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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


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    "description": "<p>Please read the steps below to upgrade your system. Not following these steps could break your instance of BETY.</p>\nPassword encryption\n<p>The previous versions of BETY would ignore the environment variable SECRET_KEY_BASE and use the default value defined in <code>config/defaults.yml</code>. <strong>If you have set SECRET_KEY_BASE and upgrade BETY you will not be able to login anymore!</strong>. It is best to remove SECRET_KEY_BASE if set and default back to the default SECRET_KEY_BASE.</p>\nThis release requires a migration.\nSteps Needed for Upgrade (Non Docker)\n<ol>\n<li>Log in to the server.</li>\n<li>cd to the Rails root directory.</li>\n<li>Run git pull to get the latest version of the master branch.</li>\n<li>Update any gems using bundle</li>\n<li>Run the migration in the new release with\n<code>bundle exec rake db:migrate RAILS_ENV=production</code></li>\n<li>Restart the Rails server with\n<code>touch tmp/restart.txt</code></li>\n</ol>\nSteps Needed for Upgrade (Docker)\n<ol>\n<li>Log in to the server</li>\n<li>cd to the directory with the docker-compose file</li>\n<li>update the version of bety (if you don't use latest)</li>\n<li>stop BETY\n<code>docker-compose rm --stop bety</code> </li>\n<li>download latest version\n<code>docker-compose pull bety</code></li>\n<li>run migration\n<code>docker-compose run --rm bety migrate</code></li>\n<li>start bety\n<code>docker-compose up -d bety</code></li>\n</ol>\nPEcAn dump script\n<p>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.</p>\nComplete list of changes\nFixes\n<ul>\n<li>#696 : actually now uses environment variable SECRET_KEY_BASE. If this was set, unset otherwise you can not login to BETY.</li>\n<li>#551 : remove GUnload message from console on page change.</li>\n<li>#672 : Added activemodel-serializers-xml Gem to restore functionality of \"original\" API XML endpoints.</li>\n<li>#674 : Upgraded comma Gem to restore CSV file downloads.</li>\n<li>#699 : when dumping users created/updated is set to date of dump, now keeps original dates.</li>\n<li>use actual information in database for load and dump scripts.</li>\n<li>update doi links <a href=\"http://dx.doi.org\">http://dx.doi.org</a> --&gt; <a href=\"https://doi.org\">https://doi.org</a></li>\n<li>fixed functions to explicitly add public. to function call and table reference. (this will require a migration)</li>\n<li>upgrade rake to 13.0.1 (dependbot fix)</li>\n<li>upgrade nokogiri to 1.10.8 (dependbot fix)</li>\n</ul>\nAdded\n<ul>\n<li>script to add new users to bety</li>\n<li>dockerfile to dump database in docker image for faster restore of database.</li>\n<li>switched to github actions instead of Travis</li>\n<li>cronjob on github actions to create pecan/db docker image nightly, will safe also with year-weak (i.e 2020-15)</li>\n</ul>", 
    "language": "eng", 
    "title": "PecanProject/bety: BETYdb 5.3.0", 
    "license": {
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    "notes": "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.", 
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    "references": [
      "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\u2010generation 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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    "publication_date": "2020-04-15", 
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