PecanProject/bety: BETYdb 4.15

Assorted new features and bug fixes, including data upload improvements

This is the first major release in three months.

Changes Pertinent to PEcAn Users

Administrators may need to do a database migration.

If the BETYdb 4.14 - hotfix release was deployed, no migrations are necessary. See "Database Changes" below.

Summary of Changes New Features

• Issue #466 Add support for an entity column in CSV files for Bulk Upload.

  An "entity" column heading in bulk upload CSV files is now recognized. The value in the column becomes the name of the entity to be used for all traits in the row. If the name matches an existing entity, that entity is re-used; otherwise a new entity will be inserted.

• Issue #471 Add "experiments" view, show, and edit pages.

  The experiments table is now viewable and editable via the BETYdb Web interface.

• The BETYdb Rails application is now aware of the association between experiments and sites.

• In the beta API, using the "key" parameter is now optional.

  This is a convenience for users trying out the API in a browser: they now merely need to be logged in and don't need to include "key=" in the query string. Those using the API programmatically need not use the "key" parameter either if they supply a username and password.

• Issue #432 In API, 'associated <tablename> ids' should be optional (off by default)

  A new parameter "associations_mode" affords control over how much information about associated tables to display. Recognized values include count (show the number of rows in another table that are associated with this item), ids (show a list of the ids of those rows), and _full_info_ (show complete information about each associated item).

• Extensions to site customization options:

  • Whether or not to show the Model I/O menu item can now be set in the application.yml file.
  • What place-holder text to show in the home page's search box can now be set in the application.yml file.
  • The citation/license/copyright and contact information included in CSV downloads now matches the (customizable) information displayed in the Web page footer (part of issue #482)

• Issue #482 Errors in search --> download, output csv

  In addition to site-appropriate citation information, downloaded CSV files now include a "raw_date" field in addition to the interpreted date previously provided. Although "raw_date" can easily be misinterpreted, it may prove useful for some use cases.

• Issue #459 Change bulk upload (via wizard or API) to allow for traits not in the trait_covariate_associations table

  Any variable name used as a heading in a CSV data file that does not conflict with any of the usual heading names and is not listed as a covariate in the trait_covariate_associations table will now be recognized as a trait variable name. It is now also an error for there to be a heading that matches a recognized covariate name unless there is a matching trait name in the heading.

• Improved and additional RSpec testing of trait-insertion API and Bulk Upload wizard.

Bug Fixes

• Issue #472 There is an HTML class that is alternately spelled "final_paginate_row" or "final_paginagte_row".

  For the most part, this has had no user-viewable effects.

• Pull Request #478 Typo in 401 message

  It now says "authentication" instead of "authenication".

• Issue #479 species vs specie in new API

  Species (singular and plural) are now referred to as such in API results.

• Issue #485 Bulk Upload doesn't handle blank entries in "notes" column.

  Previously either the "notes" column had to have a non-blank value in each row or the "notes" column had to be omitted altogether (in which case each trait inserted would have a blank note). Now it is possible to have notes for some but not all traits in the file.

Other Changes

The changes from https://github.com/PecanProject/bety/releases/tag/betydb_4.14-hotfix have been merged into the master branch. These changes have to do with the experiments table and related database tables and objects.

Steps Needed for Upgrade Database Changes

Administrators may need to do database migrations!

If BETYdb 4.14 - hotfix was deployed, no migrations are needed. If you are upgrading from the BETYdb 4.14, then there is one migration which needs to be run.

The database version for this release is 20170118205944.

Gem Installation

No new Gems need be installed.

Status of RSpec Tests

All non-pending tests pass when run in the default environment. (There is one pending test having to do with site-group editing permissions.) The tests can be run using the command

bundle exec rspec

Complete details for running the rspec tests are at https://pecan.gitbooks.io/betydb-documentation/content/automated_tests.html.