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Add notes for 2019-05-05

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Alan Orth
2019-05-05 16:45:12 +03:00
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="Categories"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
<meta name="generator" content="Hugo 0.55.3" />
<meta name="generator" content="Hugo 0.55.5" />
@ -101,18 +101,16 @@
<h2 id="2018-07-01">2018-07-01</h2>
<ul>
<li>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</li>
</ul>
<li><p>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</p>
<pre><code>$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
</code></pre>
</code></pre></li>
<ul>
<li>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</li>
</ul>
<li><p>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</p>
<pre><code>There is insufficient memory for the Java Runtime Environment to continue.
</code></pre>
</code></pre></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-07/'>Read more →</a>
</article>
@ -139,23 +137,23 @@
<li>There seems to be a problem with the CUA and L&amp;R versions in <code>pom.xml</code> because they are using SNAPSHOT and it doesn&rsquo;t build</li>
</ul></li>
<li>I added the new CCAFS Phase II Project Tag <code>PII-FP1_PACCA2</code> and merged it into the <code>5_x-prod</code> branch (<a href="https://github.com/ilri/DSpace/pull/379">#379</a>)</li>
<li>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</li>
</ul>
<li><p>I proofed and tested the ILRI author corrections that Peter sent back to me this week:</p>
<pre><code>$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
</code></pre>
</code></pre></li>
<ul>
<li>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="/cgspace-notes/2018-03/">March, 2018</a></li>
<li>Time to index ~70,000 items on CGSpace:</li>
</ul>
<li><p>I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in <a href="/cgspace-notes/2018-03/">March, 2018</a></p></li>
<li><p>Time to index ~70,000 items on CGSpace:</p>
<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
real 74m42.646s
user 8m5.056s
sys 2m7.289s
</code></pre>
</code></pre></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-06/'>Read more →</a>
</article>
@ -279,26 +277,25 @@ sys 2m7.289s
<li>I didn&rsquo;t get any load alerts from Linode and the REST and XMLUI logs don&rsquo;t show anything out of the ordinary</li>
<li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li>
<li>In dspace.log around that time I see many errors like &ldquo;Client closed the connection before file download was complete&rdquo;</li>
<li>And just before that I see this:</li>
</ul>
<li><p>And just before that I see this:</p>
<pre><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
</code></pre>
</code></pre></li>
<ul>
<li>Ah hah! So the pool was actually empty!</li>
<li>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</li>
<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</li>
<li>I notice this error quite a few times in dspace.log:</li>
</ul>
<li><p>Ah hah! So the pool was actually empty!</p></li>
<li><p>I need to increase that, let&rsquo;s try to bump it up from 50 to 75</p></li>
<li><p>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don&rsquo;t know what the hell Uptime Robot saw</p></li>
<li><p>I notice this error quite a few times in dspace.log:</p>
<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered &quot; &quot;]&quot; &quot;] &quot;&quot; at line 1, column 32.
</code></pre>
</code></pre></li>
<ul>
<li>And there are many of these errors every day for the past month:</li>
</ul>
<li><p>And there are many of these errors every day for the past month:</p>
<pre><code>$ grep -c &quot;Error while searching for sidebar facets&quot; dspace.log.*
dspace.log.2017-11-21:4
@ -344,10 +341,9 @@ dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
</code></pre>
</code></pre></li>
<ul>
<li>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let&rsquo;s Encrypt if it&rsquo;s just a handful of domains</li>
<li><p>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let&rsquo;s Encrypt if it&rsquo;s just a handful of domains</p></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
</article>
@ -400,20 +396,18 @@ dspace.log.2018-01-02:34
<h2 id="2017-11-02">2017-11-02</h2>
<ul>
<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
</ul>
<li><p>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</p>
<pre><code># grep -c &quot;CORE&quot; /var/log/nginx/access.log
0
</code></pre>
</code></pre></li>
<ul>
<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
</ul>
<li><p>Generate list of authors on CGSpace for Peter to go through and correct:</p>
<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
</code></pre>
</code></pre></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a>
</article>
@ -434,15 +428,14 @@ COPY 54701
<h2 id="2017-10-01">2017-10-01</h2>
<ul>
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
</ul>
<li><p>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</p>
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
</code></pre>
</code></pre></li>
<ul>
<li>There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</li>
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
<li><p>There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</p></li>
<li><p>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</p></li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
</article>