for data without chromosome and offset
Use LD reduced data for IBD/GRR for faster performance and better resolution of close relationships
Add an LD pruning and thinning step to rgGRR - the target composite pbed or lped has the thinned files permanently added for reuse.
This is skipped for small numbers of markers since the plink --thin 0.1 option applied to tinywga.pbed will return an empty file
which is not really ideal.
2010-04-13 11:15:35 -04:00
Jeremy Goecks
4135f39355
Enable user to change dbkey from a known key back to unspecified. This is a hack, but there's no straightforward way to accomplish this without modifying the jquery autocomplete script.
2010-04-13 10:22:27 -04:00
Kanwei Li
f6c1c2db77
- Update jQuery.jStore, JSON2
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- Fix issue with all local prefs being deleted on "collapse all"
- Refactored history display code into galaxy.base
2010-04-09 18:09:54 -04:00
Jeremy Goecks
3ba6d2dfa4
Rollback text + autocomplete for big selects. Only use text + autocomplete for dbkey.
2010-04-09 13:02:15 -04:00
Kanwei Li
34518df336
Add BedGraph datatype (wiggle-like data for intervals)
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trackster:
- Fix various UI issues
- BedGraph -> array_tree converter
2010-04-06 19:00:39 -04:00
Kanwei Li