Bugfix: operation state + Layout improvements

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.

Bugfix: Unwanted plan updates

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.

Bugfix: Large plan loading time

This minor release fixes a bug that caused large plans with completed operations to load very slowly in the designer.

Docker / Designer Improvements / Dead code removal

• You can get started using Aquarium more quickly now with the Docker installer. See the documentation for how to use it.
• The documentation has been moved around and expanded. See http://klavinslab.org/aquarium for details.
• Performance: Several key queries, especially in the designer backend, have been optimized and should result in faster page loads, particularly big plans.
• Rubocop: Style in Ruby files is now policed.
• The designer should be more functional, allowing users greater control over how they edit their plans.
• You can refer to data associated with operations via http://yourhost/uploads/operation/12345/key or http://yourhost/uploads/item/12345/key. You can put those links in text boxes to decorate your plans with data.
• The manager now has a view that shows a day's activity in graphical form.
• Several bugs have been fixed, mainly in the designer.
• Krill has been updated. In particular, show now returns a (backwards compatible) ShowResponse object with convenience routines for accessing table inputs and so on.
• Migration notes
  • Version v.2.3 deletes old tables and old columns from existing tables. Make a backup of your db and then run rake db:migrate.
  • You will need to add something like this to your config/initializers/aquarium.rb file

    Bioturk::Application.config.krill_hostname = 'localhost'

• Dead code removal: All references to tasks, metacols, oyster, and several other defunct models have been removed.

Bug fixes

This version fixes several bugs:

• Random orange arrows in designer are gone
• Extending a plan with new operations is smoother
• Fixed a bug where looking up an item's history caused a long delay
• Added before_destroy method for operations, so that field values and wires are destroyed too
• Fixed bug where the first item in a collection was always selected in the designer

In addition, we added technician statistics

Plan editing, Javascript tests, Manger convenience, and unique operation types

1. This version includes many updates to the planner. In particular, it allows
   users to edit plans even after they have started (or finished) running. Users
   can, for example, add an operation to a plan, or retry an operation that
   failed. Users can also add and remove wires.

2. The updates to the planner include text boxes, which can contain markdown code.

3. Managers can now set the status of an operation to whatever they need it to be.
   In the Manager view, click on Force next to an operation and choose the desired new
   status.

4. The plan list and plan editor are now separate items on the main task bar.

5. OperationType names are now required to be unique within a category.
   Before running the migrations, also run the rake task
   rake rename_optype_duplicates, which will make a best guess about which of
   the operations with duplicate names should be renamed and update the table.

6. The javascript code was refactored to use promises more idiomatically.

7. There is a javascript test environment, called shark, now integrated into
   Aquarium and available in development mode.

Minor bugfix

Fixes bug in which an operation with a buggy precondition could prevent other operations from updating.

Functional Cost Model + Sample Tree

This is a mostly bug-free version that includes a cost model and accounting system. It is mainly being tagged because the next set of updates are going to completely rework how sample fields are handled, resulting in rather new (and hopefully better) behavior.

Technician Interface Update

This release includes a new, more robust, and functional technician interface written in angular. The new interface is more aware of operations, has better upload management, smoother transitions between slides, and improved layout.

This release also includes a variety of bug fixes, in particular to the invoice pages.

Aquarium 2.0, First Release

This new version includes the notion of an operation, with typed inputs and outputs. Operations can be strung together in plans using a graphical editor. An inline IDE for protocols allows new operation types to be defined and the associated protocol written and tested. A new manager page enables managers to schedule and run operations easily.

Note: This version does away with tasks and oyster.