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887 lines
39 KiB
HTML
887 lines
39 KiB
HTML
<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta property="og:title" content="January, 2019" />
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<meta property="og:description" content="2019-01-02
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Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning
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I don’t see anything interesting in the web server logs around that time though:
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# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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92 40.77.167.4
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99 210.7.29.100
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120 38.126.157.45
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177 35.237.175.180
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177 40.77.167.32
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216 66.249.75.219
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225 18.203.76.93
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261 46.101.86.248
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357 207.46.13.1
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903 54.70.40.11
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-01/" /><meta property="article:published_time" content="2019-01-02T09:48:30+02:00"/>
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<meta property="article:modified_time" content="2019-01-16T17:10:50+02:00"/>
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="January, 2019"/>
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<meta name="twitter:description" content="2019-01-02
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Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning
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I don’t see anything interesting in the web server logs around that time though:
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# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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92 40.77.167.4
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99 210.7.29.100
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120 38.126.157.45
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177 35.237.175.180
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177 40.77.167.32
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216 66.249.75.219
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225 18.203.76.93
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261 46.101.86.248
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357 207.46.13.1
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903 54.70.40.11
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"/>
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<meta name="generator" content="Hugo 0.53" />
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<script type="application/ld+json">
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{
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"headline": "January, 2019",
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"url": "https://alanorth.github.io/cgspace-notes/2019-01/",
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"wordCount": "2447",
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"datePublished": "2019-01-02T09:48:30+02:00",
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"dateModified": "2019-01-16T17:10:50+02:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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},
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"keywords": "Notes"
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}
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</script>
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2019-01/">
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<title>January, 2019 | CGSpace Notes</title>
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<!-- combined, minified CSS -->
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<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-6+EGfPoOzk/n2DVJSlglKT8TV1TgIMvVcKI73IZgBswLasPBn94KommV6ilJqCXE" crossorigin="anonymous">
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</head>
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<body>
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<div class="blog-masthead">
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<div class="container">
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<nav class="nav blog-nav">
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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</nav>
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</div>
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</div>
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<header class="blog-header">
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<div class="container">
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<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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</div>
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</header>
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<div class="container">
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<div class="row">
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<div class="col-sm-8 blog-main">
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-01/">January, 2019</a></h2>
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<p class="blog-post-meta"><time datetime="2019-01-02T09:48:30+02:00">Wed Jan 02, 2019</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2019-01-02">2019-01-02</h2>
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<ul>
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<li>Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning</li>
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<li>I don’t see anything interesting in the web server logs around that time though:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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92 40.77.167.4
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99 210.7.29.100
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120 38.126.157.45
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177 35.237.175.180
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177 40.77.167.32
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216 66.249.75.219
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225 18.203.76.93
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261 46.101.86.248
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357 207.46.13.1
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903 54.70.40.11
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</code></pre>
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<ul>
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<li>Analyzing the types of requests made by the top few IPs during that time:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | grep 54.70.40.11 | grep -o -E "(bitstream|discover|handle)" | sort | uniq -c
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30 bitstream
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534 discover
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352 handle
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# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | grep 207.46.13.1 | grep -o -E "(bitstream|discover|handle)" | sort | uniq -c
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194 bitstream
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345 handle
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# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | grep 46.101.86.248 | grep -o -E "(bitstream|discover|handle)" | sort | uniq -c
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261 handle
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</code></pre>
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<ul>
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<li>It’s not clear to me what was causing the outbound traffic spike</li>
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<li>Oh nice! The once-per-year cron job for rotating the Solr statistics actually worked now (for the first time ever!):</li>
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</ul>
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<pre><code>Moving: 81742 into core statistics-2010
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Moving: 1837285 into core statistics-2011
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Moving: 3764612 into core statistics-2012
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Moving: 4557946 into core statistics-2013
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Moving: 5483684 into core statistics-2014
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Moving: 2941736 into core statistics-2015
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Moving: 5926070 into core statistics-2016
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Moving: 10562554 into core statistics-2017
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Moving: 18497180 into core statistics-2018
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</code></pre>
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<ul>
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<li>This could by why the outbound traffic rate was high, due to the S3 backup that run at 3:30AM…</li>
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<li>Run all system updates on DSpace Test (linode19) and reboot the server</li>
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</ul>
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<h2 id="2019-01-03">2019-01-03</h2>
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<ul>
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<li>Update local Docker image for DSpace PostgreSQL, re-using the existing data volume:</li>
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</ul>
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<pre><code>$ sudo docker pull postgres:9.6-alpine
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$ sudo docker rm dspacedb
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$ sudo docker run --name dspacedb -v /home/aorth/.local/lib/containers/volumes/dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
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</code></pre>
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<ul>
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<li>Testing DSpace 5.9 with Tomcat 8.5.37 on my local machine and I see that Atmire’s Listings and Reports still doesn’t work
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<ul>
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<li>After logging in via XMLUI and clicking the Listings and Reports link from the sidebar it redirects me to a JSPUI login page</li>
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<li>If I log in again there the Listings and Reports work… hmm.</li>
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</ul></li>
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<li>The JSPUI application—which Listings and Reports depends upon—also does not load, though the error is perhaps unrelated:</li>
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</ul>
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<pre><code>2019-01-03 14:45:21,727 INFO org.dspace.browse.BrowseEngine @ anonymous:session_id=9471D72242DAA05BCC87734FE3C66EA6:ip_addr=127.0.0.1:browse_mini:
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2019-01-03 14:45:21,971 INFO org.dspace.app.webui.discovery.DiscoverUtility @ facets for scope, null: 23
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2019-01-03 14:45:22,115 WARN org.dspace.app.webui.servlet.InternalErrorServlet @ :session_id=9471D72242DAA05BCC87734FE3C66EA6:internal_error:-- URL Was: http://localhost:8080/jspui/internal-error
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-- Method: GET
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-- Parameters were:
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org.apache.jasper.JasperException: /home.jsp (line: [214], column: [1]) /discovery/static-tagcloud-facet.jsp (line: [57], column: [8]) No tag [tagcloud] defined in tag library imported with prefix [dspace]
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at org.apache.jasper.compiler.DefaultErrorHandler.jspError(DefaultErrorHandler.java:41)
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at org.apache.jasper.compiler.ErrorDispatcher.dispatch(ErrorDispatcher.java:291)
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at org.apache.jasper.compiler.ErrorDispatcher.jspError(ErrorDispatcher.java:97)
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at org.apache.jasper.compiler.Parser.processIncludeDirective(Parser.java:347)
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at org.apache.jasper.compiler.Parser.parseIncludeDirective(Parser.java:380)
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at org.apache.jasper.compiler.Parser.parseDirective(Parser.java:481)
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at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1445)
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at org.apache.jasper.compiler.Parser.parseBody(Parser.java:1683)
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at org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:1016)
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at org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1291)
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at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1470)
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at org.apache.jasper.compiler.Parser.parse(Parser.java:144)
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at org.apache.jasper.compiler.ParserController.doParse(ParserController.java:244)
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at org.apache.jasper.compiler.ParserController.parse(ParserController.java:105)
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at org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:202)
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at org.apache.jasper.compiler.Compiler.compile(Compiler.java:373)
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at org.apache.jasper.compiler.Compiler.compile(Compiler.java:350)
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at org.apache.jasper.compiler.Compiler.compile(Compiler.java:334)
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at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:595)
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at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:399)
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at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
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at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
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at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:728)
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at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:470)
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at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:395)
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at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:316)
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at org.dspace.app.webui.util.JSPManager.showJSP(JSPManager.java:60)
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at org.apache.jsp.index_jsp._jspService(index_jsp.java:191)
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at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
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at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
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at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:476)
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at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
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at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
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at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
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at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
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at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
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at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
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at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
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at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
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at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:234)
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at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
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at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
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at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
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at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
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at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
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at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
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at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
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at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
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at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
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at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
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at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
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at java.lang.Thread.run(Thread.java:748)
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</code></pre>
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<ul>
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<li>I notice that I get different JSESSIONID cookies for <code>/</code> (XMLUI) and <code>/jspui</code> (JSPUI) on Tomcat 8.5.37, I wonder if it’s the same on Tomcat 7.0.92… yes I do.</li>
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<li>Hmm, on Tomcat 7.0.92 I see that I get a <code>dspace.current.user.id</code> session cookie after logging into XMLUI, and then when I browse to JSPUI I am still logged in…
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<ul>
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<li>I didn’t see that cookie being set on Tomcat 8.5.37</li>
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</ul></li>
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<li>I sent a message to the dspace-tech mailing list to ask</li>
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</ul>
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<h2 id="2019-01-04">2019-01-04</h2>
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<ul>
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<li>Linode sent a message last night that CGSpace (linode18) had high CPU usage, but I don’t see anything around that time in the web server logs:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "03/Jan/2019:1(7|8|9)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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189 207.46.13.192
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217 31.6.77.23
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340 66.249.70.29
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349 40.77.167.86
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417 34.218.226.147
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630 207.46.13.173
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710 35.237.175.180
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790 40.77.167.87
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1776 66.249.70.27
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2099 54.70.40.11
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</code></pre>
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<ul>
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<li>I’m thinking about trying to validate our <code>dc.subject</code> terms against <a href="http://aims.fao.org/agrovoc/webservices">AGROVOC webservices</a></li>
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<li>There seem to be a few APIs and the documentation is kinda confusing, but I found this REST endpoint that does work well, for example searching for <code>SOIL</code>:</li>
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</ul>
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<pre><code>$ http http://agrovoc.uniroma2.it/agrovoc/rest/v1/search?query=SOIL&lang=en
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HTTP/1.1 200 OK
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Access-Control-Allow-Origin: *
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Connection: Keep-Alive
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Content-Length: 493
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Content-Type: application/json; charset=utf-8
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Date: Fri, 04 Jan 2019 13:44:27 GMT
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Keep-Alive: timeout=5, max=100
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Server: Apache
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Strict-Transport-Security: max-age=63072000; includeSubdomains
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Vary: Accept
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X-Content-Type-Options: nosniff
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X-Frame-Options: ALLOW-FROM http://aims.fao.org
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{
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"@context": {
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"@language": "en",
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"altLabel": "skos:altLabel",
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"hiddenLabel": "skos:hiddenLabel",
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"isothes": "http://purl.org/iso25964/skos-thes#",
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"onki": "http://schema.onki.fi/onki#",
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"prefLabel": "skos:prefLabel",
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"results": {
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"@container": "@list",
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"@id": "onki:results"
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},
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"skos": "http://www.w3.org/2004/02/skos/core#",
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"type": "@type",
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"uri": "@id"
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},
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"results": [
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{
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"lang": "en",
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"prefLabel": "soil",
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"type": [
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"skos:Concept"
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],
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"uri": "http://aims.fao.org/aos/agrovoc/c_7156",
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"vocab": "agrovoc"
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}
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],
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"uri": ""
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}
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</code></pre>
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<ul>
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<li>The API does not appear to be case sensitive (searches for <code>SOIL</code> and <code>soil</code> return the same thing)</li>
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<li>I’m a bit confused that there’s no obvious return code or status when a term is not found, for example <code>SOILS</code>:</li>
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</ul>
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<pre><code>HTTP/1.1 200 OK
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Access-Control-Allow-Origin: *
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Connection: Keep-Alive
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Content-Length: 367
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Content-Type: application/json; charset=utf-8
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Date: Fri, 04 Jan 2019 13:48:31 GMT
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Keep-Alive: timeout=5, max=100
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Server: Apache
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Strict-Transport-Security: max-age=63072000; includeSubdomains
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Vary: Accept
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X-Content-Type-Options: nosniff
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X-Frame-Options: ALLOW-FROM http://aims.fao.org
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{
|
|
"@context": {
|
|
"@language": "en",
|
|
"altLabel": "skos:altLabel",
|
|
"hiddenLabel": "skos:hiddenLabel",
|
|
"isothes": "http://purl.org/iso25964/skos-thes#",
|
|
"onki": "http://schema.onki.fi/onki#",
|
|
"prefLabel": "skos:prefLabel",
|
|
"results": {
|
|
"@container": "@list",
|
|
"@id": "onki:results"
|
|
},
|
|
"skos": "http://www.w3.org/2004/02/skos/core#",
|
|
"type": "@type",
|
|
"uri": "@id"
|
|
},
|
|
"results": [],
|
|
"uri": ""
|
|
}
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I guess the <code>results</code> object will just be empty…</li>
|
|
<li>Another way would be to try with SPARQL, perhaps using the Python 2.7 <a href="https://pypi.org/project/sparql-client/">sparql-client</a>:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ python2.7 -m virtualenv /tmp/sparql
|
|
$ . /tmp/sparql/bin/activate
|
|
$ pip install sparql-client ipython
|
|
$ ipython
|
|
In [10]: import sparql
|
|
In [11]: s = sparql.Service("http://agrovoc.uniroma2.it:3030/agrovoc/sparql", "utf-8", "GET")
|
|
In [12]: statement=('PREFIX skos: <http://www.w3.org/2004/02/skos/core#> '
|
|
...: 'SELECT '
|
|
...: '?label '
|
|
...: 'WHERE { '
|
|
...: '{ ?concept skos:altLabel ?label . } UNION { ?concept skos:prefLabel ?label . } '
|
|
...: 'FILTER regex(str(?label), "^fish", "i") . '
|
|
...: '} LIMIT 10')
|
|
In [13]: result = s.query(statement)
|
|
In [14]: for row in result.fetchone():
|
|
...: print(row)
|
|
...:
|
|
(<Literal "fish catching"@en>,)
|
|
(<Literal "fish harvesting"@en>,)
|
|
(<Literal "fish meat"@en>,)
|
|
(<Literal "fish roe"@en>,)
|
|
(<Literal "fish conversion"@en>,)
|
|
(<Literal "fisheries catches (composition)"@en>,)
|
|
(<Literal "fishtail palm"@en>,)
|
|
(<Literal "fishflies"@en>,)
|
|
(<Literal "fishery biology"@en>,)
|
|
(<Literal "fish production"@en>,)
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>The SPARQL query comes from my notes in <a href="/cgspace-notes/2017-08/">2017-08</a></li>
|
|
</ul>
|
|
|
|
<h2 id="2019-01-06">2019-01-06</h2>
|
|
|
|
<ul>
|
|
<li>I built a clean DSpace 5.8 installation from the upstream <code>dspace-5.8</code> tag and the issue with the XMLUI/JSPUI login is still there with Tomcat 8.5.37
|
|
|
|
<ul>
|
|
<li>If I log into XMLUI and then nagivate to JSPUI I need to log in again</li>
|
|
<li>XMLUI does not set the <code>dspace.current.user.id</code> session cookie in Tomcat 8.5.37 for some reason</li>
|
|
<li>I sent an update to the dspace-tech mailing list to ask for more help troubleshooting</li>
|
|
</ul></li>
|
|
</ul>
|
|
|
|
<h2 id="2019-01-07">2019-01-07</h2>
|
|
|
|
<ul>
|
|
<li>I built a clean DSpace 6.3 installation from the upstream <code>dspace-6.3</code> tag and the issue with the XMLUI/JSPUI login is still there with Tomcat 8.5.37
|
|
|
|
<ul>
|
|
<li>If I log into XMLUI and then nagivate to JSPUI I need to log in again</li>
|
|
<li>XMLUI does not set the <code>dspace.current.user.id</code> session cookie in Tomcat 8.5.37 for some reason</li>
|
|
<li>I sent an update to the dspace-tech mailing list to ask for more help troubleshooting</li>
|
|
</ul></li>
|
|
</ul>
|
|
|
|
<h2 id="2019-01-08">2019-01-08</h2>
|
|
|
|
<ul>
|
|
<li>Tim Donohue responded to my thread about the cookies on the dspace-tech mailing list
|
|
|
|
<ul>
|
|
<li>He suspects it’s a change of behavior in Tomcat 8.5, and indeed I see a mention of new cookie processing in the <a href="https://tomcat.apache.org/migration-85.html#Cookies">Tomcat 8.5 migration guide</a></li>
|
|
<li>I tried to switch my XMLUI and JSPUI contexts to use the <code>LegacyCookieProcessor</code>, but it didn’t seem to help</li>
|
|
<li>I <a href="https://jira.duraspace.org/browse/DS-4140">filed DS-4140 on the DSpace issue tracker</a></li>
|
|
</ul></li>
|
|
</ul>
|
|
|
|
<h2 id="2019-01-11">2019-01-11</h2>
|
|
|
|
<ul>
|
|
<li>Tezira wrote to say she has stopped receiving the <code>DSpace Submission Approved and Archived</code> emails from CGSpace as of January 2nd
|
|
|
|
<ul>
|
|
<li>I told her that I haven’t done anything to disable it lately, but that I would check</li>
|
|
<li>Bizu also says she hasn’t received them lately</li>
|
|
</ul></li>
|
|
</ul>
|
|
|
|
<h2 id="2019-01-14">2019-01-14</h2>
|
|
|
|
<ul>
|
|
<li>Day one of CGSpace AReS meeting in Amman</li>
|
|
</ul>
|
|
|
|
<h2 id="2019-01-15">2019-01-15</h2>
|
|
|
|
<ul>
|
|
<li>Day two of CGSpace AReS meeting in Amman
|
|
|
|
<ul>
|
|
<li>Discuss possibly extending the <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> to make community and collection statistics available</li>
|
|
<li>Discuss new “final” CG Core document and some changes that we’ll need to do on CGSpace and other repositories</li>
|
|
<li>We agreed to try to stick to pure Dublin Core where possible, then use fields that exist in standard DSpace, and use “cg” namespace for everything else</li>
|
|
<li>Major changes are to move <code>dc.contributor.author</code> to <code>dc.creator</code> (which MELSpace and WorldFish are already using in their DSpace repositories)</li>
|
|
</ul></li>
|
|
<li>I am testing the speed of the WorldFish DSpace repository’s REST API and it’s five to ten times faster than CGSpace as I tested in <a href="/cgspace-notes/2018-10/">2018-10</a>:</li>
|
|
</ul>
|
|
|
|
<pre><code>$ time http --print h 'https://digitalarchive.worldfishcenter.org/rest/items?expand=metadata,bitstreams,parentCommunityList&limit=100&offset=0'
|
|
|
|
0.16s user 0.03s system 3% cpu 5.185 total
|
|
0.17s user 0.02s system 2% cpu 7.123 total
|
|
0.18s user 0.02s system 6% cpu 3.047 total
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>In other news, Linode sent a mail last night that the CPU load on CGSpace (linode18) was high, here are the top IPs in the logs around those few hours:</li>
|
|
</ul>
|
|
|
|
<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "14/Jan/2019:(17|18|19|20)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
|
|
157 31.6.77.23
|
|
192 54.70.40.11
|
|
202 66.249.64.157
|
|
207 40.77.167.204
|
|
220 157.55.39.140
|
|
326 197.156.105.116
|
|
385 207.46.13.158
|
|
1211 35.237.175.180
|
|
1830 66.249.64.155
|
|
2482 45.5.186.2
|
|
</code></pre>
|
|
|
|
<h2 id="2019-01-16">2019-01-16</h2>
|
|
|
|
<ul>
|
|
<li>Day three of CGSpace AReS meeting in Amman
|
|
|
|
<ul>
|
|
<li>We discussed CG Core 2.0 metadata and decided some action points</li>
|
|
<li>We discussed branding of AReS tool</li>
|
|
</ul></li>
|
|
<li>Notes from our CG Core 2.0 metadata discussion:
|
|
|
|
<ul>
|
|
<li>Not Dublin Core:</li>
|
|
<li>dc.subtype</li>
|
|
<li>dc.peer-reviewed</li>
|
|
<li>Dublin Core, possible action for CGSpace:</li>
|
|
<li>dc.description:
|
|
|
|
<ul>
|
|
<li>We use dc.description.abstract, dc.description (Notes), dc.description.version (Peer review status), dc.description.sponsorship (Funder)</li>
|
|
<li>Maybe move abstract to dc.description</li>
|
|
<li>Maybe notes moves to cg.description.notes???</li>
|
|
<li>Maybe move dc.description.version to cg.peer-reviewed or cg.peer-review-status???</li>
|
|
<li>Move dc.description.sponsorship to cg.contributor.donor???</li>
|
|
</ul></li>
|
|
<li>dc.subject:
|
|
|
|
<ul>
|
|
<li>Wait for guidance, evaluate technical implications (Google indexing, OAI, etc)</li>
|
|
</ul></li>
|
|
<li>Move dc.contributor.author to dc.creator</li>
|
|
<li>dc.contributor Project
|
|
|
|
<ul>
|
|
<li>Recommend against creating new fields for all projects</li>
|
|
<li>We use collections projects/themes/etc</li>
|
|
</ul></li>
|
|
<li>dc.contributor Project Lead Center
|
|
|
|
<ul>
|
|
<li>MELSpace uses cg.contributor.project-lead-institute (institute is more generic than center)</li>
|
|
<li>Maybe we use?</li>
|
|
</ul></li>
|
|
<li>dc.contributor Partner
|
|
|
|
<ul>
|
|
<li>Wait for guidance</li>
|
|
<li>MELSpace uses cg.contibutor.center (?)</li>
|
|
</ul></li>
|
|
<li>dc.contributor Donor
|
|
|
|
<ul>
|
|
<li>Use cg.contributor.donor</li>
|
|
</ul></li>
|
|
<li>dc.date
|
|
|
|
<ul>
|
|
<li>Wait for guidance, maybe move dc.date.issued?</li>
|
|
<li>dc.date.accessioned and dc.date.available are automatic in DSpace</li>
|
|
</ul></li>
|
|
<li>dc.language
|
|
|
|
<ul>
|
|
<li>Move dc.language.iso to dc.language</li>
|
|
</ul></li>
|
|
<li>dc.identifier
|
|
|
|
<ul>
|
|
<li>Move cg.identifier.url to dc.identifier</li>
|
|
</ul></li>
|
|
<li>dc.identifier bibliographicCitation
|
|
|
|
<ul>
|
|
<li>dc.identifier.citation should move to dc.bibliographicCitation</li>
|
|
</ul></li>
|
|
<li>dc.description.notes
|
|
|
|
<ul>
|
|
<li>Wait for guidance, maybe move to cg.description.notes ???</li>
|
|
</ul></li>
|
|
<li>dc.relation
|
|
|
|
<ul>
|
|
<li>Maybe move cg.link.reference</li>
|
|
<li>Perhaps consolodate cg.link.audio etc there…?</li>
|
|
</ul></li>
|
|
<li>dc.relation.isPartOf
|
|
|
|
<ul>
|
|
<li>Move dc.relation.ispartofseries to dc.relation.isPartOf</li>
|
|
</ul></li>
|
|
<li>dc.audience
|
|
|
|
<ul>
|
|
<li>Move cg.targetaudience to dc.audience</li>
|
|
</ul></li>
|
|
</ul></li>
|
|
<li>Something happened to the Solr usage statistics on CGSpace
|
|
|
|
<ul>
|
|
<li>I looked on the server and the Solr cores are there (56GB!), and I don’t see any obvious errors in dmesg or anything</li>
|
|
<li>I see that the server hasn’t been rebooted in 26 days so I rebooted it</li>
|
|
</ul></li>
|
|
<li>After reboot the Solr stats are still messed up in the Atmire Usage Stats module, it only shows 2019-01!</li>
|
|
</ul>
|
|
|
|
<p><img src="/cgspace-notes/2019/01/solr-stats-incorrect.png" alt="Solr stats fucked up" /></p>
|
|
|
|
<ul>
|
|
<li>In the Solr admin UI I see the following error:</li>
|
|
</ul>
|
|
|
|
<pre><code>statistics-2018: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Looking in the Solr log I see this:</li>
|
|
</ul>
|
|
|
|
<pre><code>2019-01-16 13:37:55,395 ERROR org.apache.solr.core.CoreContainer @ Error creating core [statistics-2018]: Error opening new searcher
|
|
org.apache.solr.common.SolrException: Error opening new searcher
|
|
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:873)
|
|
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:646)
|
|
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:491)
|
|
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:466)
|
|
at org.apache.solr.handler.admin.CoreAdminHandler.handleCreateAction(CoreAdminHandler.java:575)
|
|
at org.apache.solr.handler.admin.CoreAdminHandler.handleRequestInternal(CoreAdminHandler.java:199)
|
|
at org.apache.solr.handler.admin.CoreAdminHandler.handleRequestBody(CoreAdminHandler.java:188)
|
|
at org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:135)
|
|
at org.apache.solr.servlet.SolrDispatchFilter.handleAdminRequest(SolrDispatchFilter.java:729)
|
|
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:258)
|
|
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:207)
|
|
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
|
|
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
|
|
at org.dspace.solr.filters.LocalHostRestrictionFilter.doFilter(LocalHostRestrictionFilter.java:50)
|
|
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
|
|
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
|
|
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:221)
|
|
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
|
|
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
|
|
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
|
|
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
|
|
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180)
|
|
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)
|
|
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
|
|
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:436)
|
|
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078)
|
|
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)
|
|
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
|
|
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
|
|
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
|
|
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
|
|
at java.lang.Thread.run(Thread.java:748)
|
|
Caused by: org.apache.solr.common.SolrException: Error opening new searcher
|
|
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1565)
|
|
at org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:1677)
|
|
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:845)
|
|
... 31 more
|
|
Caused by: org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2018/data/index/write.lock
|
|
at org.apache.lucene.store.Lock.obtain(Lock.java:89)
|
|
at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:753)
|
|
at org.apache.solr.update.SolrIndexWriter.<init>(SolrIndexWriter.java:77)
|
|
at org.apache.solr.update.SolrIndexWriter.create(SolrIndexWriter.java:64)
|
|
at org.apache.solr.update.DefaultSolrCoreState.createMainIndexWriter(DefaultSolrCoreState.java:279)
|
|
at org.apache.solr.update.DefaultSolrCoreState.getIndexWriter(DefaultSolrCoreState.java:111)
|
|
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1528)
|
|
... 33 more
|
|
2019-01-16 13:37:55,401 ERROR org.apache.solr.core.SolrCore @ org.apache.solr.common.SolrException: Error CREATEing SolrCore 'statistics-2018': Unable to create core [statistics-2018] Caused by: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2018/data/index/write.lock
|
|
at org.apache.solr.handler.admin.CoreAdminHandler.handleCreateAction(CoreAdminHandler.java:613)
|
|
at org.apache.solr.handler.admin.CoreAdminHandler.handleRequestInternal(CoreAdminHandler.java:199)
|
|
at org.apache.solr.handler.admin.CoreAdminHandler.handleRequestBody(CoreAdminHandler.java:188)
|
|
at org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:135)
|
|
at org.apache.solr.servlet.SolrDispatchFilter.handleAdminRequest(SolrDispatchFilter.java:729)
|
|
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:258)
|
|
at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:207)
|
|
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
|
|
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
|
|
at org.dspace.solr.filters.LocalHostRestrictionFilter.doFilter(LocalHostRestrictionFilter.java:50)
|
|
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
|
|
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
|
|
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:221)
|
|
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
|
|
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
|
|
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
|
|
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
|
|
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180)
|
|
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)
|
|
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
|
|
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:436)
|
|
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078)
|
|
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)
|
|
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
|
|
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
|
|
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
|
|
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
|
|
at java.lang.Thread.run(Thread.java:748)
|
|
Caused by: org.apache.solr.common.SolrException: Unable to create core [statistics-2018]
|
|
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:507)
|
|
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:466)
|
|
at org.apache.solr.handler.admin.CoreAdminHandler.handleCreateAction(CoreAdminHandler.java:575)
|
|
... 27 more
|
|
Caused by: org.apache.solr.common.SolrException: Error opening new searcher
|
|
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:873)
|
|
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:646)
|
|
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:491)
|
|
... 29 more
|
|
Caused by: org.apache.solr.common.SolrException: Error opening new searcher
|
|
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1565)
|
|
at org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:1677)
|
|
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:845)
|
|
... 31 more
|
|
Caused by: org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2018/data/index/write.lock
|
|
at org.apache.lucene.store.Lock.obtain(Lock.java:89)
|
|
at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:753)
|
|
at org.apache.solr.update.SolrIndexWriter.<init>(SolrIndexWriter.java:77)
|
|
at org.apache.solr.update.SolrIndexWriter.create(SolrIndexWriter.java:64)
|
|
at org.apache.solr.update.DefaultSolrCoreState.createMainIndexWriter(DefaultSolrCoreState.java:279)
|
|
at org.apache.solr.update.DefaultSolrCoreState.getIndexWriter(DefaultSolrCoreState.java:111)
|
|
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1528)
|
|
... 33 more
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>I found some threads on StackOverflow etc discussing this and several suggested increasing the address space for the shell with ulimit</li>
|
|
<li>I added <code>ulimit -v unlimited</code> to the <code>/etc/default/tomcat7</code> and restarted Tomcat and now Solr is working again:</li>
|
|
</ul>
|
|
|
|
<p><img src="/cgspace-notes/2019/01/solr-stats-incorrect.png" alt="Solr stats working" /></p>
|
|
|
|
<ul>
|
|
<li>Some StackOverflow discussions related to this:
|
|
|
|
<ul>
|
|
<li><a href="https://stackoverflow.com/questions/2895417/solrexception-internal-server-error/3035916#3035916">https://stackoverflow.com/questions/2895417/solrexception-internal-server-error/3035916#3035916</a></li>
|
|
<li><a href="https://stackoverflow.com/questions/11683850/how-much-memory-could-vm-use">https://stackoverflow.com/questions/11683850/how-much-memory-could-vm-use</a></li>
|
|
<li><a href="https://stackoverflow.com/questions/8892143/error-when-opening-a-lucene-index-map-failed/8893684#8893684">https://stackoverflow.com/questions/8892143/error-when-opening-a-lucene-index-map-failed/8893684#8893684</a></li>
|
|
</ul></li>
|
|
<li>Abenet was asking if the Atmire Usage Stats are correct because they are over 2 million the last few months…</li>
|
|
<li>For 2019-01 alone the Usage Stats are already around 1.2 million</li>
|
|
<li>I tried to look in the nginx logs to see how many raw requests there are so far this month and it’s about 1.4 million:</li>
|
|
</ul>
|
|
|
|
<pre><code># time zcat --force /var/log/nginx/* | grep -cE "[0-9]{1,2}/Jan/2019"
|
|
1442874
|
|
|
|
real 0m17.161s
|
|
user 0m16.205s
|
|
sys 0m2.396s
|
|
</code></pre>
|
|
|
|
<h2 id="2019-01-17">2019-01-17</h2>
|
|
|
|
<ul>
|
|
<li>Send reminder to Atmire about purchasing the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=657">MQM module</a></li>
|
|
<li>Trying to decide the solid action points for CGSpace on the CG Core 2.0 metadata:
|
|
|
|
<ul>
|
|
<li>dc.description → cg.description.notes</li>
|
|
<li>dc.description.abstract → dc.abstract</li>
|
|
<li>dc.description.version → cg.peer-reviewed (or cg.peer-review-status)</li>
|
|
<li>dc.description.sponsorship → cg.contributor.donor</li>
|
|
<li>dc.contributor.author → dc.creator</li>
|
|
<li>dc.language.iso → dc.language</li>
|
|
<li>cg.identifier.url → dc.identifier</li>
|
|
<li>dc.identifier.citation → dc.bibliographicCitation</li>
|
|
<li>dc.relation.ispartofseries → dc.relation.isPartOf</li>
|
|
<li>cg.targetaudience → dc.audience</li>
|
|
</ul></li>
|
|
<li>It’s actually difficult to decide some of these because the current CG Core 2.0 document does not provide guidance or descriptions</li>
|
|
<li>Also, there is not a good Dublin Core reference (or maybe I just don’t understand?)</li>
|
|
<li>Several authoritative documents on Dublin Core appear to be:
|
|
|
|
<ul>
|
|
<li><a href="http://dublincore.org/documents/dces/">Dublin Core Metadata Element Set, Version 1.1: Reference Description</a></li>
|
|
<li><a href="http://www.dublincore.org/documents/dcmi-terms/">DCMI Metadata Terms</a></li>
|
|
</ul></li>
|
|
<li>And what is the relationship between DC and DCTERMS?</li>
|
|
<li>DSpace uses DCTERMS in the metadata it embeds in XMLUI item views!</li>
|
|
<li>We really need to look at this more carefully and see the impacts that might be made from switching core fields like languages, abstract, authors, etc</li>
|
|
<li>We can check WorldFish and MELSpace repositories to see what effects these changes have had on theirs because they have already adopted some of these changes…</li>
|
|
</ul>
|
|
|
|
<!-- vim: set sw=2 ts=2: -->
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
|
|
<h4>Recent Posts</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
|
|
<li><a href="/cgspace-notes/2019-01/">January, 2019</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-12/">December, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-11/">November, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-10/">October, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-09/">September, 2018</a></li>
|
|
|
|
</ol>
|
|
</section>
|
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|
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|
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|
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<section class="sidebar-module">
|
|
<h4>Links</h4>
|
|
<ol class="list-unstyled">
|
|
|
|
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
|
|
|
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
|
|
|
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
|
|
|
</ol>
|
|
</section>
|
|
|
|
</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p>
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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