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PecanProject/bety: BETYdb 5.3.0

Scott Rohde; Carl Crott; David LeBauer; Patrick Mulrooney; Rob Kooper; Jeremy Kemball; Jimmy Chen; Andrew Shirk; Zhengqi Yang; Max Burnette; Haotian Jiang; Yilin Dong; Uday Saraf; Michael Dietze; Chris Black; Chris Schnaufer

Please read the steps below to upgrade your system. Not following these steps could break your instance of BETY.

Password encryption

The previous versions of BETY would ignore the environment variable SECRET_KEY_BASE and use the default value defined in config/defaults.yml. If you have set SECRET_KEY_BASE and upgrade BETY you will not be able to login anymore!. It is best to remove SECRET_KEY_BASE if set and default back to the default SECRET_KEY_BASE.

This release requires a migration. Steps Needed for Upgrade (Non Docker)
  1. Log in to the server.
  2. cd to the Rails root directory.
  3. Run git pull to get the latest version of the master branch.
  4. Update any gems using bundle
  5. Run the migration in the new release with bundle exec rake db:migrate RAILS_ENV=production
  6. Restart the Rails server with touch tmp/restart.txt
Steps Needed for Upgrade (Docker)
  1. Log in to the server
  2. cd to the directory with the docker-compose file
  3. update the version of bety (if you don't use latest)
  4. stop BETY docker-compose rm --stop bety
  5. download latest version docker-compose pull bety
  6. run migration docker-compose run --rm bety migrate
  7. start bety docker-compose up -d bety
PEcAn dump script

There is a change to the script/dump.bety.sh that will keep the creation/update times of the users in the database. This is needed for future work to speed up database synchronizations. If you use the script standalone, please copy latest script.

Complete list of changes Fixes
  • #696 : actually now uses environment variable SECRET_KEY_BASE. If this was set, unset otherwise you can not login to BETY.
  • #551 : remove GUnload message from console on page change.
  • #672 : Added activemodel-serializers-xml Gem to restore functionality of "original" API XML endpoints.
  • #674 : Upgraded comma Gem to restore CSV file downloads.
  • #699 : when dumping users created/updated is set to date of dump, now keeps original dates.
  • use actual information in database for load and dump scripts.
  • update doi links http://dx.doi.org --> https://doi.org
  • fixed functions to explicitly add public. to function call and table reference. (this will require a migration)
  • upgrade rake to 13.0.1 (dependbot fix)
  • upgrade nokogiri to 1.10.8 (dependbot fix)
Added
  • script to add new users to bety
  • dockerfile to dump database in docker image for faster restore of database.
  • switched to github actions instead of Travis
  • cronjob on github actions to create pecan/db docker image nightly, will safe also with year-weak (i.e 2020-15)

Development of BETYdb is supported by the National Science Foundation (ABI #1062547, ABI #1458021), the Department of Energy (ARPA-E awards #DE-AR0000594 and DE-AR0000598), and the Energy Biosciences Institute.
Files (12.8 MB)
Name Size
PecanProject/bety-betydb_5.3.0.zip
md5:4747f832a9d693f69dad8214ff155e91
12.8 MB Download
  • LeBauer, D., Kooper, R., Mulrooney, P., Rohde, S., Wang, D., Long, S. P., & Dietze, M. C. (2018). BETYdb: a yield, trait, and ecosystem service database applied to second‐generation bioenergy feedstock production. GCB Bioenergy, 10(1), 61-71

  • LeBauer, David, Michael Dietze, Rob Kooper, Steven Long, Patrick Mulrooney, Gareth Scott Rohde, Dan Wang (2010). Biofuel Ecophysiological Traits and Yields Database (BETYdb), Energy Biosciences Institute, University of Illinois at Urbana-Champaign. doi:10.13012/J8H41PB9

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