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BETYdb 4.20 Upgrade to Rails 4.2

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


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  <identifier identifierType="DOI">10.5281/zenodo.1199667</identifier>
  <creators>
    <creator>
      <creatorName>Scott Rohde</creatorName>
      <affiliation>University of Illinois</affiliation>
    </creator>
    <creator>
      <creatorName>Carl Crott</creatorName>
    </creator>
    <creator>
      <creatorName>David LeBauer</creatorName>
      <affiliation>University of Illinois</affiliation>
    </creator>
    <creator>
      <creatorName>Patrick Mulrooney</creatorName>
    </creator>
    <creator>
      <creatorName>Rob Kooper</creatorName>
      <affiliation>National Center for Supercomputing Applications</affiliation>
    </creator>
    <creator>
      <creatorName>Jeremy Kemball</creatorName>
    </creator>
    <creator>
      <creatorName>Jimmy Chen</creatorName>
    </creator>
    <creator>
      <creatorName>Andrew Shirk</creatorName>
    </creator>
    <creator>
      <creatorName>Zhengqi Yang</creatorName>
    </creator>
    <creator>
      <creatorName>Max Burnette</creatorName>
      <affiliation>NCSA</affiliation>
    </creator>
    <creator>
      <creatorName>Haotian 	Jiang</creatorName>
    </creator>
    <creator>
      <creatorName>Yilin Dong</creatorName>
    </creator>
    <creator>
      <creatorName>Uday Saraf</creatorName>
    </creator>
    <creator>
      <creatorName>Michael Dietze</creatorName>
      <affiliation>Boston University</affiliation>
    </creator>
    <creator>
      <creatorName>Chris Black</creatorName>
    </creator>
  </creators>
  <titles>
    <title>BETYdb 4.20 Upgrade to Rails 4.2</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <dates>
    <date dateType="Issued">2018-03-15</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1199667</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/PecanProject/bety/tree/betydb_4.20</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.593027</relatedIdentifier>
  </relatedIdentifiers>
  <version>betydb_4.20</version>
  <rightsList>
    <rights rightsURI="http://www.opensource.org/licenses/NCSA">University of Illinois/NCSA Open Source License</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Draft Release Notes (Rails 4.2)&lt;/p&gt;

&lt;p&gt;Upgrade to Rails 4.2; several bug fixes. Summary of Changes&lt;/p&gt;

&lt;p&gt;This release upgrades the version of Rails used from 3.2 to 4.2.&lt;/p&gt;

&lt;p&gt;New features&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;
	&lt;p&gt;Added Rake tasks for dumping and updating SQL comments using YAML files (pull request #543).&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;On the Advanced Search page, traits and yields are now searchable by method name (pull request #506)&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;When creating or editing Managements, possible management types now include &amp;quot;thining&amp;quot; and &amp;quot;other&amp;quot; (pull request #546).&lt;/p&gt;
	&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Bug fixes&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;
	&lt;p&gt;Issue #533 (&amp;quot;Trait/entity notes don&amp;#39;t get populated through Bulk Upload Wizard&amp;quot;)&lt;/p&gt;

	&lt;p&gt;If a Bulk Upload file has a &amp;quot;notes&amp;quot; column, those notes now show up in the newly-created traits or yields.&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;Issue #552 (&amp;quot;Travis fails trying to create postgis extension.&amp;quot;)&lt;/p&gt;

	&lt;p&gt;Travis now runs RSpec successfully so builds no longer always fail.&lt;/p&gt;
	&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Other Changes&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;
	&lt;p&gt;Updated DBMS named in the README file from MySQL to PostgreSQL (long overdue).&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;Docker cleanup (pull requests #537 and #550).&lt;/p&gt;
	&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Steps Needed for Upgrade&lt;/p&gt;

&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 &lt;code&gt;git pull&lt;/code&gt; to get the lastest version of the master branch.&lt;/li&gt;
	&lt;li&gt;Run &lt;code&gt;bundle&lt;/code&gt; to upgrade several Gems (including Rails itself) and to add new Gems that are no longer part of Rails proper are that are needed to support legacy Rails behaviors until code is updated to no longer need this legacy support.&lt;/li&gt;
	&lt;li&gt;The file &lt;code&gt;config/secrets.yml&lt;/code&gt; expects a variable called &lt;code&gt;SECRET_KEY_BASE&lt;/code&gt; to be in the environment. To generate a suitable value for this variable, run &lt;code&gt;rake secret&lt;/code&gt;.&lt;/li&gt;
	&lt;li&gt;Ensure this variable is in the environment seen by the HTTP server. If you run your BETYdb app under Apache HTTP server, one way to do this is to put a directive of the form
	&lt;pre&gt;&lt;code&gt;SetEnv SECRET_KEY_BASE some_secret_key
&lt;/code&gt;&lt;/pre&gt;
	in the &lt;code&gt;&amp;lt;Directory&amp;gt;&lt;/code&gt; section of the configuration file corresponding to the BETYdb instance you have deployed.&lt;/li&gt;
	&lt;li&gt;Restart the HTTP server, e.g. &lt;code&gt;sudo apachectl restart&lt;/code&gt;.&lt;/li&gt;
&lt;/ol&gt;

&lt;p&gt;[In lieu of steps 6 and 7, you could also edit &lt;code&gt;config/secrets.yml&lt;/code&gt; directly, replacing&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;&amp;lt;%= ENV["SECRET_KEY_BASE"] %&amp;gt;
&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;with the value you generated in step 5; then restart PhusionPassenger by running &lt;code&gt;touch tmp/restart.txt&lt;/code&gt;. This is not the preferred way of doing things, however, since Git will then always show this file as modified.]&lt;/p&gt;

&lt;p&gt;Status of RSpec Tests&lt;/p&gt;

&lt;p&gt;All non-pending tests pass when run in the default environment. (There is one pending test having to do with site-group editing permissions.)&lt;/p&gt;

&lt;p&gt;Complete details for running the RSpec tests are at &lt;a href="https://pecan.gitbooks.io/betydb-documentation/content/automated_tests.html"&gt;https://pecan.gitbooks.io/betydb-documentation/content/automated_tests.html&lt;/a&gt;.&lt;/p&gt;</description>
    <description descriptionType="Other">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.</description>
    <description descriptionType="Other">{"references": ["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\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"]}</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>National Science Foundation</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/100000001</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/NSF/Directorate+for+Biological+Sciences/1062547/">1062547</awardNumber>
      <awardTitle>Collaborative Proposal: ABI Innovation: Model-data synthesis and forecasting across the upper Midwest: Partitioning uncertainty and environmental heterogeneity in ecosystem carbon</awardTitle>
    </fundingReference>
  </fundingReferences>
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