mirror of
https://github.com/alanorth/cgspace-notes.git
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357 lines
12 KiB
HTML
357 lines
12 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="November, 2017" />
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<meta property="og:description" content="2017-11-01
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The CORE developers responded to say they are looking into their bot not respecting our robots.txt
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2017-11-02
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Today there have been no hits by CORE and no alerts from Linode (coincidence?)
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# grep -c "CORE" /var/log/nginx/access.log
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0
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Generate list of authors on CGSpace for Peter to go through and correct:
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dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
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COPY 54701
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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/2017-11/" />
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<meta property="article:published_time" content="2017-11-02T09:37:54+02:00"/>
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<meta property="article:modified_time" content="2017-11-05T15:06:22+02:00"/>
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<meta name="twitter:card" content="summary"/><meta name="twitter:title" content="November, 2017"/>
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<meta name="twitter:description" content="2017-11-01
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The CORE developers responded to say they are looking into their bot not respecting our robots.txt
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2017-11-02
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Today there have been no hits by CORE and no alerts from Linode (coincidence?)
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# grep -c "CORE" /var/log/nginx/access.log
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0
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Generate list of authors on CGSpace for Peter to go through and correct:
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dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
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COPY 54701
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"/>
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<meta name="generator" content="Hugo 0.30.2" />
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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": "November, 2017",
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"url": "https://alanorth.github.io/cgspace-notes/2017-11/",
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"wordCount": "683",
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"datePublished": "2017-11-02T09:37:54+02:00",
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"dateModified": "2017-11-05T15:06:22+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/2017-11/">
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<title>November, 2017 | 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-O8wjsnz02XiyrPxnhfF6AVOv6YLBaEGRCnVF+DL3gCPBy9cieyHcpixIrVyD2JS5" 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/2017-11/">November, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-11-02T09:37:54+02:00">Thu Nov 02, 2017</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="2017-11-01">2017-11-01</h2>
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<ul>
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<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
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</ul>
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<h2 id="2017-11-02">2017-11-02</h2>
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<ul>
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<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
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</ul>
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<pre><code># grep -c "CORE" /var/log/nginx/access.log
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0
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</code></pre>
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<ul>
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<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
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</ul>
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<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
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COPY 54701
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</code></pre>
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<p></p>
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<ul>
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<li>Abenet asked if it would be possible to generate a report of items in Listing and Reports that had “International Fund for Agricultural Development” as the <em>only</em> investor</li>
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<li>I opened a ticket with Atmire to ask if this was possible: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=540">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=540</a></li>
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<li>Work on making the thumbnails in the item view clickable</li>
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<li>Basically, once you read the METS XML for an item it becomes easy to trace the structure to find the bitstream link</li>
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</ul>
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<pre><code>//mets:fileSec/mets:fileGrp[@USE='CONTENT']/mets:file/mets:FLocat[@LOCTYPE='URL']/@xlink:href
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</code></pre>
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<ul>
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<li>METS XML is available for all items with this pattern: /metadata/handle/10568/95947/mets.xml</li>
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<li>I whipped up a quick hack to print a clickable link with this URL on the thumbnail but it needs to check a few corner cases, like when there is a thumbnail but no content bitstream!</li>
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<li>Help proof fifty-three CIAT records for Sisay: <a href="https://dspacetest.cgiar.org/handle/10568/95895">https://dspacetest.cgiar.org/handle/10568/95895</a></li>
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<li>A handful of issues with <code>cg.place</code> using format like “Lima, PE” instead of “Lima, Peru”</li>
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<li>Also, some dates like with completely invalid format like “2010- 06” and “2011-3-28”</li>
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<li>I also collapsed some consecutive whitespace on a handful of fields</li>
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</ul>
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<h2 id="2017-11-03">2017-11-03</h2>
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<ul>
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<li>Atmire got back to us to say that they estimate it will take two days of labor to implement the change to Listings and Reports</li>
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<li>I said I’d ask Abenet if she wants that feature</li>
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</ul>
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<h2 id="2017-11-04">2017-11-04</h2>
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<ul>
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<li>I finished looking through Sisay’s CIAT records for the “Alianzas de Aprendizaje” data</li>
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<li>I corrected about half of the authors to standardize them</li>
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<li>Linode emailed this morning to say that the CPU usage was high again, this time at 6:14AM</li>
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<li>It’s the first time in a few days that this has happened</li>
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<li>I had a look to see what was going on, but it isn’t the CORE bot:</li>
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</ul>
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<pre><code># awk '{print $1}' /var/log/nginx/access.log | sort -n | uniq -c | sort -h | tail
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306 68.180.229.31
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323 61.148.244.116
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414 66.249.66.91
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507 40.77.167.16
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618 157.55.39.161
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652 207.46.13.103
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666 157.55.39.254
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1173 104.196.152.243
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1737 66.249.66.90
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23101 138.201.52.218
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</code></pre>
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<ul>
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<li>138.201.52.218 is from some Hetzner server, and I see it making 40,000 requests yesterday too, but none before that:</li>
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</ul>
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<pre><code># zgrep -c 138.201.52.218 /var/log/nginx/access.log*
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/var/log/nginx/access.log:24403
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/var/log/nginx/access.log.1:45958
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/var/log/nginx/access.log.2.gz:0
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/var/log/nginx/access.log.3.gz:0
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/var/log/nginx/access.log.4.gz:0
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/var/log/nginx/access.log.5.gz:0
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/var/log/nginx/access.log.6.gz:0
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</code></pre>
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<ul>
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<li>It’s clearly a bot as it’s making tens of thousands of requests, but it’s using a “normal” user agent:</li>
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</ul>
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<pre><code>Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2227.0 Safari/537.36
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</code></pre>
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<ul>
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<li>For now I don’t know what this user is!</li>
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</ul>
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<h2 id="2017-11-05">2017-11-05</h2>
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<ul>
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<li>Peter asked if I could fix the appearance of “International Livestock Research Institute” in the author lookup during item submission</li>
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<li>It looks to be just an issue with the user interface expecting authors to have both a first and last name:</li>
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</ul>
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<p><img src="/cgspace-notes/2017/11/author-lookup.png" alt="Author lookup" />
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<img src="/cgspace-notes/2017/11/add-author.png" alt="Add author" /></p>
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<ul>
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<li>But in the database the authors are correct (none with weird <code>, /</code> characters):</li>
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</ul>
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<pre><code>dspace=# select distinct text_value, authority, confidence from metadatavalue value where resource_type_id=2 and metadata_field_id=3 and text_value like 'International Livestock Research Institute%';
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text_value | authority | confidence
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--------------------------------------------+--------------------------------------+------------
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International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c | 0
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International Livestock Research Institute | f4db1627-47cd-4699-b394-bab7eba6dadc | 0
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International Livestock Research Institute | | -1
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International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c | 600
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International Livestock Research Institute | f4db1627-47cd-4699-b394-bab7eba6dadc | -1
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International Livestock Research Institute | | 600
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International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c | -1
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International Livestock Research Institute | 8f3865dc-d056-4aec-90b7-77f49ab4735c | 500
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(8 rows)
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</code></pre>
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<ul>
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<li>So I’m not sure if this is just a graphical glitch or if editors have to edit this metadata field prior to approval</li>
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<li>Looking at monitoring Tomcat’s JVM heap with Prometheus, it looks like we need to use JMX + <a href="https://github.com/prometheus/jmx_exporter">jmx_exporter</a></li>
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<li>This guide shows how to <a href="https://geekflare.com/enable-jmx-tomcat-to-monitor-administer/">enable JMX in Tomcat</a> by modifying <code>CATALINA_OPTS</code></li>
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<li>I was able to successfully connect to my local Tomcat with jconsole!</li>
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</ul>
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2017-11/">November, 2017</a></li>
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<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
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<li><a href="/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></li>
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<li><a href="/cgspace-notes/2017-09/">September, 2017</a></li>
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<li><a href="/cgspace-notes/2017-08/">August, 2017</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</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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</p>
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<p>
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<a href="#">Back to top</a>
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</p>
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</body>
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</html>
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