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HTML
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<meta property="og:title" content="October, 2021" />
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<meta property="og:description" content="2021-10-01
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Export all affiliations on CGSpace and run them against the latest RoR data dump:
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localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-10-01-affiliations.csv WITH CSV HEADER;
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$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d > /tmp/2021-10-01-affiliations.txt
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$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
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ations-matching.csv
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$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
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1879
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$ wc -l /tmp/2021-10-01-affiliations.txt
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7100 /tmp/2021-10-01-affiliations.txt
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So we have 1879/7100 (26.46%) matching already
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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/2021-10/" />
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<meta property="article:published_time" content="2021-10-01T11:14:07+03:00" />
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<meta property="article:modified_time" content="2021-10-11T20:06:42+03:00" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="October, 2021"/>
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<meta name="twitter:description" content="2021-10-01
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Export all affiliations on CGSpace and run them against the latest RoR data dump:
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localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-10-01-affiliations.csv WITH CSV HEADER;
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$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d > /tmp/2021-10-01-affiliations.txt
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$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
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ations-matching.csv
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$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
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1879
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$ wc -l /tmp/2021-10-01-affiliations.txt
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7100 /tmp/2021-10-01-affiliations.txt
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So we have 1879/7100 (26.46%) matching already
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"/>
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<meta name="generator" content="Hugo 0.88.1" />
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"headline": "October, 2021",
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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<header class="blog-header">
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<div class="container">
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2021-10/">October, 2021</a></h2>
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<p class="blog-post-meta">
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<time datetime="2021-10-01T11:14:07+03:00">Fri Oct 01, 2021</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2021-10-01">2021-10-01</h2>
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<ul>
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<li>Export all affiliations on CGSpace and run them against the latest RoR data dump:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= > \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2021-10-01-affiliations.csv WITH CSV HEADER;
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$ csvcut -c 1 /tmp/2021-10-01-affiliations.csv | sed 1d > /tmp/2021-10-01-affiliations.txt
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$ ./ilri/ror-lookup.py -i /tmp/2021-10-01-affiliations.txt -r 2021-09-23-ror-data.json -o /tmp/2021-10-01-affili
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ations-matching.csv
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$ csvgrep -c matched -m true /tmp/2021-10-01-affiliations-matching.csv | sed 1d | wc -l
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1879
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$ wc -l /tmp/2021-10-01-affiliations.txt
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7100 /tmp/2021-10-01-affiliations.txt
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</code></pre><ul>
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<li>So we have 1879/7100 (26.46%) matching already</li>
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</ul>
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<h2 id="2021-10-03">2021-10-03</h2>
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<ul>
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<li>Dominique from IWMI asked me for information about how CGSpace partners are using CGSpace APIs to feed their websites</li>
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<li>Start a fresh indexing on AReS</li>
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<li>Udana sent me his file of 292 non-IWMI publications for the Virtual library on water management
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<ul>
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<li>He added licenses</li>
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<li>I want to clean up the <code>dcterms.extent</code> field though because it has volume, issue, and pages there</li>
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<li>I cloned the column several times and extracted values based on their positions, for example:
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<ul>
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<li>Volume: <code>value.partition(":")[0]</code></li>
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<li>Issue: <code>value.partition("(")[2].partition(")")[0]</code></li>
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<li>Page: <code>"p. " + value.replace(".", "")</code></li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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<h2 id="2021-10-04">2021-10-04</h2>
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<ul>
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<li>Start looking at the last month of Solr statistics on CGSpace
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<ul>
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<li>I see a number of IPs with “normal” user agents who clearly behave like bots
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<ul>
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<li>198.15.130.18: 21,000 requests to /discover with a normal-looking user agent, from ASN 11282 (SERVERYOU, US)</li>
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<li>93.158.90.107: 8,500 requests to handle and browse links with a Firefox 84.0 user agent, from ASN 12552 (IPO-EU, SE)</li>
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<li>193.235.141.162: 4,800 requests to handle, browse, and discovery links with a Firefox 84.0 user agent, from ASN 51747 (INTERNETBOLAGET, SE)</li>
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<li>3.225.28.105: 2,900 requests to REST API for the CIAT Story Maps collection with a normal user agent, from ASN 14618 (AMAZON-AES, US)</li>
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<li>34.228.236.6: 2,800 requests to discovery for the CGIAR System community with user agent <code>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</code>, from ASN 14618 (AMAZON-AES, US)</li>
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<li>18.212.137.2: 2,800 requests to discovery for the CGIAR System community with user agent <code>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</code>, from ASN 14618 (AMAZON-AES, US)</li>
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<li>3.81.123.72: 2,800 requests to discovery and handles for the CGIAR System community with user agent <code>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</code>, from ASN 14618 (AMAZON-AES, US)</li>
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<li>3.227.16.188: 2,800 requests to discovery and handles for the CGIAR System community with user agent <code>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</code>, from ASN 14618 (AMAZON-AES, US)</li>
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</ul>
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</li>
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<li>Looking closer into the requests with this Mozilla/4.0 user agent, I see 500+ IPs using it:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console"># zcat --force /var/log/nginx/*.log* | grep 'Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)' | awk '{print $1}' | sort | uniq > /tmp/mozilla-4.0-ips.txt
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# wc -l /tmp/mozilla-4.0-ips.txt
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543 /tmp/mozilla-4.0-ips.txt
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</code></pre><ul>
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<li>Then I resolved the IPs and extracted the ones belonging to Amazon:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ ./ilri/resolve-addresses-geoip2.py -i /tmp/mozilla-4.0-ips.txt -k "$ABUSEIPDB_API_KEY" -o /tmp/mozilla-4.0-ips.csv
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$ csvgrep -c asn -m 14618 /tmp/mozilla-4.0-ips.csv | csvcut -c ip | sed 1d | tee /tmp/amazon-ips.txt | wc -l
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</code></pre><ul>
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<li>I am thinking I will purge them all, as I have several indicators that they are bots: mysterious user agent, IP owned by Amazon</li>
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<li>Even more interesting, these requests are weighted VERY heavily on the CGIAR System community:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console"> 1592 GET /handle/10947/2526
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1592 GET /handle/10947/2527
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1592 GET /handle/10947/34
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1593 GET /handle/10947/6
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1594 GET /handle/10947/1
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1598 GET /handle/10947/2515
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1598 GET /handle/10947/2516
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1599 GET /handle/10568/101335
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1599 GET /handle/10568/91688
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1599 GET /handle/10947/2517
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1599 GET /handle/10947/2518
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1599 GET /handle/10947/2519
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1599 GET /handle/10947/2708
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1599 GET /handle/10947/2871
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1600 GET /handle/10568/89342
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1600 GET /handle/10947/4467
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1607 GET /handle/10568/103816
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290382 GET /handle/10568/83389
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</code></pre><ul>
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<li>Before I purge all those I will ask someone Samuel Stacey from the System Office to hopefully get an insight…</li>
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<li>Meeting with Michael Victor, Peter, Jane, and Abenet about the future of repositories in the One CGIAR</li>
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<li>Meeting with Michelle from Altmetric about their new CSV upload system
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<ul>
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<li>I sent her some examples of Handles that have DOIs, but no linked score (yet) to see if an association will be created when she uploads them</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code class="language-csv" data-lang="csv">doi,handle
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10.1016/j.agsy.2021.103263,10568/115288
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10.3389/fgene.2021.723360,10568/115287
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10.3389/fpls.2021.720670,10568/115285
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</code></pre><ul>
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<li>Extract the AGROVOC subjects from IWMI’s 292 publications to validate them against AGROVOC:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ csvcut -c 'dcterms.subject[en_US]' ~/Downloads/2021-10-03-non-IWMI-publications.csv | sed -e 1d -e 's/||/\n/g' -e 's/"//g' | sort -u > /tmp/agrovoc.txt
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$ ./ilri/agrovoc-lookup.py -i /tmp/agrovoc-sorted.txt -o /tmp/agrovoc-matches.csv
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$ csvgrep -c 'number of matches' -m '0' /tmp/agrovoc-matches.csv | csvcut -c 1 > /tmp/invalid-agrovoc.csv
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</code></pre><h2 id="2021-10-05">2021-10-05</h2>
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<ul>
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<li>Sam put me in touch with Dodi from the System Office web team and he confirmed that the Amazon requests are not theirs
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<ul>
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<li>I added <code>Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)</code> to the list of bad bots in nginx</li>
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<li>I purged all the Amazon IPs using this user agent, as well as the few other IPs I identified yesterday</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ ./ilri/check-spider-ip-hits.sh -f /tmp/robot-ips.txt -p
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...
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Total number of bot hits purged: 465119
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</code></pre><h2 id="2021-10-06">2021-10-06</h2>
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<ul>
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<li>Thinking about how we could check for duplicates before importing
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<ul>
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<li>I found out that <a href="https://www.freecodecamp.org/news/fuzzy-string-matching-with-postgresql/">PostgreSQL has a built-in similarity function</a>:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace63= > CREATE EXTENSION pg_trgm;
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localhost/dspace63= > SELECT metadata_value_id, text_value, dspace_object_id FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=64 AND SIMILARITY(text_value,'Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines') > 0.5;
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metadata_value_id │ text_value │ dspace_object_id
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───────────────────┼────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
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3652624 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ b7f0bf12-b183-4b2f-bbd2-7a5697b0c467
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3677663 │ Molecular marker based genetic diversity assessment of Striga resistant maize inbred lines │ fb62f551-f4a5-4407-8cdc-6bff6dac399e
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(2 rows)
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</code></pre><ul>
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<li>I was able to find an exact duplicate for an IITA item by searching for its title (I already knew that these existed)</li>
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<li>I started working on a basic Python script to do this and managed to find an actual duplicate in the recent IWMI items
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<ul>
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<li>I think I will check for similar titles, and if I find them I will print out the handles for verification</li>
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<li>I could also proceed to check other metadata like type because those shouldn’t vary too much</li>
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</ul>
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</li>
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<li>I ran my new <code>check-duplicates.py</code> script on the 292 non-IWMI publications from Udana and found twelve potential duplicates
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<ul>
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<li>Upon checking them manually, I found that 7/12 were indeed already present on CGSpace!</li>
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<li>This is with the similarity threshold at 0.5. I wonder if tweaking that higher will make the script run faster and eliminate some false positives</li>
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<li>I re-ran it with higher thresholds this eliminated all false positives, but it still took 24 minutes to run for 292 items!
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<ul>
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<li>0.6: ./ilri/check-duplicates.py -i ~/Downloads/2021-10-03-non-IWMI-publications.cs 0.09s user 0.03s system 0% cpu 24:40.42 total</li>
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<li>0.7: ./ilri/check-duplicates.py -i ~/Downloads/2021-10-03-non-IWMI-publications.cs 0.12s user 0.03s system 0% cpu 24:29.15 total</li>
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<li>0.8: ./ilri/check-duplicates.py -i ~/Downloads/2021-10-03-non-IWMI-publications.cs 0.09s user 0.03s system 0% cpu 25:44.13 total</li>
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</ul>
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</li>
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</ul>
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</li>
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<li>Some minor updates to csv-metadata-quality
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<ul>
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<li>Fix two issues with regular expressions in the duplicate items and experimental language checks</li>
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<li>Add a check for items that have a DOI listed in their citation, but are missing a standalone DOI field</li>
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</ul>
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</li>
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<li>Then I ran this new version of csv-metadata-quality on an export of IWMI’s community, minus some fields I don’t want to check:</li>
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</ul>
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<pre tabindex="0"><code class="language-console" data-lang="console">$ csvcut -C 'dc.date.accessioned,dc.date.accessioned[],dc.date.accessioned[en_US],dc.date.available,dc.date.available[],dc.date.available[en_US],dcterms.issued[en_US],dcterms.issued[],dcterms.issued,dc.description.provenance[en],dc.description.provenance[en_US],dc.identifier.uri,dc.identifier.uri[],dc.identifier.uri[en_US],dcterms.abstract[en_US],dcterms.bibliographicCitation[en_US],collection' ~/Downloads/iwmi.csv > /tmp/iwmi-to-check.csv
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$ csv-metadata-quality -i /tmp/iwmi-to-check.csv -o /tmp/iwmi.csv | tee /tmp/out.log
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$ xsv split -s 2000 /tmp /tmp/iwmi.csv
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</code></pre><ul>
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<li>I noticed each CSV only had 10 or 20 corrections, mostly that none of the duplicate metadata values were removed in the CSVs…
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<ul>
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<li>I cut a subset of the fields from the main CSV and tried again, but DSpace said “no changes detected”</li>
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<li>The duplicates are definitely removed from the CSV, but DSpace doesn’t detect them</li>
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<li>I realized this is an issue I’ve had before, but forgot because I usually use csv-metadata-quality for new items, not ones already inside DSpace!</li>
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<li>I found a comment on thread on the dspace-tech mailing list from helix84 in 2015 (“No changes were detected” when importing metadata via XMLUI") where he says:</li>
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</ul>
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</li>
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</ul>
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<blockquote>
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<p>It’s very likely that multiple values in a single field are being compared as an unordered set rather than an ordered list.
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Try doing it in two imports. In first import, remove all authors. In second import, add them in the new order.</p>
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</blockquote>
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<ul>
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<li>Shit, so that’s worth looking into…</li>
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</ul>
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<h2 id="2021-10-07">2021-10-07</h2>
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<ul>
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<li>I decided to upload the cleaned IWMI community by moving the cleaned metadata field from <code>dcterms.subject[en_US]</code> to <code>dcterms.subject[en_Fu]</code> temporarily, uploading them, then moving them back, and uploading again
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<ul>
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<li>I started by copying just a handful of fields from the iwmi.csv community export:</li>
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</ul>
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</li>
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</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ csvcut -c 'id,cg.contributor.affiliation[en_US],cg.coverage.country[en_US],cg.coverage.iso3166-alpha2[en_US],cg.coverage.subregion[en_US],cg.identifier.doi[en_US],cg.identifier.iwmilibrary[en_US],cg.identifier.url[en_US],cg.isijournal[en_US],cg.issn[en_US],cg.river.basin[en_US],dc.contributor.author[en_US],dcterms.subject[en_US]' ~/Downloads/iwmi.csv > /tmp/iwmi-duplicate-metadata.csv
|
||
# Copy and blank columns in OpenRefine
|
||
$ csv-metadata-quality -i ~/Downloads/2021-10-07-IWMI-duplicate-metadata-csv.csv -o /tmp/iwmi-duplicates-cleaned.csv | tee /tmp/out.log
|
||
$ xsv split -s 2000 /tmp /tmp/iwmi-duplicates-cleaned.csv
|
||
</code></pre><ul>
|
||
<li>It takes a few hours per 2,000 items because DSpace processes them so slowly… sigh…</li>
|
||
</ul>
|
||
<h2 id="2021-10-08">2021-10-08</h2>
|
||
<ul>
|
||
<li>I decided to update these records in PostgreSQL instead of via several CSV batches, as there were several others to normalize too:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">cgspace=# SELECT DISTINCT text_lang, count(text_lang) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) GROUP BY text_lang ORDER BY count DESC;
|
||
text_lang | count
|
||
-----------+---------
|
||
en_US | 2603711
|
||
en_Fu | 115568
|
||
en | 8818
|
||
| 5286
|
||
fr | 2
|
||
vn | 2
|
||
| 0
|
||
(7 rows)
|
||
cgspace=# BEGIN;
|
||
cgspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN ('en_Fu', 'en', '');
|
||
UPDATE 129673
|
||
cgspace=# COMMIT;
|
||
</code></pre><ul>
|
||
<li>So all this effort to remove ~400 duplicate metadata values in the IWMI community hmmm:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ grep -c 'Removing duplicate value' /tmp/out.log
|
||
391
|
||
</code></pre><ul>
|
||
<li>I tried to export ILRI’s community, but ran into the export bug (DS-4211)
|
||
<ul>
|
||
<li>After applying the patch on my local instance I was able to export, but found many duplicate items in the CSV (as I also noticed in 2021-02):</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ csvcut -c id /tmp/ilri-duplicate-metadata.csv | sed '1d' | wc -l
|
||
32070
|
||
$ csvcut -c id /tmp/ilri-duplicate-metadata.csv | sort -u | sed '1d' | wc -l
|
||
19315
|
||
</code></pre><ul>
|
||
<li>It seems there are only about 200 duplicate values in this subset of fields in ILRI’s community:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ grep -c 'Removing duplicate value' /tmp/out.log
|
||
220
|
||
</code></pre><ul>
|
||
<li>I found a cool way to select only the items with corrections
|
||
<ul>
|
||
<li>First, extract a handful of fields from the CSV with csvcut</li>
|
||
<li>Second, clean the CSV with csv-metadata-quality</li>
|
||
<li>Third, rename the columns to something obvious in the cleaned CSV</li>
|
||
<li>Fourth, use csvjoin to merge the cleaned file with the original</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ csvcut -c 'id,cg.contributor.affiliation[en_US],cg.coverage.country[en_US],cg.coverage.iso3166-alpha2[en_US],cg.coverage.subregion[en_US],cg.identifier.doi[en_US],cg.identifier.url[en_US],cg.isijournal[en_US],cg.issn[en_US],dc.contributor.author[en_US],dcterms.subject[en_US]' /tmp/ilri.csv | csvsort | uniq > /tmp/ilri-deduplicated-items.csv
|
||
$ csv-metadata-quality -i /tmp/ilri-deduplicated-items.csv -o /tmp/ilri-deduplicated-items-cleaned.csv | tee /tmp/out.log
|
||
$ sed -i -e '1s/en_US/en_Fu/g' /tmp/ilri-deduplicated-items-cleaned.csv
|
||
$ csvjoin -c id /tmp/ilri-deduplicated-items.csv /tmp/ilri-deduplicated-items-cleaned.csv > /tmp/ilri-deduplicated-items-cleaned-joined.csv
|
||
</code></pre><ul>
|
||
<li>Then I imported the file into OpenRefine and used a custom text facet with a GREL like this to identify the rows with changes:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>if(cells['dcterms.subject[en_US]'].value == cells['dcterms.subject[en_Fu]'].value,"same","different")
|
||
</code></pre><ul>
|
||
<li>For these rows I starred them and then blanked out the original field so DSpace would see it as a removal, and add the new column
|
||
<ul>
|
||
<li>After these are uploaded I will normalize the <code>text_lang</code> fields in PostgreSQL again</li>
|
||
</ul>
|
||
</li>
|
||
<li>I did the same for CIAT but there were over 7,000 duplicate metadata values! Hard to believe:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ grep -c 'Removing duplicate value' /tmp/out.log
|
||
7720
|
||
</code></pre><ul>
|
||
<li>I applied these to the CIAT community, so in total that’s over 8,000 duplicate metadata values removed in a handful of fields…</li>
|
||
</ul>
|
||
<h2 id="2021-10-09">2021-10-09</h2>
|
||
<ul>
|
||
<li>I did similar metadata cleanups for CCAFS and IITA too, but there were only a few hundred duplicates there</li>
|
||
<li>Also of note, there are some other fixes too, for example in IITA’s community:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ grep -c -E '(Fixing|Removing) (duplicate|excessive|invalid)' /tmp/out.log
|
||
249
|
||
</code></pre><ul>
|
||
<li>I ran a full Discovery re-indexing on CGSpace</li>
|
||
<li>Then I exported all of CGSpace and extracted the ISSNs and ISBNs:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ csvcut -c 'id,cg.issn[en_US],dc.identifier.issn[en_US],cg.isbn[en_US],dc.identifier.isbn[en_US]' /tmp/cgspace.csv > /tmp/cgspace-issn-isbn.csv
|
||
</code></pre><ul>
|
||
<li>I did cleanups on about seventy items with invalid and mixed ISSNs/ISBNs</li>
|
||
</ul>
|
||
<h2 id="2021-10-10">2021-10-10</h2>
|
||
<ul>
|
||
<li>Start testing DSpace 7.1-SNAPSHOT to see if it has the duplicate item bug on <code>metadata-export</code> (DS-4211)</li>
|
||
<li>First create a new PostgreSQL 13 container:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ podman run --name dspacedb13 -v dspacedb13_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5433:5432 -d postgres:13-alpine
|
||
$ createuser -h localhost -p 5433 -U postgres --pwprompt dspacetest
|
||
$ createdb -h localhost -p 5433 -U postgres -O dspacetest --encoding=UNICODE dspace7
|
||
$ psql -h localhost -p 5433 -U postgres dspace7 -c 'CREATE EXTENSION pgcrypto;'
|
||
</code></pre><ul>
|
||
<li>Then edit setting in <code>dspace/config/local.cfg</code> and build the backend server with Java 11:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ mvn package
|
||
$ cd dspace/target/dspace-installer
|
||
$ ant fresh_install
|
||
# fix database not being fully ready, causing Tomcat to fail to start the server application
|
||
$ ~/dspace7/bin/dspace database migrate
|
||
</code></pre><ul>
|
||
<li>Copy Solr configs and start Solr:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ cp -Rv ~/dspace7/solr/* ~/src/solr-8.8.2/server/solr/configsets
|
||
$ ~/src/solr-8.8.2/bin/solr start
|
||
</code></pre><ul>
|
||
<li>Start my local Tomcat 9 instance:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ systemctl --user start tomcat9@dspace7
|
||
</code></pre><ul>
|
||
<li>This works, so now I will drop the default database and import a dump from CGSpace</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ systemctl --user stop tomcat9@dspace7
|
||
$ dropdb -h localhost -p 5433 -U postgres dspace7
|
||
$ createdb -h localhost -p 5433 -U postgres -O dspacetest --encoding=UNICODE dspace7
|
||
$ psql -h localhost -p 5433 -U postgres -c 'alter user dspacetest superuser;'
|
||
$ pg_restore -h localhost -p 5433 -U postgres -d dspace7 -O --role=dspacetest -h localhost dspace-2021-10-09.backup
|
||
$ psql -h localhost -p 5433 -U postgres -c 'alter user dspacetest nosuperuser;'
|
||
</code></pre><ul>
|
||
<li>Delete Atmire migrations and some others that were “unresolved”:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ psql -h localhost -p 5433 -U postgres dspace7 -c "DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%';"
|
||
$ psql -h localhost -p 5433 -U postgres dspace7 -c "DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');"
|
||
</code></pre><ul>
|
||
<li>Now DSpace 7 starts with my CGSpace data… nice
|
||
<ul>
|
||
<li>The Discovery indexing still takes seven hours… fuck</li>
|
||
</ul>
|
||
</li>
|
||
<li>I tested the <code>metadata-export</code> on DSpace 7.1-SNAPSHOT and it still has the duplicate items issue introduced by DS-4211
|
||
<ul>
|
||
<li>I filed a GitHub issue and notified nwoodward: <a href="https://github.com/DSpace/DSpace/issues/7988">https://github.com/DSpace/DSpace/issues/7988</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>Start a full reindex on AReS</li>
|
||
</ul>
|
||
<h2 id="2021-10-11">2021-10-11</h2>
|
||
<ul>
|
||
<li>Start a full Discovery reindex on my local DSpace 6.3 instance:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ /usr/bin/time -f %M:%e chrt -b 0 ~/dspace63/bin/dspace index-discovery -b
|
||
Loading @mire database changes for module MQM
|
||
Changes have been processed
|
||
836140:6543.6
|
||
</code></pre><ul>
|
||
<li>So that’s 1.8 hours versus 7 on DSpace 7, with the same database!</li>
|
||
<li>Several users wrote to me that CGSpace was slow recently
|
||
<ul>
|
||
<li>Looking at the PostgreSQL database I see connections look normal, but locks for <code>dspaceWeb</code> are high:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">$ psql -c 'SELECT * FROM pg_stat_activity' | wc -l
|
||
53
|
||
$ psql -c "SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" | wc -l
|
||
1697
|
||
$ psql -c "SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid WHERE application_name='dspaceWeb'" | wc -l
|
||
1681
|
||
</code></pre><ul>
|
||
<li>Looking at Munin, I see there are indeed a higher number of locks starting on the morning of 2021-10-07:</li>
|
||
</ul>
|
||
<p><img src="/cgspace-notes/2021/10/postgres_locks_ALL-week.png" alt="PostgreSQL locks week"></p>
|
||
<ul>
|
||
<li>The only thing I did on 2021-10-07 was import a few thousand metadata corrections…</li>
|
||
<li>I restarted PostgreSQL (instead of restarting Tomcat), so let’s see if that helps</li>
|
||
<li>I filed <a href="https://github.com/DSpace/DSpace/issues/7989">a bug for the DSpace 6/7 duplicate values metadata import issue</a></li>
|
||
<li>I tested the two patches for removing abandoned submissions from the workflow but unfortunately it seems that they are for the configurable aka XML workflow, and we are using the basic workflow</li>
|
||
<li>I discussed PostgreSQL issues with some people on the DSpace Slack
|
||
<ul>
|
||
<li>Looking at postgresqltuner.pl and <a href="https://pgtune.leopard.in.ua">https://pgtune.leopard.in.ua</a> I realized that there were some settings that I hadn’t changed in a few years that I probably need to re-evaluate</li>
|
||
<li>For example, <code>random_page_cost</code> is recommended to be 1.1 in the PostgreSQL 10 docs (default is 4.0, but we use 1 since 2017 when it came up in Hacker News)</li>
|
||
<li>Also, <code>effective_io_concurrency</code> is recommended to be “hundreds” if you are using an SSD (default is 1)</li>
|
||
</ul>
|
||
</li>
|
||
<li>I also enabled the <code>pg_stat_statements</code> extension to try to understand what queries are being run the most often, and how long they take</li>
|
||
</ul>
|
||
<h2 id="2021-10-12">2021-10-12</h2>
|
||
<ul>
|
||
<li>I looked again at the duplicate items query I was doing with trigrams recently and found a few new things
|
||
<ul>
|
||
<li>Looking at the <code>EXPLAIN ANALYZE</code> plan for the query I noticed it wasn’t using any indexes</li>
|
||
<li>I <a href="https://dba.stackexchange.com/questions/103821/best-index-for-similarity-function/103823">read on StackExchange</a> that, if we want to make use of indexes, we need to use the similarity operator (<code>%</code>), not the function <code>similarity()</code> because “index support is bound to operators in Postgres, not to functions”</li>
|
||
<li>A note about the query plan output is that we need to read it from the bottom up!</li>
|
||
<li>So with the similary operator we need to set the threshold like this now:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace= > SET pg_trgm.similarity_threshold = 0.5;
|
||
</code></pre><ul>
|
||
<li>Next I experimented with using GIN or GiST indexes on <code>metadatavalue</code>, but they were slower than the existing DSpace indexes
|
||
<ul>
|
||
<li>I tested a few variations of the query I had been using and found it’s <em>much</em> faster if I use the similarity operator and keep the condition that object IDs are in the item table…</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace= > SELECT text_value, dspace_object_id FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=64 AND text_value % 'Traditional knowledge affects soil management ability of smallholder farmers in marginal areas';
|
||
text_value │ dspace_object_id
|
||
────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
|
||
Traditional knowledge affects soil management ability of smallholder farmers in marginal areas │ 7af059af-9cd7-431b-8a79-7514896ca7dc
|
||
(1 row)
|
||
|
||
Time: 739.948 ms
|
||
</code></pre><ul>
|
||
<li>Now this script runs in four minutes (versus twenty-four!) and it still finds the same seven duplicates! Amazing!</li>
|
||
<li>I still don’t understand the differences in the query plan well enough, but I see it is using the DSpace default indexes and the results are accurate</li>
|
||
<li>So to summarize, the best to the worst query, all returning the same result:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code class="language-console" data-lang="console">localhost/dspace= > SET pg_trgm.similarity_threshold = 0.6;
|
||
localhost/dspace= > SELECT text_value, dspace_object_id FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=64 AND text_value % 'Traditional knowledge affects soil management ability of smallholder farmers in marginal areas';
|
||
text_value │ dspace_object_id
|
||
────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
|
||
Traditional knowledge affects soil management ability of smallholder farmers in marginal areas │ 7af059af-9cd7-431b-8a79-7514896ca7dc
|
||
(1 row)
|
||
|
||
Time: 683.165 ms
|
||
Time: 635.364 ms
|
||
Time: 674.666 ms
|
||
|
||
localhost/dspace= > DISCARD ALL;
|
||
localhost/dspace= > SET pg_trgm.similarity_threshold = 0.6;
|
||
localhost/dspace= > SELECT text_value, dspace_object_id FROM metadatavalue WHERE metadata_field_id=64 AND text_value % 'Traditional knowledge affects soil management ability of smallholder farmers in marginal areas';
|
||
text_value │ dspace_object_id
|
||
────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
|
||
Traditional knowledge affects soil management ability of smallholder farmers in marginal areas │ 7af059af-9cd7-431b-8a79-7514896ca7dc
|
||
(1 row)
|
||
|
||
Time: 1584.765 ms (00:01.585)
|
||
Time: 1665.594 ms (00:01.666)
|
||
Time: 1623.726 ms (00:01.624)
|
||
|
||
localhost/dspace= > DISCARD ALL;
|
||
localhost/dspace= > SELECT text_value, dspace_object_id FROM metadatavalue WHERE metadata_field_id=64 AND SIMILARITY(text_value,'Traditional knowledge affects soil management ability of smallholder farmers in marginal areas') > 0.6;
|
||
text_value │ dspace_object_id
|
||
────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
|
||
Traditional knowledge affects soil management ability of smallholder farmers in marginal areas │ 7af059af-9cd7-431b-8a79-7514896ca7dc
|
||
(1 row)
|
||
|
||
Time: 4028.939 ms (00:04.029)
|
||
Time: 4022.239 ms (00:04.022)
|
||
Time: 4061.820 ms (00:04.062)
|
||
|
||
localhost/dspace= > DISCARD ALL;
|
||
localhost/dspace= > SELECT text_value, dspace_object_id FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=64 AND SIMILARITY(text_value,'Traditional knowledge affects soil management ability of smallholder farmers in marginal areas') > 0.6;
|
||
text_value │ dspace_object_id
|
||
────────────────────────────────────────────────────────────────────────────────────────────────┼──────────────────────────────────────
|
||
Traditional knowledge affects soil management ability of smallholder farmers in marginal areas │ 7af059af-9cd7-431b-8a79-7514896ca7dc
|
||
(1 row)
|
||
|
||
Time: 4358.713 ms (00:04.359)
|
||
Time: 4301.248 ms (00:04.301)
|
||
Time: 4417.909 ms (00:04.418)
|
||
</code></pre><h2 id="2021-10-13">2021-10-13</h2>
|
||
<ul>
|
||
<li>I looked into the <a href="https://github.com/DSpace/DSpace/issues/7946">REST API issue where fields without qualifiers throw an HTTP 500</a>
|
||
<ul>
|
||
<li>The fix is to check if the qualifier is not null AND not empty in dspace-api</li>
|
||
<li>I submitted a fix: <a href="https://github.com/DSpace/DSpace/pull/7993">https://github.com/DSpace/DSpace/pull/7993</a></li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2021-10-14">2021-10-14</h2>
|
||
<ul>
|
||
<li>Someone in the DSpace community already posted a fix for the DSpace 6/7 duplicate items export bug!
|
||
<ul>
|
||
<li>I tested it and it works so I left feedback: <a href="https://github.com/DSpace/DSpace/pull/7995">https://github.com/DSpace/DSpace/pull/7995</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>Altmetric support got back to us about the missing DOI–Handle link and said it was due to the TLS certificate chain on CGSpace
|
||
<ul>
|
||
<li>I checked and everything is actually working fine, so it could be their backend servers are old and don’t support the new Let’s Encrypt trust path</li>
|
||
<li>I asked them to put me in touch with their backend developers directly</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2021-10-17">2021-10-17</h2>
|
||
<ul>
|
||
<li>Revert the ssl-cert change on the Ansible infrastructure scripts so that nginx uses a manually generated “snakeoil” TLS certificate
|
||
<ul>
|
||
<li>The ssl-cert one is easier because it’s automatic, but they include the hostname in the bogus cert so it’s an unecessary leak of information</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/2021-10/">October, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-09/">September, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-08/">August, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-07/">July, 2021</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2021-06/">June, 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>
|
||
|
||
|
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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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<a href="#">Back to top</a>
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