bety: BETYdb 3.3

This incorporates a major new feature--the Bulk Upload Wizard--and also includes bug fixes from the last several sprints. It was deployed to www.betydb.org on December 5, 2014.

Major Changes

Administrators either need to run bundle install to install several new Ruby Gems or configure bundler to ignore the Gems in the 'debug' group. (The 'debug' group is needed only for running RSpec tests using the Selenium JavaScript driver.) Also, to avoid the installation of capybara-webkit, the group to ignore is now called 'javascript_testing', so if you never installed it and don't want to install it, configure Bundler to ignore the 'javascript_testing' group.

(Note: Unless you have difficulty installing the Gems used for testing, there is really no compelling reason not to install them.)

To ignore the 'debug' group, either run

bundle install --without debug

or, if you are sure your other Gems are up-to-date, you can just run

bundle config --local without debug

To ignore the 'javascript_testing' group (thus avoiding installation of capybara-webkit), substitute 'javascript_testing' for 'debug' in either of these two commands. To ignore both, run

bundle install --without debug javascript_testing

or

bundle config --local without debug:javascript_testing

Or, to ignore ALL gems except those needed in the production environment, ignore all the other groups:

bundle install --without debug javascript_testing test development

or

bundle config --local without debug:javascript_testing:test:development

Note that bundle install --without takes a space-separated list, but bundle config without takes a colon-separated one.

Summary of Changes New Features

• A wizard for bulk upload of data has been added (currently only available to administrators).
• An easy method has been provided to debug RSpec tests using the Selenium JavaScript driver together with breakpoints (see the updated Wiki page for Automated Tests).
• Distinct pages now have distinct titles, making the site more accessible for those using screen readers and making navigation of the site using the browser history possible.

Minor Improvements

• Redmine issue #2599 ("Different pages of BetyDB should have different titles."): Formerly, every page on the site had the same title ("Energy Biosciences Institute"). This meant that if one had been clicking around the site for awhile and then looked at the browser history, all the recent entries in the history list would appear to be exactly the same. Now the default title is "BETYdb: " followed by the path/filename portion of the URL of the page.

• New validations have been added to the Create and Update pages for some tables. For example, it is now checked that yield values are non-negative.

• The rake notes:todo task has been redefined so that it finds not only source-code comments beginning with "TODO", but also those beginning with "TO-DO" or "to-do".

Bug Fixes

These bugs have been fixed:

• Redmine issue #2406 ("Searching is broken on Ensembles, Inputs, Runs, and Workflows pages.") Searches on these pages have now been fixed.

• Redmine issue #2486 ("Baffling trait-creation error.")

• Redmine issue #2604 ("Application error when unsuccessfully updating a yield."

Status of RSpec Tests

• All tests now pass when run in the default environment and can be run using the command

  bundle exec rspec

  Complete details for running the rspec tests are on the updated Wiki page at https://github.com/PecanProject/bety/wiki/Automated-Tests