Jeremy Goecks
abea9f8f76
Make VCF a first-class type in trackster. Added VCF data provider and VCF tracks type to trackster; new functionality is used to show reference base and alternate base for SNPs in VCF tracks. Also refactored data providers so that they inherit from a base provider.
2010-10-07 21:26:21 -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
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
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
Kanwei Li
65a474b9a0
trackster: Move "Add Tracks" button to main pane, UI tweaks for overview
2010-09-29 13:56:09 -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
Ramkrishna Chakrabarty
b8d1b02a55
interactivity bug fixed in mutation viz tool
2010-09-20 14:58:59 -04:00
Ramkrishna Chakrabarty
1bac740073
mutation viz tool
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- now the tool requires the user to enter the specific columns indicating ref base, position, and start of a sample
- added an interactive zoom option. when this option is selected, the image can be zoomed in or out using the mouse wheel.
- fixed the firefox & opera problems in displaying the svg image
2010-09-20 12:07:09 -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
Dannon Baker
5a28632683
Tweak to prevent workflow output indicator icon from getting out of sync. And repack.
2010-09-10 12:14:30 -04:00
Dannon Baker
e629c020d2
Packed scripts.
2010-09-10 12:05:30 -04:00
Dannon Baker
74f9454636
Workflow changes-
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Output flagging now has a third faded icon, and tooltip, and aligns properly on multiline outputs.
ToolForm width now properly calculated, taking into account the length of input and output rows.
-Max width is 250px, min is 150px.
Output extensions are now properly separated by ', ' (including space) instead of just slammed together.
Fixed a bug where a newly created node had no outputs array.
2010-09-10 11:59:38 -04:00
Jeremy Goecks
9e44caf592
UI improvements for annotating items: more descriptive messages and larger targets.
2010-09-08 17:52:01 -04:00
Dannon Baker
85e7c42ba8
Flagging of workflow outputs from within the workflow editor itself.
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Hover over any output, click the asterisk to flag/unflag an output as a workflow-wide output.
2010-09-08 15:24:15 -04:00
Kanwei Li
a541704a4a
trackster: Fix drawing of features being cut off at bottom, added dropdown to track name for setting overview, and preferences in the future
2010-09-02 18:46:23 -04:00
Kanwei Li
4ea8dd779b
trackster: Changing display mode from "Auto" now fetches additional detail data and displays features. Displays error messages in canvas elements if present. Limit number of features displayed in one tile due to above feature. Fix bugs in visualization creation from form
2010-09-01 18:20:42 -04:00
Dannon Baker
894e1a43c3
Repacked workflow editor.
2010-08-31 11:58:59 -04:00
Dannon Baker
a7aab68bbc
Constrain connection to correct outputs when using ChangeDatatypeAction in workflow editor.
2010-08-30 18:48:08 -04:00
Dannon Baker
1d7a117da0
Workflow Fix- Enabled connection of nodes using ChangeDatatypeAction in the editor pane.
2010-08-30 18:38:35 -04:00
Kanwei Li
ab8217d1e9
trackster: fix use of an old variable
2010-08-27 15:43:11 -04:00
Kanwei Li
d8ad672ecf
trackster: make "go-to" navigation inline, activated when chrom position is clicked. Drag-zoom overlay should now cover entire viewport (was missing a bit at bottom)
2010-08-26 19:04:55 -04:00
Kanwei Li
2b1d895ecf
Repack js
2010-08-26 12:14:04 -04:00
Kanwei Li
4f291405f6
trackster: Overview track, viz cloning, "Go-to" specific location, UI fixes
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- Each track now has an Overview checkbox that will set the initial chromosome-wide view of that track to become the overview
- Visualizations that users own or are shared with can now be cloned
- Go-to feature lets users go directly to a certain chrom (eg "chr1"), or chrom and position ("chr1:1-100,000,000")
- Fix double flushing when creating converter
- Line tracks display mode is now inline
- Use smaller font for tracks
- Fix web-kit bug where using scrollbar would also trigger viewport dragging
- Fix Line tracks jumping around when changing position
- Made default Line track height 80px from 100px
- Fix drag-zoom overlay appearing at top of header instead of Label track
- Minor grid refactoring
2010-08-26 12:12:32 -04:00
Dannon Baker
1d6896a316
Fix for the issue where multiple of the same action on separate outputs of a single tool were being overwritten as one.
2010-08-26 08:10:12 -04:00
Kanwei Li
4bd9e909b7
Use image_path for workflows and show_modal instead of relative paths
2010-08-20 15:00:52 -04:00
Dannon Baker
6803dea808
Workflow Output Tagging
2010-08-19 23:18:56 -04:00
Kanwei Li
0ec45350aa
trackster: Show counts for summary view by default, but only when text can fit in. Fix summary view off-by-pixel bug. Display Mode is now only initialized once and stays the same while switching chroms.
2010-08-09 20:01:02 -04:00
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