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Add notes for 2019-11-28
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<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
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<meta property="og:type" content="website" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
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<meta property="og:updated_time" content="2019-11-04T12:20:30+02:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="CGSpace Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.59.1" />
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<meta name="generator" content="Hugo 0.60.0" />
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@ -100,10 +99,9 @@
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</p>
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</header>
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<h2 id="2018-04-01">2018-04-01</h2>
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<h2 id="20180401">2018-04-01</h2>
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<ul>
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<li>I tried to test something on DSpace Test but noticed that it’s down since god knows when</li>
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<li>I tried to test something on DSpace Test but noticed that it's down since god knows when</li>
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<li>Catalina logs at least show some memory errors yesterday:</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-04/'>Read more →</a>
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</p>
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</header>
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<h2 id="2018-03-02">2018-03-02</h2>
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<h2 id="20180302">2018-03-02</h2>
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<ul>
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<li>Export a CSV of the IITA community metadata for Martin Mueller</li>
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</ul>
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@ -145,13 +142,12 @@
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</p>
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</header>
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<h2 id="2018-02-01">2018-02-01</h2>
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<h2 id="20180201">2018-02-01</h2>
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<ul>
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<li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li>
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<li>We don’t need to distinguish between internal and external works, so that makes it just a simple list</li>
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<li>We don't need to distinguish between internal and external works, so that makes it just a simple list</li>
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<li>Yesterday I figured out how to monitor DSpace sessions using JMX</li>
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<li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu’s <code>munin-plugins-java</code> package and used the stuff I discovered about JMX <a href="/cgspace-notes/2018-01/">in 2018-01</a></li>
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<li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu's <code>munin-plugins-java</code> package and used the stuff I discovered about JMX <a href="/cgspace-notes/2018-01/">in 2018-01</a></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-02/'>Read more →</a>
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</article>
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</p>
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</header>
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<h2 id="2018-01-02">2018-01-02</h2>
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<h2 id="20180102">2018-01-02</h2>
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<ul>
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<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
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<li>I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary</li>
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<li>I didn't get any load alerts from Linode and the REST and XMLUI logs don't show anything out of the ordinary</li>
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<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>
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<li>In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”</li>
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<li><p>And just before that I see this:</p>
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<li>And just before that I see this:</li>
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</ul>
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<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].
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</code></pre></li>
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<li><p>Ah hah! So the pool was actually empty!</p></li>
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<li><p>I need to increase that, let’s try to bump it up from 50 to 75</p></li>
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<li><p>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw</p></li>
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<li><p>I notice this error quite a few times in dspace.log:</p>
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</code></pre><ul>
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<li>Ah hah! So the pool was actually empty!</li>
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<li>I need to increase that, let's try to bump it up from 50 to 75</li>
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<li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don't know what the hell Uptime Robot saw</li>
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<li>I notice this error quite a few times in dspace.log:</li>
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</ul>
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<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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</code></pre></li>
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<li><p>And there are many of these errors every day for the past month:</p>
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</code></pre><ul>
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<li>And there are many of these errors every day for the past month:</li>
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</ul>
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<pre><code>$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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dspace.log.2017-11-22:1
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@ -241,9 +230,8 @@ dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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</code></pre></li>
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<li><p>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains</p></li>
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</code></pre><ul>
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<li>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let's Encrypt if it's just a handful of domains</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
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</article>
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</p>
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</header>
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<h2 id="2017-12-01">2017-12-01</h2>
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<h2 id="20171201">2017-12-01</h2>
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<ul>
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<li>Uptime Robot noticed that CGSpace went down</li>
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<li>The logs say “Timeout waiting for idle object”</li>
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@ -287,27 +274,22 @@ dspace.log.2018-01-02:34
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</p>
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</header>
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<h2 id="2017-11-01">2017-11-01</h2>
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<h2 id="20171101">2017-11-01</h2>
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<ul>
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<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
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</ul>
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<h2 id="2017-11-02">2017-11-02</h2>
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<h2 id="20171102">2017-11-02</h2>
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<ul>
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<li><p>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</p>
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<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
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</ul>
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<pre><code># grep -c "CORE" /var/log/nginx/access.log
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0
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</code></pre></li>
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<li><p>Generate list of authors on CGSpace for Peter to go through and correct:</p>
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</code></pre><ul>
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<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
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</ul>
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<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;
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COPY 54701
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</code></pre></li>
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</ul>
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a>
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</article>
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@ -325,17 +307,14 @@ COPY 54701
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</p>
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</header>
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<h2 id="2017-10-01">2017-10-01</h2>
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<h2 id="20171001">2017-10-01</h2>
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<ul>
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<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>
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<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>
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</ul>
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<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
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</code></pre></li>
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<li><p>There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</p></li>
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<li><p>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</p></li>
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</code></pre><ul>
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<li>There appears to be a pattern but I'll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</li>
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<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
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</article>
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</p>
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</header>
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<h2 id="2017-09-06">2017-09-06</h2>
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<h2 id="20170906">2017-09-06</h2>
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<ul>
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<li>Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two hours</li>
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</ul>
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<h2 id="2017-09-07">2017-09-07</h2>
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<h2 id="20170907">2017-09-07</h2>
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<ul>
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<li>Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account is both in the approvers step as well as the group</li>
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<li>Ask Sisay to clean up the WLE approvers a bit, as Marianne's user account is both in the approvers step as well as the group</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-09/'>Read more →</a>
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</article>
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@ -402,22 +378,21 @@ COPY 54701
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</p>
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</header>
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<h2 id="2017-08-01">2017-08-01</h2>
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<h2 id="20170801">2017-08-01</h2>
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<ul>
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<li>Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours</li>
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<li>I looked in the Activity pane of the Admin Control Panel and it seems that Google, Baidu, Yahoo, and Bing are all crawling with massive numbers of bots concurrently (~100 total, mostly Baidu and Google)</li>
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<li>The good thing is that, according to <code>dspace.log.2017-08-01</code>, they are all using the same Tomcat session</li>
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<li>This means our Tomcat Crawler Session Valve is working</li>
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<li>But many of the bots are browsing dynamic URLs like:
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<ul>
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<li>/handle/10568/3353/discover</li>
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<li>/handle/10568/16510/browse</li>
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</ul></li>
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</ul>
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</li>
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<li>The <code>robots.txt</code> only blocks the top-level <code>/discover</code> and <code>/browse</code> URLs… we will need to find a way to forbid them from accessing these!</li>
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<li>Relevant issue from DSpace Jira (semi resolved in DSpace 6.0): <a href="https://jira.duraspace.org/browse/DS-2962">https://jira.duraspace.org/browse/DS-2962</a></li>
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<li>It turns out that we’re already adding the <code>X-Robots-Tag "none"</code> HTTP header, but this only forbids the search engine from <em>indexing</em> the page, not crawling it!</li>
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<li>It turns out that we're already adding the <code>X-Robots-Tag "none"</code> HTTP header, but this only forbids the search engine from <em>indexing</em> the page, not crawling it!</li>
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<li>Also, the bot has to successfully browse the page first so it can receive the HTTP header…</li>
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<li>We might actually have to <em>block</em> these requests with HTTP 403 depending on the user agent</li>
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<li>Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415</li>
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