2. Clean up the code that renders the jquery file browser plugin - things work much cleaner now. One remaining item is handing the issue where rsh / ssh keys are not set. Also clean up a lot of code related to manual file transfers in the requests_admin controller.
3. In addition to the new ManualDataTransferPlugin, add the Pacific Biosciences SMRTPortalPlugin that automatically transfers files produced by SMRT Portal to a Galaxy data library.
4. Add the external service type config for Pac Bio SMRT Portal version 1.1.0.
1. Enhance importing library dataset into the current history by now allowing the user to select from a list of existing histories or create a new named history ( similar to copying datasets ).  This feature is available for a specific library dataset, a folder ( or root folder ), when selecting multiple datasets from in a library,  and on the results page for searched library datasets.
2. Add Brad Chapman's latest patch for fixing the lucene search implementation
3. Eliminate searches on dataset state for both whoosh and lucene searches
4. Clarify the objects being searched in the regular search and advanced search boxes in the data libraries grids.
5. Add the ability to perform certain actions on 1 or more selected library datasets on the results page for searched library datasets.
6. Add a "select all" checkbox to the browse_library.mako template.
7. Fixed library functional tests accordingly.
- sequencer table now populated with the unique sequencer in the request_type table
- sequencer_type is introduced which defines a sequencer
- support for sequencer (create, delete, edit)
- added support for a simple sequencer for backward compatibility
- added support for Solid sequencer
- tweaked the request_type api methods. removed the sequencer login info.
Additional effort is needed to abstract more previously existing functionality out of web controllers.
Add script that is able to create a sequencer configuration for the sample tracking system using API.
- eliminated the transfer_datasets.ini config file
- eliminated the data transfer user
- now the admin user initiating the data transfer is used as the data transfer user.
- the admin user is provided the add_library_item permission before data transfer if they dont have it
- sample update & data transfer amqp messages now includes api_key
- added web api methods to update requests, samples using restful api
- removed the old ad-doc web api
- modified the data transfer code to use this api
- code cleanup
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.
- first pass for state change mechanism for multiple samples
- UI enhancements: checkboxes to select samples & selectfield to select specific operation
- removed state change UI for individual samples in the sample_events page
next is selecting library for multiple samples
Greg Von Kuster