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This minor release fixes a few bugs and cleans up the UI.
- Larger space for viewing/designing plans.
- Links to items, collections, and parts to collections are clearer and the popups more informative.
- Templates remain selected when added to a plan.
- Fixed a bug where members could not be added to groups.
- New convenience methods in collection (data_matrix_values) and field_value (part).
- Fix a bug where setting data for a collection from a matrix (a) duplicated part associations and (b) did not check for duplicate keys in data_associations.
- Fixed a "feature" where the designer would reassign items for inputs if the originally assigned items were deleted.
Rails 4.2: We have upgraded from Rails 3.2 to Rails 4.2, and upgraded almost all associated gems to their latest versions. You will need to update your bundle:
bundle update rails bundle install
Note that due to the upgrade to Rails 4.2, some updates to your protocol code may be necessary. In particular, Rails 4.2 no longer treats ActiveRecord::Relation objects as mutable arrays. So any mutator methods applied to such code, such as Array.reject! will no longer work. This version of Aquarium makes it easier to find such situations using the new test_all page described below.
Collections: This release includes an improved collections model in which parts of collections are first class Items, instead of sample ids. As a result, parts can have data associations, histories, and anything else an Item has. In addition, there is a spiffy new collection editor so you can build a collection and its associated data before sending it to a workflow. Your database will need to be migrated after you pull these changes using the following commands. Make sure to make a backup of your database before migrating!
rake db:migrate rake collections:migrate
The first line adds a new join table model called PartAssociation. The second line ports all your existing collections to the new data structure. You may also have to check whether your protocols use any old methods expecting collection.data to have a :matrix entry, as in collection.data["matrix"], which no longer works. Instead, use should be changed to collection.matrix, which will still return a set matrix of sample ids. Also, collection.set(r,c,sample) now explicitly expects sample to either be a sample id or a Sample object. Storing arbitrary information in collection matrices is not allow. Instead use DataAssociations with either the collection or parts of the collection.
Testing: More model testing has been written and can be found in /spec/models. In addition, we have included new front end tests, mainly of the Designer, using Cyprus. These tests are in /ui. Finally, operation types can be tested all on one page at http://your.aquarium.instance/operation_types/test_all.html.
Other: The release includes the following minor changes and bug fixes as well:
- Computing validations in the Designer now ignores errored-out operations, so you can extend plans containing them.
- Start and stop times are correctly displayed for multi-day operations in activity monitor. The activity monitor is also remembered with a cookie now.
- OperationTypes can now have DataAssociations and there is a tab in Developer to manage them.
- If you get logged out for some reason, Aquarium is better at informing you that this is the case.
- Aquarium now formally disallows SampleTypes with the same name.
- When editing an ObjectType, its SampleType reference is no longer always reset to the first sample type.
- There are now cute 404 and 505 pages.
- You can scroll through an item's history in the item popup.
This release fixes an issue where in some cases item choices were not deleted after reassigning itemless samples to I/O in the designer.
This version fixes a bug where saving a plan after saving data associations put operations into the wrong state. It also includes a number of minor layout improvements to the UI.
This version fixes a bug where saving a data association associated with a plan having operations whose status is "planning" and then extending it caused the newly added operations to have status "pending" regardless of their position in the plan.