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BETYdb 4.4 now with access to twice as much data

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@gsrohde gsrohde released this 14 Oct 22:14
· 837 commits to master since this release


Summary of Changes

This release implements a number of long-standing requests for changes to database tables, implements some new features, and fixes several bugs.

Administrators need to do a database migration. See "Database Changes" below.

Access to 'unchecked' data through web interface and API

Data are marked as 'unchecked' when they are first entered, and marked 'checked' after they have been independently compared to their source. QAQC is an ongoing effort, but most of the data are valid, so we have decided to make all unchecked data available. Previously, only checked data were available. Data flagged as incorrect are still marked as such and are are only accessible to administrators and data managers.

Unchecked data have previously been available to PEcAn users.

QAQC is a community effort - please report incorrect data as well as any data that you use and compare with an original publication or source of data, or another database / independent review.

New BETYdb chat room on Gitter

Join the chat at

New Features

New Workflow Attributes

The Workflows model now includes a "notes" attribute and a link to the users table.

Advanced Search Option to View Unchecked Traits and Yields

The Advanced Search page now includes a check-box for optionally including unchecked data in the search results.

Link to New Gitter Chat Page

We're now on Gitter. A link to the Gitter chat page has been added to the footer. Just like the one above).

Option to Log Rake Tasks to STDOUT

The new log rake task can be used to redirect logging of subsequent tasks in the command-line task list to standard output. This is particularly useful when running migrations: By running the migration as

rake log db:migrate

the user can easily see what SQL commands were used to effect the migration.

Steps Needed for Upgrade

Database Changes (if applicable)

Administrators need to do database migrations!

There are three migrations associated with this release:

  1. The first alters the view traits_and_yields_view so that unchecked rows are included.
  2. The second adds new attributes notes and user_id (along with a foreign-key constraint for the latter) to the workflows table.
  3. The third removes the dataformat attribute from the formats table.

The database version for this release is 20151914182146.

Status of RSpec Tests

  • There are now 246 RSpec tests that don't involve Javascript. These pass consistently, and may be run with the command

    bundle exec rspec -t ~js
  • There are 28 RSpec tests that involve Javascript. Most of these pass consistently, but occassionally one of these tests will fail intermittently. (This may be a timing-related issue.) These tests may be run with the command

    bundle exec rspec -t js

If one of these tests fails, the output will show the command needed to re-run the failing test. Often, the test will pass on a second try.

(Complete details for running the rspec tests are on the Wiki pages at .)

Bug Fixes

Fixed Typo in Mangements List

A typo in the management types list prevented fertilizer_other_rate and fungicide from appearing in the selection drop-down for choosing a management type in the New and Edit Management pages. This has been fixed.

Edit Species Displays Errors Properly

A validation error when attempting to edit a species was causing the "We're sorry, but something went wrong" page to be displayed. Now the user is correctly returned to the Edit page with a displayed list of validation errors.

Searching Formats Fixed

Searches on the "Listing Formats" were broken when the mime_type column in the formats table was replaced by a key into the mimetypes table. This has been fixed.

Show Pages for Runs Fixed

The show pages for runs was broken when the start_date and end_date columns were removed from the runs table. This has been fixed.