Software Open Access

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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    <subfield code="x">LeBauer, D., Kooper, R., Mulrooney, P., Rohde, S., Wang, D., Long, S. P., &amp; 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</subfield>
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    <subfield code="x">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</subfield>
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    <subfield code="a">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.</subfield>
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    <subfield code="a">&lt;p&gt;Please read the steps below to upgrade your system. Not following these steps could break your instance of BETY.&lt;/p&gt;
Password encryption
&lt;p&gt;The previous versions of BETY would ignore the environment variable SECRET_KEY_BASE and use the default value defined in &lt;code&gt;config/defaults.yml&lt;/code&gt;. &lt;strong&gt;If you have set SECRET_KEY_BASE and upgrade BETY you will not be able to login anymore!&lt;/strong&gt;. It is best to remove SECRET_KEY_BASE if set and default back to the default SECRET_KEY_BASE.&lt;/p&gt;
This release requires a migration.
Steps Needed for Upgrade (Non Docker)
&lt;ol&gt;
&lt;li&gt;Log in to the server.&lt;/li&gt;
&lt;li&gt;cd to the Rails root directory.&lt;/li&gt;
&lt;li&gt;Run git pull to get the latest version of the master branch.&lt;/li&gt;
&lt;li&gt;Update any gems using bundle&lt;/li&gt;
&lt;li&gt;Run the migration in the new release with
&lt;code&gt;bundle exec rake db:migrate RAILS_ENV=production&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Restart the Rails server with
&lt;code&gt;touch tmp/restart.txt&lt;/code&gt;&lt;/li&gt;
&lt;/ol&gt;
Steps Needed for Upgrade (Docker)
&lt;ol&gt;
&lt;li&gt;Log in to the server&lt;/li&gt;
&lt;li&gt;cd to the directory with the docker-compose file&lt;/li&gt;
&lt;li&gt;update the version of bety (if you don't use latest)&lt;/li&gt;
&lt;li&gt;stop BETY
&lt;code&gt;docker-compose rm --stop bety&lt;/code&gt; &lt;/li&gt;
&lt;li&gt;download latest version
&lt;code&gt;docker-compose pull bety&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;run migration
&lt;code&gt;docker-compose run --rm bety migrate&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;start bety
&lt;code&gt;docker-compose up -d bety&lt;/code&gt;&lt;/li&gt;
&lt;/ol&gt;
PEcAn dump script
&lt;p&gt;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.&lt;/p&gt;
Complete list of changes
Fixes
&lt;ul&gt;
&lt;li&gt;#696 : actually now uses environment variable SECRET_KEY_BASE. If this was set, unset otherwise you can not login to BETY.&lt;/li&gt;
&lt;li&gt;#551 : remove GUnload message from console on page change.&lt;/li&gt;
&lt;li&gt;#672 : Added activemodel-serializers-xml Gem to restore functionality of "original" API XML endpoints.&lt;/li&gt;
&lt;li&gt;#674 : Upgraded comma Gem to restore CSV file downloads.&lt;/li&gt;
&lt;li&gt;#699 : when dumping users created/updated is set to date of dump, now keeps original dates.&lt;/li&gt;
&lt;li&gt;use actual information in database for load and dump scripts.&lt;/li&gt;
&lt;li&gt;update doi links &lt;a href="http://dx.doi.org"&gt;http://dx.doi.org&lt;/a&gt; --&amp;gt; &lt;a href="https://doi.org"&gt;https://doi.org&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;fixed functions to explicitly add public. to function call and table reference. (this will require a migration)&lt;/li&gt;
&lt;li&gt;upgrade rake to 13.0.1 (dependbot fix)&lt;/li&gt;
&lt;li&gt;upgrade nokogiri to 1.10.8 (dependbot fix)&lt;/li&gt;
&lt;/ul&gt;
Added
&lt;ul&gt;
&lt;li&gt;script to add new users to bety&lt;/li&gt;
&lt;li&gt;dockerfile to dump database in docker image for faster restore of database.&lt;/li&gt;
&lt;li&gt;switched to github actions instead of Travis&lt;/li&gt;
&lt;li&gt;cronjob on github actions to create pecan/db docker image nightly, will safe also with year-weak (i.e 2020-15)&lt;/li&gt;
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    <subfield code="a">https://github.com/PecanProject/bety/tree/betydb_5.3.0</subfield>
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