mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-14 02:47:05 +01:00
426 lines
18 KiB
HTML
426 lines
18 KiB
HTML
<!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 0.82.0" />
|
|
|
|
|
|
|
|
<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.ffbfea088a9a1666ec65c3a8cb4906e2a0e4f92dc70dbbf400a125ad2422123a.js" integrity="sha256-/7/qCIqaFmbsZcOoy0kG4qDk+S3HDbv0AKElrSQiEjo=" 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><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><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><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><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><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><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><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><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><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><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><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><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><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><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><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/2021-03/">March, 2021</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2021-02/">February, 2021</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2021-01/">January, 2021</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2020-12/">December, 2020</a></li>
|
|
|
|
<li><a href="/cgspace-notes/cgspace-dspace6-upgrade/">CGSpace DSpace 6 Upgrade</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>
|