<!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="May, 2016" /> <meta property="og:description" content="2016-05-01 Since yesterday there have been 10,000 REST errors and the site has been unstable again I have blocked access to the API now There are 3,000 IPs accessing the REST API in a 24-hour period! # awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l 3168 " /> <meta property="og:type" content="article" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-05/" /> <meta property="article:published_time" content="2016-05-01T23:06:00+03:00" /> <meta property="article:modified_time" content="2020-04-13T15:30:24+03:00" /> <meta name="twitter:card" content="summary"/> <meta name="twitter:title" content="May, 2016"/> <meta name="twitter:description" content="2016-05-01 Since yesterday there have been 10,000 REST errors and the site has been unstable again I have blocked access to the API now There are 3,000 IPs accessing the REST API in a 24-hour period! # awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l 3168 "/> <meta name="generator" content="Hugo 0.92.0" /> <script type="application/ld+json"> { "@context": "http://schema.org", "@type": "BlogPosting", "headline": "May, 2016", "url": "https://alanorth.github.io/cgspace-notes/2016-05/", "wordCount": "1349", "datePublished": "2016-05-01T23:06:00+03:00", "dateModified": "2020-04-13T15:30:24+03:00", "author": { "@type": "Person", "name": "Alan Orth" }, "keywords": "Notes" } </script> <link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2016-05/"> <title>May, 2016 | CGSpace Notes</title> <!-- combined, minified CSS --> <link href="https://alanorth.github.io/cgspace-notes/css/style.beb8012edc08ba10be012f079d618dc243812267efe62e11f22fe49618f976a4.css" rel="stylesheet" integrity="sha256-vrgBLtwIuhC+AS8HnWGNwkOBImfv5i4R8i/klhj5dqQ=" crossorigin="anonymous"> <!-- minified Font Awesome for SVG icons --> <script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz+lcnA=" crossorigin="anonymous"></script> <!-- RSS 2.0 feed --> </head> <body> <div class="blog-masthead"> <div class="container"> <nav class="nav blog-nav"> <a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a> </nav> </div> </div> <header class="blog-header"> <div class="container"> <h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1> <p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p> </div> </header> <div class="container"> <div class="row"> <div class="col-sm-8 blog-main"> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-05/">May, 2016</a></h2> <p class="blog-post-meta"> <time datetime="2016-05-01T23:06:00+03:00">Sun May 01, 2016</time> in <span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a> </p> </header> <h2 id="2016-05-01">2016-05-01</h2> <ul> <li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li> <li>I have blocked access to the API now</li> <li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li> </ul> <pre tabindex="0"><code># awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l 3168 </code></pre><ul> <li>The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29</li> <li>100% of the requests coming from Ethiopia are like this and result in an HTTP 500:</li> </ul> <pre tabindex="0"><code>GET /rest/handle/10568/NaN?expand=parentCommunityList,metadata HTTP/1.1 </code></pre><ul> <li>For now I’ll block just the Ethiopian IP</li> <li>The owner of that application has said that the <code>NaN</code> (not a number) is an error in his code and he’ll fix it</li> </ul> <h2 id="2016-05-03">2016-05-03</h2> <ul> <li>Update nginx to 1.10.x branch on CGSpace</li> <li>Fix a reference to <code>dc.type.output</code> in Discovery that I had missed when we migrated to <code>dc.type</code> last month (<a href="https://github.com/ilri/DSpace/pull/223">#223</a>)</li> </ul> <p><img src="/cgspace-notes/2016/05/discovery-types.png" alt="Item type in Discovery results"></p> <h2 id="2016-05-06">2016-05-06</h2> <ul> <li>DSpace Test is down, <code>catalina.out</code> has lots of messages about heap space from some time yesterday (!)</li> <li>It looks like Sisay was doing some batch imports</li> <li>Hmm, also disk space is full</li> <li>I decided to blow away the solr indexes, since they are 50GB and we don’t really need all the Atmire stuff there right now</li> <li>I will re-generate the Discovery indexes after re-deploying</li> <li>Testing <code>renew-letsencrypt.sh</code> script for nginx</li> </ul> <pre tabindex="0"><code>#!/usr/bin/env bash readonly SERVICE_BIN=/usr/sbin/service readonly LETSENCRYPT_BIN=/opt/letsencrypt/letsencrypt-auto # stop nginx so LE can listen on port 443 $SERVICE_BIN nginx stop $LETSENCRYPT_BIN renew -nvv --standalone --standalone-supported-challenges tls-sni-01 > /var/log/letsencrypt/renew.log 2>&1 LE_RESULT=$? $SERVICE_BIN nginx start if [[ "$LE_RESULT" != 0 ]]; then echo 'Automated renewal failed:' cat /var/log/letsencrypt/renew.log exit 1 fi </code></pre><ul> <li>Seems to work well</li> </ul> <h2 id="2016-05-10">2016-05-10</h2> <ul> <li>Start looking at more metadata migrations</li> <li>There are lots of fields in <code>dcterms</code> namespace that look interesting, like: <ul> <li>dcterms.type</li> <li>dcterms.spatial</li> </ul> </li> <li>Not sure what <code>dcterms</code> is…</li> <li>Looks like these were <a href="https://wiki.lyrasis.org/display/DSDOC5x/Metadata+and+Bitstream+Format+Registries#MetadataandBitstreamFormatRegistries-DublinCoreTermsRegistry(DCTERMS)">added in DSpace 4</a> to allow for future work to make DSpace more flexible</li> <li>CGSpace’s <code>dc</code> registry has 96 items, and the default DSpace one has 73.</li> </ul> <h2 id="2016-05-11">2016-05-11</h2> <ul> <li> <p>Identify and propose the next phase of CGSpace fields to migrate:</p> <ul> <li>dc.title.jtitle → cg.title.journal</li> <li>dc.identifier.status → cg.identifier.status</li> <li>dc.river.basin → cg.river.basin</li> <li>dc.Species → cg.species</li> <li>dc.targetaudience → cg.targetaudience</li> <li>dc.fulltextstatus → cg.fulltextstatus</li> <li>dc.editon → cg.edition</li> <li>dc.isijournal → cg.isijournal</li> </ul> </li> <li> <p>Start a test rebase of the <code>5_x-prod</code> branch on top of the <code>dspace-5.5</code> tag</p> </li> <li> <p>There were a handful of conflicts that I didn’t understand</p> </li> <li> <p>After completing the rebase I tried to build with the module versions Atmire had indicated as being 5.5 ready but I got this error:</p> </li> </ul> <pre tabindex="0"><code>[ERROR] Failed to execute goal on project additions: Could not resolve dependencies for project org.dspace.modules:additions:jar:5.5: Could not find artifact com.atmire:atmire-metadata-quality-api:jar:5.5-2.10.1-0 in sonatype-releases (https://oss.sonatype.org/content/repositories/releases/) -> [Help 1] </code></pre><ul> <li>I’ve sent them a question about it</li> <li>A user mentioned having problems with uploading a 33 MB PDF</li> <li>I told her I would increase the limit temporarily tomorrow morning</li> <li>Turns out she was able to decrease the size of the PDF so we didn’t have to do anything</li> </ul> <h2 id="2016-05-12">2016-05-12</h2> <ul> <li>Looks like the issue that Abenet was having a few days ago with “Connection Reset” in Firefox might be due to a Firefox 46 issue: <a href="https://bugzilla.mozilla.org/show_bug.cgi?id=1268775">https://bugzilla.mozilla.org/show_bug.cgi?id=1268775</a></li> <li>I finally found a copy of the latest CG Core metadata guidelines and it looks like we can add a few more fields to our next migration: <ul> <li>dc.rplace.region → cg.coverage.region</li> <li>dc.cplace.country → cg.coverage.country</li> </ul> </li> <li>Questions for CG people: <ul> <li>Our <code>dc.place</code> and <code>dc.srplace.subregion</code> could both map to <code>cg.coverage.admin-unit</code>?</li> <li>Should we use <code>dc.contributor.crp</code> or <code>cg.contributor.crp</code> for the CRP (ours is <code>dc.crsubject.crpsubject</code>)?</li> <li>Our <code>dc.contributor.affiliation</code> and <code>dc.contributor.corporate</code> could both map to <code>dc.contributor</code> and possibly <code>dc.contributor.center</code> depending on if it’s a CG center or not</li> <li><code>dc.title.jtitle</code> could either map to <code>dc.publisher</code> or <code>dc.source</code> depending on how you read things</li> </ul> </li> <li>Found ~200 messed up CIAT values in <code>dc.publisher</code>:</li> </ul> <pre tabindex="0"><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to "% %"; </code></pre><h2 id="2016-05-13">2016-05-13</h2> <ul> <li>More theorizing about CGcore</li> <li>Add two new fields: <ul> <li>dc.srplace.subregion → cg.coverage.admin-unit</li> <li>dc.place → cg.place</li> </ul> </li> <li><code>dc.place</code> is our own field, so it’s easy to move</li> <li>I’ve removed <code>dc.title.jtitle</code> from the list for now because there’s no use moving it out of DC until we know where it will go (see discussion yesterday)</li> </ul> <h2 id="2016-05-18">2016-05-18</h2> <ul> <li>Work on 707 CCAFS records</li> <li>They have thumbnails on Flickr and elsewhere</li> <li>In OpenRefine I created a new <code>filename</code> column based on the <code>thumbnail</code> column with the following GREL:</li> </ul> <pre tabindex="0"><code>if(cells['thumbnails'].value.contains('hqdefault'), cells['thumbnails'].value.split('/')[-2] + '.jpg', cells['thumbnails'].value.split('/')[-1]) </code></pre><ul> <li>Because ~400 records had the same filename on Flickr (hqdefault.jpg) but different UUIDs in the URL</li> <li>So for the <code>hqdefault.jpg</code> ones I just take the UUID (-2) and use it as the filename</li> <li>Before importing with SAFBuilder I tested adding “__bundle:THUMBNAIL” to the <code>filename</code> column and it works fine</li> </ul> <h2 id="2016-05-19">2016-05-19</h2> <ul> <li>More quality control on <code>filename</code> field of CCAFS records to make processing in shell and SAFBuilder more reliable:</li> </ul> <pre tabindex="0"><code>value.replace('_','').replace('-','') </code></pre><ul> <li>We need to hold off on moving <code>dc.Species</code> to <code>cg.species</code> because it is only used for plants, and might be better to move it to something like <code>cg.species.plant</code></li> <li>And <code>dc.identifier.fund</code> is MOSTLY used for CPWF project identifier but has some other sponsorship things <ul> <li>We should move PN*, SG*, CBA, IA, and PHASE* values to <code>cg.identifier.cpwfproject</code></li> <li>The rest, like BMGF and USAID etc, might have to go to either <code>dc.description.sponsorship</code> or <code>cg.identifier.fund</code> (not sure yet)</li> <li>There are also some mistakes in CPWF’s things, like “PN 47”</li> <li>This ought to catch all the CPWF values (there don’t appear to be and SG* values):</li> </ul> </li> </ul> <pre tabindex="0"><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA'); </code></pre><h2 id="2016-05-20">2016-05-20</h2> <ul> <li>More work on CCAFS Video and Images records</li> <li>For SAFBuilder we need to modify filename column to have the thumbnail bundle:</li> </ul> <pre tabindex="0"><code>value + "__bundle:THUMBNAIL" </code></pre><ul> <li>Also, I fixed some weird characters using OpenRefine’s transform with the following GREL:</li> </ul> <pre tabindex="0"><code>value.replace(/\u0081/,'') </code></pre><ul> <li>Write shell script to resize thumbnails with height larger than 400: <a href="https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256">https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256</a></li> <li>Upload 707 CCAFS records to DSpace Test</li> <li>A few miscellaneous fixes for XMLUI display niggles (spaces in item lists and link target <code>_black</code>): <a href="https://github.com/ilri/DSpace/pull/224">#224</a></li> <li>Work on configuration changes for Phase 2 metadata migrations</li> </ul> <h2 id="2016-05-23">2016-05-23</h2> <ul> <li>Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine</li> <li>LibreOffice excludes empty cells when it exports and all the fields shift over to the left and cause URLs to go to Subjects, etc.</li> <li>Google Docs does this better, but somehow reorders the rows and when I paste the thumbnail/filename row in they don’t match!</li> <li>I will have to try later</li> </ul> <h2 id="2016-05-30">2016-05-30</h2> <ul> <li>Export CCAFS video and image records from DSpace Test using the migrate option (<code>-m</code>):</li> </ul> <pre tabindex="0"><code>$ mkdir ~/ccafs-images $ /home/dspacetest.cgiar.org/bin/dspace export -t COLLECTION -i 10568/79355 -d ~/ccafs-images -n 0 -m </code></pre><ul> <li>And then import to CGSpace:</li> </ul> <pre tabindex="0"><code>$ JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/70974 --source /tmp/ccafs-images --mapfile=/tmp/ccafs-images-may30.map &> /tmp/ccafs-images-may30.log </code></pre><ul> <li>But now we have double authors for “CGIAR Research Program on Climate Change, Agriculture and Food Security” in the authority</li> <li>I’m trying to do a Discovery index before messing with the authority index</li> <li>Looks like we are missing the <code>index-authority</code> cron job, so who knows what’s up with our authority index</li> <li>Run system updates on DSpace Test, re-deploy code, and reboot the server</li> <li>Clean up and import ~200 CTA records to CGSpace via CSV like:</li> </ul> <pre tabindex="0"><code>$ export JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" $ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA-May30/CTA-42229.csv &> ~/CTA-May30/CTA-42229.log </code></pre><ul> <li>Discovery indexing took a few hours for some reason, and after that I started the <code>index-authority</code> script</li> </ul> <pre tabindex="0"><code>$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace index-authority </code></pre><h2 id="2016-05-31">2016-05-31</h2> <ul> <li>The <code>index-authority</code> script ran over night and was finished in the morning</li> <li>Hopefully this was because we haven’t been running it regularly and it will speed up next time</li> <li>I am running it again with a timer to see:</li> </ul> <pre tabindex="0"><code>$ time /home/cgspace.cgiar.org/bin/dspace index-authority Retrieving all data Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer Cleaning the old index Writing new data All done ! real 37m26.538s user 2m24.627s sys 0m20.540s </code></pre><ul> <li>Update <code>tomcat7</code> crontab on CGSpace and DSpace Test to have the <code>index-authority</code> script that we were missing</li> <li>Add new ILRI subject and CCAFS project tags to <code>input-forms.xml</code> (<a href="https://github.com/ilri/DSpace/pull/226">#226</a>, <a href="https://github.com/ilri/DSpace/pull/225">#225</a>)</li> <li>Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.</li> <li>Re-sync DSpace Test data with CGSpace</li> <li>Clean up and import ~65 more CTA items into CGSpace</li> </ul> </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/2022-01/">January, 2022</a></li> <li><a href="/cgspace-notes/2021-12/">December, 2021</a></li> <li><a href="/cgspace-notes/2021-11/">November, 2021</a></li> <li><a href="/cgspace-notes/2021-10/">October, 2021</a></li> <li><a href="/cgspace-notes/2021-09/">September, 2021</a></li> </ol> </section> <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> </div> <!-- /.row --> </div> <!-- /.container --> <footer class="blog-footer"> <p dir="auto"> Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>. </p> <p> <a href="#">Back to top</a> </p> </footer> </body> </html>