cgspace-notes/docs/2019-01/index.html

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Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning
I don&rsquo;t see anything interesting in the web server logs around that time though:


# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;02/Jan/2019:0(1|2|3)&quot; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
     92 40.77.167.4
     99 210.7.29.100
    120 38.126.157.45
    177 35.237.175.180
    177 40.77.167.32
    216 66.249.75.219
    225 18.203.76.93
    261 46.101.86.248
    357 207.46.13.1
    903 54.70.40.11
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Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning
I don&rsquo;t see anything interesting in the web server logs around that time though:


# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;02/Jan/2019:0(1|2|3)&quot; | awk &#39;{print $1}&#39; | sort | uniq -c | sort -n | tail -n 10
     92 40.77.167.4
     99 210.7.29.100
    120 38.126.157.45
    177 35.237.175.180
    177 40.77.167.32
    216 66.249.75.219
    225 18.203.76.93
    261 46.101.86.248
    357 207.46.13.1
    903 54.70.40.11
"/>
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    <h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-01/">January, 2019</a></h2>
    <p class="blog-post-meta"><time datetime="2019-01-02T09:48:30&#43;02:00">Wed Jan 02, 2019</time> by Alan Orth in 

<i class="fa fa-tag" aria-hidden="true"></i>&nbsp;<a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>

</p>
  </header>
  <h2 id="2019-01-02">2019-01-02</h2>

<ul>
<li>Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning</li>
<li>I don&rsquo;t see anything interesting in the web server logs around that time though:</li>
</ul>

<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;02/Jan/2019:0(1|2|3)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
     92 40.77.167.4
     99 210.7.29.100
    120 38.126.157.45
    177 35.237.175.180
    177 40.77.167.32
    216 66.249.75.219
    225 18.203.76.93
    261 46.101.86.248
    357 207.46.13.1
    903 54.70.40.11
</code></pre>

<ul>
<li>Analyzing the types of requests made by the top few IPs during that time:</li>
</ul>

<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;02/Jan/2019:0(1|2|3)&quot; | grep 54.70.40.11 | grep -o -E &quot;(bitstream|discover|handle)&quot; | sort | uniq -c
     30 bitstream
    534 discover
    352 handle
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;02/Jan/2019:0(1|2|3)&quot; | grep 207.46.13.1 | grep -o -E &quot;(bitstream|discover|handle)&quot; | sort | uniq -c
    194 bitstream
    345 handle
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;02/Jan/2019:0(1|2|3)&quot; | grep 46.101.86.248 | grep -o -E &quot;(bitstream|discover|handle)&quot; | sort | uniq -c
    261 handle
</code></pre>

<ul>
<li>It&rsquo;s not clear to me what was causing the outbound traffic spike</li>
<li>Oh nice! The once-per-year cron job for rotating the Solr statistics actually worked now (for the first time ever!):</li>
</ul>

<pre><code>Moving: 81742 into core statistics-2010
Moving: 1837285 into core statistics-2011
Moving: 3764612 into core statistics-2012
Moving: 4557946 into core statistics-2013
Moving: 5483684 into core statistics-2014
Moving: 2941736 into core statistics-2015
Moving: 5926070 into core statistics-2016
Moving: 10562554 into core statistics-2017
Moving: 18497180 into core statistics-2018
</code></pre>

<ul>
<li>This could by why the outbound traffic rate was high, due to the S3 backup that run at 3:30AM&hellip;</li>
<li>Run all system updates on DSpace Test (linode19) and reboot the server</li>
</ul>

<h2 id="2019-01-03">2019-01-03</h2>

<ul>
<li>Update local Docker image for DSpace PostgreSQL, re-using the existing data volume:</li>
</ul>

<pre><code>$ sudo docker pull postgres:9.6-alpine
$ sudo docker rm dspacedb
$ 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
</code></pre>

<ul>
<li>Testing DSpace 5.9 with Tomcat 8.5.37 on my local machine and I see that Atmire&rsquo;s Listings and Reports still doesn&rsquo;t work

<ul>
<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>
<li>If I log in again there the Listings and Reports work&hellip; hmm.</li>
</ul></li>
<li>The JSPUI application—which Listings and Reports depends upon—also does not load, though the error is perhaps unrelated:</li>
</ul>

<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:
2019-01-03 14:45:21,971 INFO  org.dspace.app.webui.discovery.DiscoverUtility @ facets for scope, null: 23
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
-- Method: GET
-- Parameters were:

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]
    at org.apache.jasper.compiler.DefaultErrorHandler.jspError(DefaultErrorHandler.java:41)
    at org.apache.jasper.compiler.ErrorDispatcher.dispatch(ErrorDispatcher.java:291)
    at org.apache.jasper.compiler.ErrorDispatcher.jspError(ErrorDispatcher.java:97)
    at org.apache.jasper.compiler.Parser.processIncludeDirective(Parser.java:347)
    at org.apache.jasper.compiler.Parser.parseIncludeDirective(Parser.java:380)
    at org.apache.jasper.compiler.Parser.parseDirective(Parser.java:481)
    at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1445)
    at org.apache.jasper.compiler.Parser.parseBody(Parser.java:1683)
    at org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:1016)
    at org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1291)
    at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1470)
    at org.apache.jasper.compiler.Parser.parse(Parser.java:144)
    at org.apache.jasper.compiler.ParserController.doParse(ParserController.java:244)
    at org.apache.jasper.compiler.ParserController.parse(ParserController.java:105)
    at org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:202)
    at org.apache.jasper.compiler.Compiler.compile(Compiler.java:373)
    at org.apache.jasper.compiler.Compiler.compile(Compiler.java:350)
    at org.apache.jasper.compiler.Compiler.compile(Compiler.java:334)
    at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:595)
    at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:399)
    at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
    at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:728)
    at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:470)
    at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:395)
    at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:316)
    at org.dspace.app.webui.util.JSPManager.showJSP(JSPManager.java:60)
    at org.apache.jsp.index_jsp._jspService(index_jsp.java:191)
    at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
    at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:476)
    at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
    at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
    at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:234)
    at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
    at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
    at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
    at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
    at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
    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)
</code></pre>

<ul>
<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&rsquo;s the same on Tomcat 7.0.92&hellip; yes I do.</li>
<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&hellip;

<ul>
<li>I didn&rsquo;t see that cookie being set on Tomcat 8.5.37</li>
</ul></li>
<li>I sent a message to the dspace-tech mailing list to ask</li>
</ul>

<h2 id="2019-01-04">2019-01-04</h2>

<ul>
<li>Linode sent a message last night that CGSpace (linode18) had high CPU usage, but I don&rsquo;t see anything around that time in the web server logs:</li>
</ul>

<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E &quot;03/Jan/2019:1(7|8|9)&quot; | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
    189 207.46.13.192
    217 31.6.77.23
    340 66.249.70.29
    349 40.77.167.86
    417 34.218.226.147
    630 207.46.13.173
    710 35.237.175.180
    790 40.77.167.87
   1776 66.249.70.27
   2099 54.70.40.11
</code></pre>

<ul>
<li>I&rsquo;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>
<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>
</ul>

<pre><code>$ http http://agrovoc.uniroma2.it/agrovoc/rest/v1/search?query=SOIL&amp;lang=en
HTTP/1.1 200 OK
Access-Control-Allow-Origin: *
Connection: Keep-Alive
Content-Length: 493
Content-Type: application/json; charset=utf-8
Date: Fri, 04 Jan 2019 13:44:27 GMT
Keep-Alive: timeout=5, max=100
Server: Apache
Strict-Transport-Security: max-age=63072000; includeSubdomains
Vary: Accept
X-Content-Type-Options: nosniff
X-Frame-Options: ALLOW-FROM http://aims.fao.org

{
    &quot;@context&quot;: {
        &quot;@language&quot;: &quot;en&quot;,
        &quot;altLabel&quot;: &quot;skos:altLabel&quot;,
        &quot;hiddenLabel&quot;: &quot;skos:hiddenLabel&quot;,
        &quot;isothes&quot;: &quot;http://purl.org/iso25964/skos-thes#&quot;,
        &quot;onki&quot;: &quot;http://schema.onki.fi/onki#&quot;,
        &quot;prefLabel&quot;: &quot;skos:prefLabel&quot;,
        &quot;results&quot;: {
            &quot;@container&quot;: &quot;@list&quot;,
            &quot;@id&quot;: &quot;onki:results&quot;
        },
        &quot;skos&quot;: &quot;http://www.w3.org/2004/02/skos/core#&quot;,
        &quot;type&quot;: &quot;@type&quot;,
        &quot;uri&quot;: &quot;@id&quot;
    },
    &quot;results&quot;: [
        {
            &quot;lang&quot;: &quot;en&quot;,
            &quot;prefLabel&quot;: &quot;soil&quot;,
            &quot;type&quot;: [
                &quot;skos:Concept&quot;
            ],
            &quot;uri&quot;: &quot;http://aims.fao.org/aos/agrovoc/c_7156&quot;,
            &quot;vocab&quot;: &quot;agrovoc&quot;
        }
    ],
    &quot;uri&quot;: &quot;&quot;
}
</code></pre>

<ul>
<li>The API does not appear to be case sensitive (searches for <code>SOIL</code> and <code>soil</code> return the same thing)</li>
<li>I&rsquo;m a bit confused that there&rsquo;s no obvious return code or status when a term is not found, for example <code>SOILS</code>:</li>
</ul>

<pre><code>HTTP/1.1 200 OK
Access-Control-Allow-Origin: *
Connection: Keep-Alive
Content-Length: 367
Content-Type: application/json; charset=utf-8
Date: Fri, 04 Jan 2019 13:48:31 GMT
Keep-Alive: timeout=5, max=100
Server: Apache
Strict-Transport-Security: max-age=63072000; includeSubdomains
Vary: Accept
X-Content-Type-Options: nosniff
X-Frame-Options: ALLOW-FROM http://aims.fao.org

{
    &quot;@context&quot;: {
        &quot;@language&quot;: &quot;en&quot;,
        &quot;altLabel&quot;: &quot;skos:altLabel&quot;,
        &quot;hiddenLabel&quot;: &quot;skos:hiddenLabel&quot;,
        &quot;isothes&quot;: &quot;http://purl.org/iso25964/skos-thes#&quot;,
        &quot;onki&quot;: &quot;http://schema.onki.fi/onki#&quot;,
        &quot;prefLabel&quot;: &quot;skos:prefLabel&quot;,
        &quot;results&quot;: {
            &quot;@container&quot;: &quot;@list&quot;,
            &quot;@id&quot;: &quot;onki:results&quot;
        },
        &quot;skos&quot;: &quot;http://www.w3.org/2004/02/skos/core#&quot;,
        &quot;type&quot;: &quot;@type&quot;,
        &quot;uri&quot;: &quot;@id&quot;
    },
    &quot;results&quot;: [],
    &quot;uri&quot;: &quot;&quot;
}
</code></pre>

<ul>
<li>I guess the <code>results</code> object will just be empty&hellip;</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(&quot;http://agrovoc.uniroma2.it:3030/agrovoc/sparql&quot;, &quot;utf-8&quot;, &quot;GET&quot;)
In [12]: statement=('PREFIX skos: &lt;http://www.w3.org/2004/02/skos/core#&gt; '
    ...: 'SELECT '
    ...: '?label '
    ...: 'WHERE { '
    ...: '{  ?concept  skos:altLabel ?label . } UNION {  ?concept  skos:prefLabel ?label . } '
    ...: 'FILTER regex(str(?label), &quot;^fish&quot;, &quot;i&quot;) . '
    ...: '} LIMIT 10')
In [13]: result = s.query(statement)
In [14]: for row in result.fetchone():
   ...:     print(row)
   ...:
(&lt;Literal &quot;fish catching&quot;@en&gt;,)
(&lt;Literal &quot;fish harvesting&quot;@en&gt;,)
(&lt;Literal &quot;fish meat&quot;@en&gt;,)
(&lt;Literal &quot;fish roe&quot;@en&gt;,)
(&lt;Literal &quot;fish conversion&quot;@en&gt;,)
(&lt;Literal &quot;fisheries catches (composition)&quot;@en&gt;,)
(&lt;Literal &quot;fishtail palm&quot;@en&gt;,)
(&lt;Literal &quot;fishflies&quot;@en&gt;,)
(&lt;Literal &quot;fishery biology&quot;@en&gt;,)
(&lt;Literal &quot;fish production&quot;@en&gt;,)
</code></pre>

<ul>
<li>The SPARQL query comes from my notes in <a href="/cgspace-notes/2017-08/">2017-08</a></li>
</ul>

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    <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>
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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>
      
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</html>
Add notes for 2019-01-02 2019-01-02 08:59:01 +01:00			`<!DOCTYPE html>`
			`<html lang="en">`

			`<head>`
			`<meta charset="utf-8">`
			`<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">`

			`<meta property="og:title" content="January, 2019" />`
			`<meta property="og:description" content="2019-01-02`


			`Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning`
			`I don’t see anything interesting in the web server logs around that time though:`


			`# 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`
			`92 40.77.167.4`
			`99 210.7.29.100`
			`120 38.126.157.45`
			`177 35.237.175.180`
			`177 40.77.167.32`
			`216 66.249.75.219`
			`225 18.203.76.93`
			`261 46.101.86.248`
			`357 207.46.13.1`
			`903 54.70.40.11`
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			`Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning`
			`I don’t see anything interesting in the web server logs around that time though:`


			`# 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`
			`92 40.77.167.4`
			`99 210.7.29.100`
			`120 38.126.157.45`
			`177 35.237.175.180`
			`177 40.77.167.32`
			`216 66.249.75.219`
			`225 18.203.76.93`
			`261 46.101.86.248`
			`357 207.46.13.1`
			`903 54.70.40.11`
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			`<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2019-01/">January, 2019</a></h2>`
			`<p class="blog-post-meta"><time datetime="2019-01-02T09:48:30+02:00">Wed Jan 02, 2019</time> by Alan Orth in`

			`<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>`

			`</p>`
			`</header>`
			`<h2 id="2019-01-02">2019-01-02</h2>`

			`<ul>`
			`<li>Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning</li>`
			`<li>I don’t see anything interesting in the web server logs around that time though:</li>`
			`</ul>`

			`<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`
			`92 40.77.167.4`
			`99 210.7.29.100`
			`120 38.126.157.45`
			`177 35.237.175.180`
			`177 40.77.167.32`
			`216 66.249.75.219`
			`225 18.203.76.93`
			`261 46.101.86.248`
			`357 207.46.13.1`
			`903 54.70.40.11`
			`</code></pre>`

			`<ul>`
			`<li>Analyzing the types of requests made by the top few IPs during that time:</li>`
			`</ul>`

			`<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`
			`30 bitstream`
			`534 discover`
			`352 handle`
			`# 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`
			`194 bitstream`
			`345 handle`
			`# 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`
			`261 handle`
			`</code></pre>`

			`<ul>`
			`<li>It’s not clear to me what was causing the outbound traffic spike</li>`
Update notes for 2019-01-02 2019-01-02 09:28:26 +01:00			`<li>Oh nice! The once-per-year cron job for rotating the Solr statistics actually worked now (for the first time ever!):</li>`
			`</ul>`

			`<pre><code>Moving: 81742 into core statistics-2010`
			`Moving: 1837285 into core statistics-2011`
			`Moving: 3764612 into core statistics-2012`
			`Moving: 4557946 into core statistics-2013`
			`Moving: 5483684 into core statistics-2014`
			`Moving: 2941736 into core statistics-2015`
			`Moving: 5926070 into core statistics-2016`
			`Moving: 10562554 into core statistics-2017`
			`Moving: 18497180 into core statistics-2018`
			`</code></pre>`

			`<ul>`
			`<li>This could by why the outbound traffic rate was high, due to the S3 backup that run at 3:30AM…</li>`
Update notes for 2019-01-02 2019-01-02 19:52:39 +01:00			`<li>Run all system updates on DSpace Test (linode19) and reboot the server</li>`
Add notes for 2019-01-02 2019-01-02 08:59:01 +01:00			`</ul>`

Add notes for 2019-01-03 2019-01-03 10:52:26 +01:00			`<h2 id="2019-01-03">2019-01-03</h2>`

			`<ul>`
			`<li>Update local Docker image for DSpace PostgreSQL, re-using the existing data volume:</li>`
			`</ul>`

			`<pre><code>$ sudo docker pull postgres:9.6-alpine`
			`$ sudo docker rm dspacedb`
			`$ 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`
			`</code></pre>`

Add notes for 2019-01-04 2019-01-04 19:38:11 +01:00			`<ul>`
			`<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`

			`<ul>`
			`<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>`
			`<li>If I log in again there the Listings and Reports work… hmm.</li>`
			`</ul></li>`
			`<li>The JSPUI application—which Listings and Reports depends upon—also does not load, though the error is perhaps unrelated:</li>`
			`</ul>`

			`<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:`
			`2019-01-03 14:45:21,971 INFO org.dspace.app.webui.discovery.DiscoverUtility @ facets for scope, null: 23`
			`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`
			`-- Method: GET`
			`-- Parameters were:`

			`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]`
			`at org.apache.jasper.compiler.DefaultErrorHandler.jspError(DefaultErrorHandler.java:41)`
			`at org.apache.jasper.compiler.ErrorDispatcher.dispatch(ErrorDispatcher.java:291)`
			`at org.apache.jasper.compiler.ErrorDispatcher.jspError(ErrorDispatcher.java:97)`
			`at org.apache.jasper.compiler.Parser.processIncludeDirective(Parser.java:347)`
			`at org.apache.jasper.compiler.Parser.parseIncludeDirective(Parser.java:380)`
			`at org.apache.jasper.compiler.Parser.parseDirective(Parser.java:481)`
			`at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1445)`
			`at org.apache.jasper.compiler.Parser.parseBody(Parser.java:1683)`
			`at org.apache.jasper.compiler.Parser.parseOptionalBody(Parser.java:1016)`
			`at org.apache.jasper.compiler.Parser.parseCustomTag(Parser.java:1291)`
			`at org.apache.jasper.compiler.Parser.parseElements(Parser.java:1470)`
			`at org.apache.jasper.compiler.Parser.parse(Parser.java:144)`
			`at org.apache.jasper.compiler.ParserController.doParse(ParserController.java:244)`
			`at org.apache.jasper.compiler.ParserController.parse(ParserController.java:105)`
			`at org.apache.jasper.compiler.Compiler.generateJava(Compiler.java:202)`
			`at org.apache.jasper.compiler.Compiler.compile(Compiler.java:373)`
			`at org.apache.jasper.compiler.Compiler.compile(Compiler.java:350)`
			`at org.apache.jasper.compiler.Compiler.compile(Compiler.java:334)`
			`at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:595)`
			`at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:399)`
			`at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)`
			`at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)`
			`at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)`
			`at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)`
			`at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)`
			`at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)`
			`at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)`
			`at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)`
			`at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:728)`
			`at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:470)`
			`at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:395)`
			`at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:316)`
			`at org.dspace.app.webui.util.JSPManager.showJSP(JSPManager.java:60)`
			`at org.apache.jsp.index_jsp._jspService(index_jsp.java:191)`
			`at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)`
			`at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)`
			`at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:476)`
			`at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)`
			`at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)`
			`at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)`
			`at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)`
			`at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)`
			`at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)`
			`at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)`
			`at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)`
			`at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)`
			`at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)`
			`at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)`
			`at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)`
			`at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)`
			`at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)`
			`at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)`
			`at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)`
			`at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:234)`
			`at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)`
			`at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)`
			`at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)`
			`at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)`
			`at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)`
			`at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)`
			`at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)`
			`at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)`
			`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)`
			`</code></pre>`

			`<ul>`
			`<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>`
			`<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…`

			`<ul>`
			`<li>I didn’t see that cookie being set on Tomcat 8.5.37</li>`
			`</ul></li>`
			`<li>I sent a message to the dspace-tech mailing list to ask</li>`
			`</ul>`

			`<h2 id="2019-01-04">2019-01-04</h2>`

			`<ul>`
			`<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>`
			`</ul>`

			`<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`
			`189 207.46.13.192`
			`217 31.6.77.23`
			`340 66.249.70.29`
			`349 40.77.167.86`
			`417 34.218.226.147`
			`630 207.46.13.173`
			`710 35.237.175.180`
			`790 40.77.167.87`
			`1776 66.249.70.27`
			`2099 54.70.40.11`
			`</code></pre>`

			`<ul>`
			`<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>`
			`<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>`
			`</ul>`

			`<pre><code>$ http http://agrovoc.uniroma2.it/agrovoc/rest/v1/search?query=SOIL&lang=en`
			`HTTP/1.1 200 OK`
			`Access-Control-Allow-Origin: *`
			`Connection: Keep-Alive`
			`Content-Length: 493`
			`Content-Type: application/json; charset=utf-8`
			`Date: Fri, 04 Jan 2019 13:44:27 GMT`
			`Keep-Alive: timeout=5, max=100`
			`Server: Apache`
			`Strict-Transport-Security: max-age=63072000; includeSubdomains`
			`Vary: Accept`
			`X-Content-Type-Options: nosniff`
			`X-Frame-Options: ALLOW-FROM http://aims.fao.org`

			`{`
			`"@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": [`
			`{`
			`"lang": "en",`
			`"prefLabel": "soil",`
			`"type": [`
			`"skos:Concept"`
			`],`
			`"uri": "http://aims.fao.org/aos/agrovoc/c_7156",`
			`"vocab": "agrovoc"`
			`}`
			`],`
			`"uri": ""`
			`}`
			`</code></pre>`

			`<ul>`
			`<li>The API does not appear to be case sensitive (searches for <code>SOIL</code> and <code>soil</code> return the same thing)</li>`
			`<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>`
			`</ul>`

			`<pre><code>HTTP/1.1 200 OK`
			`Access-Control-Allow-Origin: *`
			`Connection: Keep-Alive`
			`Content-Length: 367`
			`Content-Type: application/json; charset=utf-8`
			`Date: Fri, 04 Jan 2019 13:48:31 GMT`
			`Keep-Alive: timeout=5, max=100`
			`Server: Apache`
			`Strict-Transport-Security: max-age=63072000; includeSubdomains`
			`Vary: Accept`
			`X-Content-Type-Options: nosniff`
			`X-Frame-Options: ALLOW-FROM http://aims.fao.org`

			`{`
			`"@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>`

Add notes for 2019-01-02 2019-01-02 08:59:01 +01:00			`<!-- vim: set sw=2 ts=2: -->`





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			`<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>`

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			`<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>`

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