connections
2) Added a script for packing the javascripts, everything is now repacked
with yui-compressor (the packed versions are slightly large, but they
gzip better resulting in an overall reduction).
the history options page for "Construct workflow" link. It allows you to
select which steps from the current history you want to convert.
This is currently not very robust to changes in tool configuration, so old
histories may cause errors. This will be fixable to some extent, but we'll
probably need to go back and look at the past changes to tool configs and
define some migration rules.
- Fixing an event bug in jquery.ui
- Fixing positioning of canvas iframe
- Working around a weird canvas drawing issue (see HACK in galaxy.workflow_editor.canvas.js)
- Removing some JavaScript 1.6 methods
- Workflows have a simple database representation (StoredWorkflow)
- Workflow step parameters can be manipulated
- Workflows can be saved and loaded
- Many improvements to workflow editing interface
2) General interface cleanup
- Styles for the overall layout have been moved from the index page to
CSS files, colors for layout backgrounds and borders and such can now
be configured in the colors.ini file
- Styles and javascript code for dialogs and popupmenus (code is currently
in the workflow editor but will be moved out after more testing)
- Can add steps (tool invocations) to the workflow
- Can modify options for tools that do not use dynamic options or nesting
- Can connect outputs to inputs, the editor does check type compatibility
(however this breaks down completely for the "input" type)
There is no way to save or run workflows yet (and not data model for them).
You'll need to set "enable_beta_features = True" in your config for this to
be accessible.
TODO: Allow annotations to be specified for all species in the file, not just the
'primary' organism (as specified by the dbkey). Metadata for sequences will need to be
fleshed out more first (i.e. store all species present in the file).
customized styles can still use the new layout). Changed the config parameter
to enable the new layout to "use_new_layout" (since it has nothing to do with style!!!)
NEXT PERSON TO UPDATE TEST PLEASE ADD
[app:universe]
use_new_layout=true
Enhance history template to only display at supported site if dataset not empty.
Commented out wormbase and flybase builds until we get the correct data automatically.
They are somewhat independent (you can use the new layout with the old style
and vice versa) but they belong together.
Tested in Firefox, Safari, IE5.5, IE6, but there are still some features
to be implemented before this is ready for 'main'.
To use, first add "new_style_june_2007=true" to the app:universe section of
universe_wsgi.ini (this gives you the new layout). Second change document_root
to "%(here)s/static/june_2007_style/blue" in the app:static_style section.
Style Features: simplifications, fewer 'hatched' images, space savings in some
places, small changes to the color scheme (same general feel, but the colors
are better matched). Main changes are to history, the new style support nested
datasets much better.
Layout features: no framesets (just iframes, some of which can be replaced with divs and ajax down the road). Frames are resizable and hideable. Tools can provide width hints and history will automatically hide (try UCSC main to see this).
Also, the consolidation makes the total file size substantially smaller. In addition, there is a "scripts/packed" directory that contains highly compressed versions of the javascript files. This should be used for production deployment. The initial load size is reduced by ~80%, before considering gzip and caching.
Fixed a bug in the unit test for new gff version 3 format in sniff.py.
Tweaked the biomart tool so that it will not display problm Info: text in history.
This commit includes some stuff for future GBrowse integration, but nothing included should pose any problems with the current environment.
Anton Nekrutenko