mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-26 00:18:21 +01:00
539 lines
25 KiB
HTML
539 lines
25 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="March, 2020" />
|
|
<meta property="og:description" content="2020-03-02
|
|
|
|
Update dspace-statistics-api for DSpace 6+ UUIDs
|
|
|
|
Tag version 1.2.0 on GitHub
|
|
|
|
|
|
Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased SolrUpgradePre6xStatistics.java
|
|
|
|
You need to download this into the DSpace 6.x source and compile it
|
|
|
|
|
|
" />
|
|
<meta property="og:type" content="article" />
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-03/" />
|
|
<meta property="article:published_time" content="2020-03-02T12:31:30+02:00" />
|
|
<meta property="article:modified_time" content="2020-04-02T12:33:41+03:00" />
|
|
|
|
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="March, 2020"/>
|
|
<meta name="twitter:description" content="2020-03-02
|
|
|
|
Update dspace-statistics-api for DSpace 6+ UUIDs
|
|
|
|
Tag version 1.2.0 on GitHub
|
|
|
|
|
|
Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased SolrUpgradePre6xStatistics.java
|
|
|
|
You need to download this into the DSpace 6.x source and compile it
|
|
|
|
|
|
"/>
|
|
<meta name="generator" content="Hugo 0.125.7">
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "BlogPosting",
|
|
"headline": "March, 2020",
|
|
"url": "https://alanorth.github.io/cgspace-notes/2020-03/",
|
|
"wordCount": "2001",
|
|
"datePublished": "2020-03-02T12:31:30+02:00",
|
|
"dateModified": "2020-04-02T12:33:41+03:00",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"keywords": "Notes"
|
|
}
|
|
</script>
|
|
|
|
|
|
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2020-03/">
|
|
|
|
<title>March, 2020 | CGSpace Notes</title>
|
|
|
|
|
|
<!-- combined, minified CSS -->
|
|
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.c6ba80bc50669557645abe05f86b73cc5af84408ed20f1551a267bc19ece8228.css" rel="stylesheet" integrity="sha256-xrqAvFBmlVdkWr4F+GtzzFr4RAjtIPFVGiZ7wZ7Ogig=" 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/2020-03/">March, 2020</a></h2>
|
|
<p class="blog-post-meta">
|
|
<time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time>
|
|
in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2020-03-02">2020-03-02</h2>
|
|
<ul>
|
|
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
|
|
<ul>
|
|
<li>Tag version 1.2.0 on GitHub</li>
|
|
</ul>
|
|
</li>
|
|
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
|
|
<ul>
|
|
<li>You need to download this into the DSpace 6.x source and compile it</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ export JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8"
|
|
$ ~/dspace63/bin/dspace solr-upgrade-statistics-6x
|
|
</code></pre><h2 id="2020-03-03">2020-03-03</h2>
|
|
<ul>
|
|
<li>Skype with Peter and Abenet to discuss the CG Core survey
|
|
<ul>
|
|
<li>We also discussed some other CGSpace issues</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-03-04">2020-03-04</h2>
|
|
<ul>
|
|
<li>Abenet asked me to add some new ILRI subjects to CGSpace
|
|
<ul>
|
|
<li>I <a href="https://github.com/ilri/DSpace/commit/b51a242e773bd8658d3cab4ac883975708b00386">updated the input-forms.xml</a> in our <code>5_x-prod</code> branch on GitHub</li>
|
|
<li>Abenet said we are changing <code>HEALTH</code> to <code>HUMAN HEALTH</code> so I need to fix those using my <code>fix-metadata-values.py</code> script:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ ./fix-metadata-values.py -i 2020-03-04-fix-1-ilri-subject.csv -db dspace -u dspace -p 'fuuu' -f cg.subject.ilri -m 203 -t correct -d
|
|
</code></pre><ul>
|
|
<li>But I have not run it on CGSpace yet because we want to ask Peter if he is sure about it…</li>
|
|
<li>Send a message to Macaroni Bros to ask them about their Drupal module and its readiness for DSpace 6 UUIDs</li>
|
|
</ul>
|
|
<h2 id="2020-03-05">2020-03-05</h2>
|
|
<ul>
|
|
<li>I found a very <a href="https://lucene.apache.org/solr/guide/8_1/solr-system-requirements.html#lucene-solr-prior-to-7-0">interesting comment on the Solr 8.1 guide</a> about Java compatibility:</li>
|
|
</ul>
|
|
<blockquote>
|
|
<p>Lucene/Solr 7.0 was the first version that successfully passed our tests using Java 9 and higher. You should avoid Java 9 or later for Lucene/Solr 6.x or earlier.</p>
|
|
</blockquote>
|
|
<h2 id="2020-03-08">2020-03-08</h2>
|
|
<ul>
|
|
<li>I want to try to consolidate our yearly Solr statistics cores back into one <code>statistics</code> core using the solr-import-export-json tool</li>
|
|
<li>I will try it on DSpace test, doing one year at a time:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ ./run.sh -s http://localhost:8081/solr/statistics-2010 -a export -o /tmp/statistics-2010.json -k uid
|
|
$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o /tmp/statistics-2010.json -k uid
|
|
$ curl -s "http://localhost:8081/solr/statistics-2010/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>time:2010*</query></delete>"
|
|
$ ./run.sh -s http://localhost:8081/solr/statistics-2011 -a export -o /tmp/statistics-2011.json -k uid
|
|
$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o /tmp/statistics-2011.json -k uid
|
|
$ curl -s "http://localhost:8081/solr/statistics-2011/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>time:2011*</query></delete>"
|
|
$ ./run.sh -s http://localhost:8081/solr/statistics -a import -o /tmp/statistics-2012.json -k uid
|
|
$ curl -s 'http://localhost:8081/solr/statistics/select?q=time:2012*&rows=0&wt=json&indent=true' | grep numFound
|
|
"response":{"numFound":3761989,"start":0,"docs":[]
|
|
$ curl -s 'http://localhost:8081/solr/statistics-2012/select?q=time:2012*&rows=0&wt=json&indent=true' | grep numFound
|
|
"response":{"numFound":3761989,"start":0,"docs":[]
|
|
$ curl -s "http://localhost:8081/solr/statistics-2012/update?softCommit=true" -H "Content-Type: text/xml" --data-binary "<delete><query>time:2012*</query></delete>"
|
|
</code></pre><ul>
|
|
<li>I will do this for as many cores as I can (disk space limited) and then monitor the effect on the system and JVM memory usage
|
|
<ul>
|
|
<li>Exporting half years might work, using a filter query with months as a regular expression:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ ./run.sh -s http://localhost:8081/solr/statistics-2014 -a export -o /tmp/statistics-2014-1.json -k uid -f 'time:/2014-0[1-6].*/'
|
|
</code></pre><ul>
|
|
<li>Upgrade PostgreSQL from 9.6 to 10 on DSpace Test (linode19)
|
|
<ul>
|
|
<li>I’ve been running it for one month in my local environment, and others have reported on the dspace-tech mailing list that they are using 10 and 11</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre tabindex="0"><code># apt install postgresql-10 postgresql-contrib-10
|
|
# systemctl stop tomcat7
|
|
# pg_ctlcluster 9.6 main stop
|
|
# tar -cvzpf var-lib-postgresql-9.6.tar.gz /var/lib/postgresql/9.6
|
|
# tar -cvzpf etc-postgresql-9.6.tar.gz /etc/postgresql/9.6
|
|
# pg_ctlcluster 10 main stop
|
|
# pg_dropcluster 10 main
|
|
# pg_upgradecluster 9.6 main
|
|
# pg_dropcluster 9.6 main
|
|
# dpkg -l | grep postgresql | grep 9.6 | awk '{print $2}' | xargs dpkg -r
|
|
</code></pre><h2 id="2020-03-09">2020-03-09</h2>
|
|
<ul>
|
|
<li>Peter noticed that the Solr stats were not showing anything before 2020
|
|
<ul>
|
|
<li>I had to restart Tomcat three times before all cores loaded properly…</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-03-10">2020-03-10</h2>
|
|
<ul>
|
|
<li>Fix some logic issues in the nginx config
|
|
<ul>
|
|
<li>Use generic blocking of <code>[Bb]ot</code> and <code>[Cc]rawl</code> and <code>[Ss]pider</code> in the “badbots” rate limiting logic instead of trying to list them all one by one (bots should not be trying to index dynamic pages <em>no matter what</em> so we punish hard here)</li>
|
|
<li>We were not properly forwarding the remote IP address to Tomcat in all nginx location blocks, which led some locations to log a hit from 127.0.0.1 (because we need to explicitly add the global proxy params when setting other headers in location blocks)</li>
|
|
<li>Unfortunately this affected the REST API and there are a few hundred thousand requests from this user agent:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 (.NET CLR 3.5.30729)
|
|
</code></pre><ul>
|
|
<li>It seems to only be a problem in the last week:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code># zgrep -c 64.225.40.66 /var/log/nginx/rest.log.{1..9}
|
|
/var/log/nginx/rest.log.1:0
|
|
/var/log/nginx/rest.log.2:0
|
|
/var/log/nginx/rest.log.3:0
|
|
/var/log/nginx/rest.log.4:3625
|
|
/var/log/nginx/rest.log.5:27458
|
|
/var/log/nginx/rest.log.6:0
|
|
/var/log/nginx/rest.log.7:0
|
|
/var/log/nginx/rest.log.8:0
|
|
/var/log/nginx/rest.log.9:0
|
|
</code></pre><ul>
|
|
<li>In Solr the IP is 127.0.0.1, but in the nginx logs I can luckily see the real IP (64.225.40.66), which is on Digital Ocean</li>
|
|
<li>I will purge them from Solr statistics:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>userAgent:"Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2.13) Gecko/20101203 Firefox/3.6.13 (.NET CLR 3.5.30729)"</query></delete>'
|
|
</code></pre><ul>
|
|
<li>Another user agent that seems to be a bot is:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)
|
|
</code></pre><ul>
|
|
<li>In Solr the IP is 127.0.0.1 because of the misconfiguration, but in nginx’s logs I see it belongs to three IPs on Online.net in France:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code># zcat /var/log/nginx/access.log.*.gz /var/log/nginx/rest.log.*.gz | grep 'Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)' | awk '{print $1}' | sort | uniq -c
|
|
63090 163.172.68.99
|
|
183428 163.172.70.248
|
|
147608 163.172.71.24
|
|
</code></pre><ul>
|
|
<li>It is making 10,000 to 40,000 requests to XMLUI per day…</li>
|
|
</ul>
|
|
<pre tabindex="0"><code># zgrep -c 'Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)' /var/log/nginx/access.log.{1..9}
|
|
/var/log/nginx/access.log.30.gz:18687
|
|
/var/log/nginx/access.log.31.gz:28936
|
|
/var/log/nginx/access.log.32.gz:36402
|
|
/var/log/nginx/access.log.33.gz:38886
|
|
/var/log/nginx/access.log.34.gz:30607
|
|
/var/log/nginx/access.log.35.gz:19040
|
|
/var/log/nginx/access.log.36.gz:10780
|
|
/var/log/nginx/access.log.37.gz:5808
|
|
/var/log/nginx/access.log.38.gz:3100
|
|
/var/log/nginx/access.log.39.gz:1485
|
|
/var/log/nginx/access.log.3.gz:2898
|
|
/var/log/nginx/access.log.40.gz:373
|
|
/var/log/nginx/access.log.41.gz:3909
|
|
/var/log/nginx/access.log.42.gz:4729
|
|
/var/log/nginx/access.log.43.gz:3906
|
|
</code></pre><ul>
|
|
<li>I will purge those hits too!</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ curl -s "http://localhost:8081/solr/statistics/update?softCommit=true" -H "Content-Type: text/xml" --data-binary '<delete><query>userAgent:"Mozilla/5.0 ((Windows; U; Windows NT 6.1; fr; rv:1.9.2) Gecko/20100115 Firefox/3.6)"</query></delete>'
|
|
</code></pre><ul>
|
|
<li>Shit, and something happened and a few thousand hits from user agents with “Bot” in their user agent got through
|
|
<ul>
|
|
<li>I need to re-run the <code>check-bot-hits.sh</code> script with the standard COUNTER-Robots list again, but add my own versions of a few because the script/Solr doesn’t support case-insensitive regular expressions:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ ./check-spider-hits.sh -f /tmp/bots -d -p
|
|
(DEBUG) Using spiders pattern file: /tmp/bots
|
|
(DEBUG) Checking for hits from spider: Citoid
|
|
Purging 11 hits from Citoid in statistics
|
|
(DEBUG) Checking for hits from spider: ecointernet
|
|
Purging 375 hits from ecointernet in statistics
|
|
(DEBUG) Checking for hits from spider: ^Pattern\/[0-9]
|
|
Purging 1 hits from ^Pattern\/[0-9] in statistics
|
|
(DEBUG) Checking for hits from spider: sqlmap
|
|
(DEBUG) Checking for hits from spider: Typhoeus
|
|
Purging 6 hits from Typhoeus in statistics
|
|
(DEBUG) Checking for hits from spider: 7siters
|
|
(DEBUG) Checking for hits from spider: Apache-HttpClient
|
|
Purging 3178 hits from Apache-HttpClient in statistics
|
|
|
|
Total number of bot hits purged: 3571
|
|
|
|
$ ./check-spider-hits.sh -f /tmp/bots -d -p
|
|
(DEBUG) Using spiders pattern file: /tmp/bots
|
|
(DEBUG) Checking for hits from spider: [Bb]ot
|
|
Purging 8317 hits from [Bb]ot in statistics
|
|
(DEBUG) Checking for hits from spider: [Cc]rawl
|
|
Purging 1314 hits from [Cc]rawl in statistics
|
|
(DEBUG) Checking for hits from spider: [Ss]pider
|
|
Purging 62 hits from [Ss]pider in statistics
|
|
(DEBUG) Checking for hits from spider: Citoid
|
|
(DEBUG) Checking for hits from spider: ecointernet
|
|
(DEBUG) Checking for hits from spider: ^Pattern\/[0-9]
|
|
(DEBUG) Checking for hits from spider: sqlmap
|
|
(DEBUG) Checking for hits from spider: Typhoeus
|
|
(DEBUG) Checking for hits from spider: 7siters
|
|
(DEBUG) Checking for hits from spider: Apache-HttpClient
|
|
</code></pre><h2 id="2020-03-11">2020-03-11</h2>
|
|
<ul>
|
|
<li>Ask Michael Victor for permission to create a new Linode server for DSpace Test</li>
|
|
</ul>
|
|
<h2 id="2020-3-12">2020-3-12</h2>
|
|
<ul>
|
|
<li>I’m working on the 170 IITA records on <a href="https://dspacetest.cgiar.org/handle/10568/106567">DSpace Test</a> from January finally
|
|
<ul>
|
|
<li>It’s been two months since I last looked and I want to do a thorough check to make sure Bosede didn’t introduce any new issues, but I want to consolidate all the text languages for these records so it’s easier to check them in OpenRefine</li>
|
|
<li>First I got a list of IDs from <code>csvcut</code> and then I updated the text languages for only those records:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>dspace=# SELECT DISTINCT text_lang, COUNT(*) FROM metadatavalue WHERE resource_type_id=2 AND resource_id in (111295,111294,111293,111292,111291,111290,111288,111286,111285,111284,111283,111282,111281,111280,111279,111278,111277,111276,111275,111274,111273,111272,111271,111270,111269,111268,111267,111266,111265,111264,111263,111262,111261,111260,111259,111258,111257,111256,111255,111254,111253,111252,111251,111250,111249,111248,111247,111246,111245,111244,111243,111242,111241,111240,111238,111237,111236,111235,111234,111233,111232,111231,111230,111229,111228,111227,111226,111225,111224,111223,111222,111221,111220,111219,111218,111217,111216,111215,111214,111213,111212,111211,111209,111208,111207,111206,111205,111204,111203,111202,111201,111200,111199,111198,111197,111196,111195,111194,111193,111192,111191,111190,111189,111188,111187,111186,111185,111184,111183,111182,111181,111180,111179,111178,111177,111176,111175,111174,111173,111172,111171,111170,111169,111168,111299,111298,111297,111296,111167,111166,111165,111164,111163,111162,111161,111160,111159,111158,111157,111156,111155,111154,111153,111152,111151,111150,111149,111148,111147,111146,111145,111144,111143,111142,111141,111140,111139,111138,111137,111136,111135,111134,111133,111132,111131,111129,111128,111127,111126,111125) GROUP BY text_lang ORDER BY count;
|
|
</code></pre><ul>
|
|
<li>Then I exported the metadata from DSpace Test and imported it into OpenRefine
|
|
<ul>
|
|
<li>I corrected one invalid AGROVOC subject using my <code>csv-metadata-quality</code> script</li>
|
|
</ul>
|
|
</li>
|
|
<li>I exported a new list of affiliations from the database, added line numbers with <code>csvcut</code>, and then validated them in OpenRefine using <code>reconcile-csv</code>:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2020-03-12-affiliations.csv WITH CSV HEADER;`
|
|
dspace=# \q
|
|
$ csvcut -l -c 0 /tmp/2020-03-12-affiliations.csv | sed -e 's/^line_number/id/' -e 's/text_value/name/' > /tmp/affiliations.csv
|
|
$ lein run /tmp/affiliations.csv name id
|
|
</code></pre><ul>
|
|
<li>I always forget how to copy the reconciled values in OpenRefine, but you need to make a new column and populate it using this GREL: <code>if(cell.recon.matched, cell.recon.match.name, value)</code></li>
|
|
<li>I mapped all 170 items to their appropriate collections based on type and uploaded them to CGSpace</li>
|
|
</ul>
|
|
<h2 id="2020-03-16">2020-03-16</h2>
|
|
<ul>
|
|
<li>I’m looking at the CPU usage of CGSpace (linode18) over the past year and I see we <em>rarely</em> even go over two CPUs on average sustained usage:</li>
|
|
</ul>
|
|
<p><img src="/cgspace-notes/2020/03/cgspace-cpu-year.png" alt="linode18 CPU usage year"></p>
|
|
<ul>
|
|
<li>Also clearly visible is the effect of CPU steal in 2019-03</li>
|
|
</ul>
|
|
<p><img src="/cgspace-notes/2020/03/cgspace-memory-year.png" alt="linode18 RAM usage year"></p>
|
|
<p><img src="/cgspace-notes/2020/03/cgspace-heap-year.png" alt="linode18 JVM heap usage year"></p>
|
|
<ul>
|
|
<li>At max we have committed 10GB of RAM, the rest is used opportunistically by the filesystem cache, likely for Solr
|
|
<ul>
|
|
<li>There was a huge drop in 2019-07 when I changed the JVM settings</li>
|
|
<li>I think we should re-evaluate our deployment and perhaps target a different instance type and add block storage for assetstore (as we determined Linode’s block storage to be too slow for Solr)</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-03-17">2020-03-17</h2>
|
|
<ul>
|
|
<li>Update the PostgreSQL JDBC driver to version 42.2.11</li>
|
|
<li>Maria from Bioversity asked me to add a new field for the combined subjects of Bioversity and CIAT, since they merged recently
|
|
<ul>
|
|
<li>We will use <code>cg.subject.alliancebiovciat</code></li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-03-18">2020-03-18</h2>
|
|
<ul>
|
|
<li>Provision new Linode server (linode26) for DSpace Test to replace the current linode19 server</li>
|
|
<li>Improve DSpace role of <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a>
|
|
<ul>
|
|
<li>We should install npm packages in the DSpace user’s home directory instead of globally as root</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-03-19">2020-03-19</h2>
|
|
<ul>
|
|
<li>Finalized migration of DSpace Test to linode26 and removed linode19</li>
|
|
</ul>
|
|
<h2 id="2020-03-22">2020-03-22</h2>
|
|
<ul>
|
|
<li>Look over the AReS ToRs sent by Enrico and Moayad and add a few notes about missing GitHub issues
|
|
<ul>
|
|
<li>Hopefully now they can start working on the development!</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-03-24">2020-03-24</h2>
|
|
<ul>
|
|
<li>Skype meeting about CGSpace with Peter and Abenet</li>
|
|
</ul>
|
|
<h2 id="2020-03-25">2020-03-25</h2>
|
|
<ul>
|
|
<li>I sent Atmire a message to ask if they managed to start working on the DSpace 6 port, as the last communication was twenty-six days ago when they said they were going to secure technical resources to do so</li>
|
|
<li>Start adapting the <code>dspace</code> role in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> for DSpace 6 support</li>
|
|
</ul>
|
|
<h2 id="2020-03-26">2020-03-26</h2>
|
|
<ul>
|
|
<li>More work adapting the <code>dspace</code> role in our Ansible infrastructure scripts to DSpace 6</li>
|
|
<li>Update Tomcat to version 7.0.103 in the Ansible infrastrcutrue playbooks and deploy on DSpace Test (linode26)</li>
|
|
<li>Maria sent me a few new ORCID identifiers from Bioversity so I combined them with our existing ones, filtered the unique ones, and then resolved their names using my <code>resolve-orcids.py</code> script:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity-orcids | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2020-03-26-combined-orcids.txt
|
|
$ ./resolve-orcids.py -i /tmp/2020-03-26-combined-orcids.txt -o /tmp/2020-03-26-combined-names.txt -d
|
|
# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents)
|
|
$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
|
|
</code></pre><ul>
|
|
<li>I checked the database for likely matches to the author name and then created a CSV with the author names and ORCID iDs:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>dc.contributor.author,cg.creator.id
|
|
"King, Brian","Brian King: 0000-0002-7056-9214"
|
|
"Ortiz-Crespo, Berta","Berta Ortiz-Crespo: 0000-0002-6664-0815"
|
|
"Ekesa, Beatrice","Beatrice Ekesa: 0000-0002-2630-258X"
|
|
"Ekesa, B.","Beatrice Ekesa: 0000-0002-2630-258X"
|
|
"Ekesa, B.N.","Beatrice Ekesa: 0000-0002-2630-258X"
|
|
"Gullotta, G.","Gaia Gullotta: 0000-0002-2240-3869"
|
|
</code></pre><ul>
|
|
<li>Running the <code>add-orcid-identifiers-csv.py</code> script I added 32 ORCID iDs to items on CGSpace!</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ ./add-orcid-identifiers-csv.py -i /tmp/2020-03-26-ciat-orcids.csv -db dspace -u dspace -p 'fuuu'
|
|
</code></pre><ul>
|
|
<li>Udana from IWMI asked about some items that are missing Altmetric donuts on CGSpace
|
|
<ul>
|
|
<li><a href="https://hdl.handle.net/10568/103225">One of them</a> had a link to the paper on Nature, but was missing a DOI</li>
|
|
<li><a href="https://hdl.handle.net/10568/106899">The second item</a> had no donut so I <a href="https://twitter.com/mralanorth/status/1243158045540134913">tweeted its handle</a></li>
|
|
<li><a href="https://hdl.handle.net/10568/107258">The third item</a> also had no handle so I <a href="https://twitter.com/mralanorth/status/1243158786392625153">tweeted it</a> as well</li>
|
|
</ul>
|
|
</li>
|
|
<li>Abenet pointed out <a href="https://hdl.handle.net/10568/106573">one item</a> that she had tweeted last week that is missing a donut as well, so I <a href="https://twitter.com/mralanorth/status/1243163710241345536">tweeted it</a> too</li>
|
|
</ul>
|
|
<h2 id="2020-03-29">2020-03-29</h2>
|
|
<ul>
|
|
<li>Add two more Bioversity ORCID iDs to CGSpace and then tag ~70 of the authors’ existing publications in the database using this CSV with my <code>add-orcid-identifiers-csv.py</code> script:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>dc.contributor.author,cg.creator.id
|
|
"Snook, L.K.","Laura Snook: 0000-0002-9168-1301"
|
|
"Snook, L.","Laura Snook: 0000-0002-9168-1301"
|
|
"Zheng, S.J.","Sijun Zheng: 0000-0003-1550-3738"
|
|
"Zheng, S.","Sijun Zheng: 0000-0003-1550-3738"
|
|
</code></pre><ul>
|
|
<li>Deploy latest Bioversity and CIAT updates on CGSpace (linode18) and DSpace Test (linode26)</li>
|
|
<li>Deploy latest Ansible infrastructure playbooks on CGSpace and DSpace Test to get the latest dspace-statistics-api (v1.1.1) and Tomcat (7.0.103) versions</li>
|
|
<li>Run system updates on CGSpace and DSpace Test and reboot them
|
|
<ul>
|
|
<li>After reboot all the Solr statistics cores came back up on the first time on both servers (yay)</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<!-- raw HTML omitted -->
|
|
|
|
|
|
|
|
|
|
|
|
</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/2024-05/">May, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-04/">April, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-02/">February, 2024</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2024-01/">January, 2024</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>
|