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Run system updates and reboot DSpace Test
2017-07-04
Merge changes for WLE Phase II theme rename (#329)
Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:
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Run system updates and reboot DSpace Test
2017-07-04
Merge changes for WLE Phase II theme rename (#329)
Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-07/">July, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-07-01T18:03:52+03:00">Sat Jul 01, 2017</time> by Alan Orth in
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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<h2 id="2017-07-01">2017-07-01</h2>
<ul>
<li>Run system updates and reboot DSpace Test</li>
</ul>
<h2 id="2017-07-04">2017-07-04</h2>
<ul>
<li>Merge changes for WLE Phase II theme rename (<a href="https://github.com/ilri/DSpace/pull/329">#329</a>)</li>
<li>Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace</li>
<li>We can use PostgreSQL’s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li>
</ul>
<p></p>
<pre><code>$ psql dspacenew -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=5 order by element, qualifier;' | sed -r 's:^-\[ RECORD (.*) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]*) +\| (.*): <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::'
</code></pre>
<ul>
<li>The <code>sed</code> script is from a post on the <a href="https://www.postgresql.org/message-id/437E44A5.508%40ultimeth.com">PostgreSQL mailing list</a></li>
<li>Abenet says the ILRI board wants to be able to have “lead author” for every item, so I’ve whipped up a WIP test in the <code>5_x-lead-author</code> branch</li>
<li>It works but is still very rough and we haven’t thought out the whole lifecycle yet</li>
</ul>
<p><img src="/cgspace-notes/2017/07/lead-author-test.png" alt="Testing lead author in submission form" /></p>
<ul>
<li>I assume that “lead author” would actually be the first question on the item submission form</li>
<li>We also need to check to see which ORCID authority core this uses, because it seems to be using an entirely new one rather than the one for <code>dc.contributor.author</code> (which makes sense of course, but fuck, all the author problems aren’t bad enough?!)</li>
<li>Also would need to edit XMLUI item displays to incorporate this into authors list</li>
<li>And fuck, then anyone consuming our data via REST / OAI will not notice that we have an author outside of <code>dc.contributor.authors</code>… ugh</li>
<li>What if we modify the item submission form to use <a href="https://wiki.duraspace.org/display/DSDOC5x/Submission+User+Interface#SubmissionUserInterface-ItemtypeBasedMetadataCollection"><code>type-bind</code> fields to show/hide certain fields depending on the type</a>?</li>
</ul>
<h2 id="2017-07-05">2017-07-05</h2>
<ul>
<li>Adjust WLE Research Theme to include both Phase I and II on the submission form according to editor feedback (<a href="https://github.com/ilri/DSpace/pull/330">#330</a>)</li>
<li>Generate list of fields in the current CGSpace <code>cg</code> scheme so we can record them properly in the metadata registry:</li>
</ul>
<pre><code>$ psql dspace -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=2 order by element, qualifier;' | sed -r 's:^-\[ RECORD (.*) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]*) +\| (.*): <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::' > cg-types.xml
</code></pre>
<ul>
<li>CGSpace was unavailable briefly, and I saw this error in the DSpace log file:</li>
</ul>
<pre><code>2017-07-05 13:05:36,452 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
org.postgresql.util.PSQLException: FATAL: remaining connection slots are reserved for non-replication superuser connections
</code></pre>
<ul>
<li>Looking at the <code>pg_stat_activity</code> table I saw there were indeed 98 active connections to PostgreSQL, and at this time the limit is 100, so that makes sense</li>
<li>Tsega restarted Tomcat and it’s working now</li>
<li>Abenet said she was generating a report with Atmire’s CUA module, so it could be due to that?</li>
<li>Looking in the logs I see this random error again that I should report to DSpace:</li>
</ul>
<pre><code>2017-07-05 13:50:07,196 ERROR org.dspace.statistics.SolrLogger @ COUNTRY ERROR: EU
</code></pre>
<ul>
<li>Seems to come from <code>dspace-api/src/main/java/org/dspace/statistics/SolrLogger.java</code></li>
</ul>
<h2 id="2017-07-06">2017-07-06</h2>
<ul>
<li>Sisay tried to help by making a <a href="https://github.com/ilri/DSpace/pull/331">pull request for the RTB flagships</a> but there are formatting errors, unrelated changes, and the flagship names are not in the style I requested</li>
<li>Abenet talked to CIP and they said they are actually ok with using collection names rather than adding a new metadata field</li>
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<li><a href="/cgspace-notes/2017-07/">July, 2017</a></li>
<li><a href="/cgspace-notes/2017-06/">June, 2017</a></li>
<li><a href="/cgspace-notes/2017-05/">May, 2017</a></li>
<li><a href="/cgspace-notes/2017-04/">April, 2017</a></li>
<li><a href="/cgspace-notes/2017-03/">March, 2017</a></li>
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