BETYdb 3.2.1

This incorporates fixes for two bugs discovered during the September 5, 2014 sprint. It was deployed to www.betydb.org on September 5, 2014.

Changes Pertinent to PEcAn Users

Administrators need to do database migrations!
See "Database Changes" below.

Summary of Changes

Database Changes

Administrators need to do database migrations!

The database version for this release is 20140904221818.

• The user_id columns of the modeltypes and modeltypes_formats tables have been changed to big ints to match their referent.
• The views which use the geometry column of the sites table have been updated so that they behave correctly when the column value is a polygon rather than a point.

Bug Fixes

• The change to the views fixes the advanced search page, which has been broken since polygons were entered into the sites table.

Status of RSpec Tests

• All tests now pass when run in the default environment.
  (Complete details for running the rspec tests are on the updated Wiki page at https://github.com/PecanProject/bety/wiki/Testing)

BETYdb 3.2

This incorporates the features and bug fixes from the Augsut 20, 2014 sprint and a few from the July 18 sprint. It was deployed to www.betydb.org on August 27, 2014.

Changes Pertinent to PEcAn Users

Administrators need to do database migrations!
See "Database Changes" below.

Creation and modification of ensembles, posteriors, runs, and workflows is no longer possible through the BetyDB web interface. This now must be done through PEcAn.

Release Highlights

• The pages for adding and editing traits has been improved with a more logical layout of the attribute fields; and the panel for editing trait covariates has been moved to a side bar.
• Users now have the ability to edit information for variables associated with formats.
• New model types can be created in BETY and can be associated with PFTs as well as models.
• Model types can now have a list of required inputs needed to run the model.
• The "New" and "Edit" pages for ensembles, runs, and workflows have been removed as this functionality has been passed off to the PEcAn software.

Summary of Changes

Database Changes

Administrators need to do database migrations!

The database version for this release is 20140729045640.

• A new modeltypes table has been added, and the textual model_type columns in the models and the pfts tables have been replaced by references to rows of the new table.
• A new modeltypes_formats table has been added; this allows one to specify what file formats are needed for execution in PEcAn as well as what tags are used to specify these files as inputs in the pecan.xml file.

Minor Changes and Improvements

• P and HSD have been removed from the list of stat names that may be selected when adding or editing traits or yields.
• The interface for associating variables with a format has been improved.

Bug Fixes

• The Willow map legend has been fixed.
• The code that generates images for the priors listing now references the correct version of R.

Status of RSpec Tests

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

  rspec
  

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

BETYdb 3.1 hotfix 1

This release applies an urgent fix to release BETYdb 3.1 to fix site searches.

BETYdb 3.1

WARNING WARNING

The migration in this release will potentially remove some information. If you have sites that have a latitude and longitude, but no elevation, the latitude and longitude will be lost! You can check to see if you are affected by running the following SQL statement: select id, lat, lon from sites where lat is not null and masl is null; all sites returned are affected. To fix these sites (and set the elevation to -999, you can run the following command update sites set masl=-999 where lat is not null and masl is null;. You will have to execute this BEFORE the migration

WARNING WARNING

This incorporates the features and bug fixes from the July 18, 2014 sprint. It was deployed to www.betydb.org on August 1, 2014.

Major Changes!

Administrators need to do database migrations, update their database.yml file, add the PostGIS extension to their database and possibly install new packages to support PostGIS!

In the best case scenario, the following steps should suffice to carry out the upgrade:

1. Add the PostGIS extension to your PostgreSQL installation if needed.

2. Run psql -d bety -c 'CREATE EXTENSION postgis;' to add PostGIS to your copy of the bety database. (If you aren't yourself a superuser for your PostgreSQL installation, add the -U <some superuser> flag to this command, e.g. -U postgres. Or possibly run using sudo: sudo -u postgres psql ....)

3. If you wish to be able to run RSpec tests, also add the PostGIS extension to template1. (Repeat the above command with "template1" in place of "bety".)

4. Modify your config/database.yml file by replacing each "adapter: postgresql" line by "adapter: postgis". Also, if you created a section for the test_js environment, you may eliminate it. This environment is no longer used.

5. Run the bundler to install the new PostGIS-related gems: bundle install (Note: If you have trouble installing the RSpec test-related gems (capybara-webkit in particular can be difficult), you can run the bundler with the --without option to skip gems only needed by the test environment: bundle install --without test. This is a "remembered" option, and to undo it, you will need to run bundle config --delete without. Alternatively, you can simply comment out problem test-related gems in your copy of the Gemfile. For example, if capybara-webkit installation is a problem, simply comment out that line. You will still be able to run RSpec on the tests that don't require it. See the testing wiki at https://github.com/PecanProject/bety/wiki/Testing for details.)

6. Run the database migrations for your development and/or production database:

   rake db:migrate
   

   and/or

   RAILS_ENV=production rake db:migrate
   

7. Restart your rails server (or run touch tmp/restart.txt if running under apache).

Release Highlights

• The advanced search page now supports searching trait and yield data by the author or year of the associated citation.
• The database and Rails software now supports PostGIS.
• All rspec tests now pass when run in the default testing environment, which now includes capybara-webkit for running Javascript-related tests. The test_js environment is no longer supported. Testing instructions have been greatly simplified. See the testing wiki at https://github.com/PecanProject/bety/wiki/Testing for details.

Summary of Changes

Database Changes

Administrators need to do database migrations!

The database version for this release is 20140708232320.

• The database now uses the PostGIS extension.
• The the lat, lon, masl, and espg columns have been eliminated from the sites table. Location information is now represented by the new "geometry" column, which has type "geometry", at type only available under PostGIS.

New Features

• Non-administrative users can now edit their own user profile.

Minor Improvements

• The "Sites >>" link has been removed from the Traits and Yields listing pages since it doesn't fit with the usual data-entry workflow.
• The species view page has been correctly styled to be consistent with other pages of the site and has been greatly simplified.
• The Sites list page has been updated to be consistent with other list pages, combining the various action controls into a single "Actions" column, and using buttons rather than links for the controls.
• Associated covariates (if any) are now listed on the trait show page.
• Unlinking covariates from a trait now works correctly and is much easier.
• Statistics for traits and yields now appear in a single column in an easy-to-read form on the traits and the yields index pages.
• Numerous RSpec tests have been added.
• The feedback tab has been made less obtrusive.

Bug Fixes

• Minor problems causing some of the RSpec tests to fail when run with capybara-webkit enabled have been fixed. All tests now pass when run in the default "test" environment.
• The Workflows listing page is now viewable.
• The Methods listing is now viewable by both Administrators and Managers, and the link to the listing does not appear for users with lesser privileges.

Status of RSpec Tests

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

  rspec
  

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

BETYdb 3.0.5.2

This incorporates the features and bug fixes from the July 1, 2014 sprint. It was deployed to www.betydb.org on July 7, 2014.

Release Highlights

• Allow users with manager access or higher to use provenance tables (RM 2007)
• Data editors can now include site and treatment information when adding yields data.
• A Feedback tab has been added conspicuously to all pages to allow easy submission of feedback.

Summary of Changes

Database Changes

Administrators need to do database migrations!

The database version for this release is 20140624185610

• schema.rb has been deprecated, is no longer part of the git repository, and is no longer automatically created by various rake scripts.
• sites.mat now has type numeric(4, 2) instead of being an integer.
• The pfts table has a new model_type column.
• A join table for posteriors and ensembles has been added.

New Features

• A Feedback tab has been added conspicuously to all pages to allow easy submission of feedback.
• Users with manager access or higher are now allowed to use provenance tables (RM 2007)
• Data editors can now include site and treatment information when adding and editing yields data.

Minor Improvements

• The sites lists on the inputs forms are now sorted.
• The Runs menu now appears in sorted order.
• Trait covariates are now listed on the trait Show page.
• Links from the treatments page to the traits and yields pages now go to the trait and yield listings rather than to the forms for new traits and yields.

Bug Fixes

• Generation of images for the Priors listing has been fixed.
• Posteriors can no longer be edited through the BetyDB web interface.

Status of RSpec Tests

(Generally we don't release code until all RSpec tests pass, but we have made an exception in this case.)

• All tests pass in the default test environment except "Posteriors search search on posteriors should show search result on current page" at line 18 of spec/features/posterior_search_spec.rb; this is because this test requires the capybara-webkit gem, which isn't included in the "test" environment. This should pass in the "test_js" environment, which does include this gem, but there is currently a routing error bug involving the jQuery libraries that causes this and several other tests to fail when run in the test_js environment.

BETYdb 3.0.3.9 hotfix 1

This release applies an urgent fix to release BETYdb 3.0.3.9 to allow persons entering yield data to set the site and treatment information for a yield entry.

BETYdb 3.0.3.9

This incorporates the features and bug fixes from the June 17, 2014 sprint. It was deployed to www.betydb.org on June 20, 2014.

Release Highlights

• New links to updated documentation, moved key documents to Authorea; added schema navigation using SchemaSpy (#43).
• New user requests sent to all users with administrative privileges (#56, RM #1707)
• Updated database schema. See below

Summary of Changes

Database Changes

Administrators need to do database migrations!

The database version for this release is 20140617163304.

• New fields in variables table to support cf-style variable naming (#59)
• Added pft type to pfts table
• Added posterior_samples, projects, and current_posteriors tables
• Removed posteriors_runs table
• Removed model_path from models table

New Features

• A schema browser has been added to conveniently show the database structure.
• Configuration changes make it now possible to run under Ruby 2.

Minor Improvements

• More intuitive navigation: back buttons have been replaced by "All Records" buttons that go to a page showing all the records of the type being shown or edited
• Added tests
  • Added capybara webkit gem to support JavaScript-related tests; see notes in deployment wiki.
• Restyled pages

Bug Fixes

• Fixed search function on Posteriors and Managements pages (RM #1908 and #1922)
• New User form now shows the "reason" input area when user requests elevated access (RM #2085)
• It is now possible to edit site and treatment on the Traits edition page (RM #1881)

BETYdb 3.0.3

Switched from MySQL to PostgreSQL backward dependency will remain until addition of PostGIS geoms for sites

BETYdb 2.1.1

Added Advanced Search page with maps

BETYdb 2.0.2

Site Redesign