- until now, lastz will (mostly) ignore alignments in masked regions since soft-masking has been enabled.  Now the default has changed to disable soft masking, and an option has been added to the tool to enable it if desired.
- the functional test framework now allows for a new "sort" attribute in the output tag for functional tests.  For example:  <output name="output1" file="lastz_wrapper_out4.tabular" sort="True" />
If set to True, the output dataset will be sorted prior to comparing.  This is needed for the lastz tool since multiple threads generate output randomly if the input file has more than 1 sequence.  The default is False.
- Decode the id of a folder prior when retrieving from the database - fixes the bug reported by Guru.
- only display check boxes on a grid if there are operations to perform
- asynchronous uploads will now properly handle associated library templates
- miscellaneous fixes for issues introduced in the library code merge in change set 3194:4743015d9a57
- move / merge all duplicate methods from the library_and library_admin controllers into the library_common controller
- move / merge all duplicate mako templates into the ~/library/common directory
- make the admin view library browser a grid
- all library item ids are now encoded
- added request_events table
- removed 'state' field in the request table
- added 'new' & 'rejected' request states
- color coded request states in the request grid
Grids framework
- added a confirm flag in grid operations which require confirmation before going through with operation
- report form now defaults to include the users email address if they are logged in
- email now includes the id of both the dataset and the history, the hid and hda.display_name(), and a link to the history
- admin users now have "view" access to any history and dataset ( this uses the new ~/history/view?id=... feature )
- moved all supported binary data types to the new binary.py
- changed GeneTrack data type to subclass from Text rather than Binary
- added Sff data type to datatypes_conf.xml.sample
- merged test_sniffinad_and_metadata_settings.py test scritp into test_get_data.py
- added several additional functional test for data types to test_get_data.py
- fixed some bugs in upload.py when uploading binary data types
- added a foreign key in the galaxy_user table to the form_values table
- separate user info page for viewing/editing user info
- user addresses added to user info page
- The genetrack controller is no longer used ( I'll delete it soon ), so the GeneTrack application is now loosely coupled
- Merge the 2 new_dataset.mako templates into one common code module name library_dataset_common.mako
- Rename all of the library upload form fields to have the same names as the history upload form fields
- Eliminate a 2nd runtool_btn from being rendered on the same form in tool_form.mako
- Fix bug and add functional tests to cover uploading a library dataset that does not include a template
Greg Von Kuster