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538 lines
21 KiB
HTML
538 lines
21 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="2019-01-06T11:50:26+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": "1240",
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"datePublished": "2019-01-02T09:48:30+02:00",
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"dateModified": "2019-01-06T11:50:26+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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{
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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>
|
|
|
|
<!-- vim: set sw=2 ts=2: -->
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|
|
|
|
|
|
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|
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|
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</article>
|
|
|
|
|
|
|
|
</div> <!-- /.blog-main -->
|
|
|
|
<aside class="col-sm-3 ml-auto blog-sidebar">
|
|
|
|
|
|
|
|
<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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|
|
<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>
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</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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