366 lines
16 KiB
HTML
366 lines
16 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="September, 2020" />
|
|
<meta property="og:description" content="2020-09-02
|
|
|
|
Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS
|
|
The AReS Explorer hasn’t updated its index since 2020-08-22 when I last forced it
|
|
|
|
I restarted it again now and told Moayad that the automatic indexing isn’t working
|
|
|
|
|
|
Add Alliance of Bioversity International and CIAT to affiliations on CGSpace
|
|
Abenet told me that the general search text on AReS doesn’t get reset when you use the “Reset Filters” button
|
|
|
|
I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39
|
|
|
|
|
|
I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40
|
|
" />
|
|
<meta property="og:type" content="article" />
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-09/" />
|
|
<meta property="article:published_time" content="2020-09-02T15:35:54+03:00" />
|
|
<meta property="article:modified_time" content="2020-09-04T13:32:16+03:00" />
|
|
|
|
<meta name="twitter:card" content="summary"/>
|
|
<meta name="twitter:title" content="September, 2020"/>
|
|
<meta name="twitter:description" content="2020-09-02
|
|
|
|
Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS
|
|
The AReS Explorer hasn’t updated its index since 2020-08-22 when I last forced it
|
|
|
|
I restarted it again now and told Moayad that the automatic indexing isn’t working
|
|
|
|
|
|
Add Alliance of Bioversity International and CIAT to affiliations on CGSpace
|
|
Abenet told me that the general search text on AReS doesn’t get reset when you use the “Reset Filters” button
|
|
|
|
I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39
|
|
|
|
|
|
I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40
|
|
"/>
|
|
<meta name="generator" content="Hugo 0.74.3" />
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "BlogPosting",
|
|
"headline": "September, 2020",
|
|
"url": "https://alanorth.github.io/cgspace-notes/2020-09/",
|
|
"wordCount": "838",
|
|
"datePublished": "2020-09-02T15:35:54+03:00",
|
|
"dateModified": "2020-09-04T13:32:16+03:00",
|
|
"author": {
|
|
"@type": "Person",
|
|
"name": "Alan Orth"
|
|
},
|
|
"keywords": "Notes"
|
|
}
|
|
</script>
|
|
|
|
|
|
|
|
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2020-09/">
|
|
|
|
<title>September, 2020 | CGSpace Notes</title>
|
|
|
|
|
|
<!-- combined, minified CSS -->
|
|
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.6da5c906cc7a8fbb93f31cd2316c5dbe3f19ac4aa6bfb066f1243045b8f6061e.css" rel="stylesheet" integrity="sha256-baXJBsx6j7uT8xzSMWxdvj8ZrEqmv7Bm8SQwRbj2Bh4=" crossorigin="anonymous">
|
|
|
|
|
|
<!-- minified Font Awesome for SVG icons -->
|
|
|
|
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f3d2a1f5980bab30ddd0d8cadbd496475309fc48e2b1d052c5c09e6facffcb0f.js" integrity="sha256-89Kh9ZgLqzDd0NjK29SWR1MJ/EjisdBSxcCeb6z/yw8=" 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/2020-09/">September, 2020</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2020-09-02T15:35:54+03:00">Wed Sep 02, 2020</time> by Alan Orth in
|
|
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2020-09-02">2020-09-02</h2>
|
|
<ul>
|
|
<li>Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS</li>
|
|
<li>The AReS Explorer hasn’t updated its index since 2020-08-22 when I last forced it
|
|
<ul>
|
|
<li>I restarted it again now and told Moayad that the automatic indexing isn’t working</li>
|
|
</ul>
|
|
</li>
|
|
<li>Add <code>Alliance of Bioversity International and CIAT</code> to affiliations on CGSpace</li>
|
|
<li>Abenet told me that the general search text on AReS doesn’t get reset when you use the “Reset Filters” button
|
|
<ul>
|
|
<li>I filed a bug on OpenRXV: <a href="https://github.com/ilri/OpenRXV/issues/39">https://github.com/ilri/OpenRXV/issues/39</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>I filed an issue on OpenRXV to make some minor edits to the admin UI: <a href="https://github.com/ilri/OpenRXV/issues/40">https://github.com/ilri/OpenRXV/issues/40</a></li>
|
|
</ul>
|
|
<ul>
|
|
<li>I ran the country code tagger on CGSpace:</li>
|
|
</ul>
|
|
<pre><code>$ time chrt -b 0 dspace curate -t countrycodetagger -i all -r - -l 500 -s object | tee /tmp/2020-09-02-countrycodetagger.log
|
|
...
|
|
real 2m10.516s
|
|
user 1m43.953s
|
|
sys 0m15.192s
|
|
$ grep -c added /tmp/2020-09-02-countrycodetagger.log
|
|
39
|
|
</code></pre><ul>
|
|
<li>I still need to create a cron job for this…</li>
|
|
<li>Sisay and Abenet said they can’t log in with LDAP on DSpace Test (DSpace 6)
|
|
<ul>
|
|
<li>I tried and I can’t either… but it is working on CGSpace</li>
|
|
<li>The error on DSpace 6 is:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code>2020-09-02 12:03:10,666 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=A629116488DCC467E1EA2062A2E2EFD7:ip_addr=92.220.02.201:failed_login:no DN found for user aorth
|
|
</code></pre><ul>
|
|
<li>I tried to query LDAP directly using the application credentials with ldapsearch and it works:</li>
|
|
</ul>
|
|
<pre><code>$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b "dc=cgiarad,dc=org" -D "applicationaccount@cgiarad.org" -W "(sAMAccountName=me)"
|
|
</code></pre><ul>
|
|
<li>According to the <a href="https://wiki.lyrasis.org/display/DSDOC6x/Authentication+Plugins#AuthenticationPlugins-LDAPAuthentication">DSpace 6 docs</a> we need to escape commas in our LDAP parameters due to the new configuration system
|
|
<ul>
|
|
<li>I added the commas and restarted DSpace (though technically we shouldn’t need to restart due to the new config system hot reloading configs)</li>
|
|
<li>Run all system updates on DSpace Test (linode26) and reboot it</li>
|
|
<li>After the restart LDAP login works…</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-09-03">2020-09-03</h2>
|
|
<ul>
|
|
<li>Fix some erroneous “review status” fields that Abenet noticed on AReS
|
|
<ul>
|
|
<li>I used my <code>fix-metadata-values.py</code> and <code>delete-metadata-values.py</code> scripts with the following input files:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code>$ cat 2020-09-03-fix-review-status.csv
|
|
dc.description.version,correct
|
|
Externally Peer Reviewed,Peer Review
|
|
Peer Reviewed,Peer Review
|
|
Peer review,Peer Review
|
|
Peer reviewed,Peer Review
|
|
Peer-Reviewed,Peer Review
|
|
Peer-reviewed,Peer Review
|
|
peer Review,Peer Review
|
|
$ cat 2020-09-03-delete-review-status.csv
|
|
dc.description.version
|
|
Report
|
|
Formally Published
|
|
Poster
|
|
Unrefereed reprint
|
|
$ ./delete-metadata-values.py -i 2020-09-03-delete-review-status.csv -db dspace -u dspace -p 'fuuu' -f dc.description.version -m 68
|
|
$ ./fix-metadata-values.py -i 2020-09-03-fix-review-status.csv -db dspace -u dspace -p 'fuuu' -f dc.description.version -t 'correct' -m 68
|
|
</code></pre><ul>
|
|
<li>Start reviewing 95 items for IITA (20201stbatch)
|
|
<ul>
|
|
<li>I used my <a href="https://github.com/ilri/csv-metadata-quality">csv-metadata-quality</a> tool to check and fix some low-hanging fruit first</li>
|
|
<li>This fixed a few unnecessary Unicode, excessive whitespace, invalid multi-value separator, and duplicate metadata values</li>
|
|
<li>Then I looked at the data in OpenRefine and noticed some things:
|
|
<ul>
|
|
<li>All issue dates use year only, but some have months in the citation so they could be more specific</li>
|
|
<li>I normalized all the DOIs to use “<a href="https://doi.org">https://doi.org</a>” format</li>
|
|
<li>I fixed a few AGROVOC subjects with a simple GREL: <code>value.replace("GRAINS","GRAIN").replace("SOILS","SOIL").replace("CORN","MAIZE")</code></li>
|
|
<li>But there are a few more that are invalid that she will have to look at</li>
|
|
<li>I uploaded the items to <a href="https://dspacetest.cgiar.org/handle/10568/108357">DSpace Test</a> and it was apparently successful but I get these errors to the console:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code>Thu Sep 03 12:26:33 CEST 2020 | Query:containerItem:ea7a2648-180d-4fce-bdc5-c3aa2304fc58
|
|
Error while updating
|
|
java.lang.NullPointerException
|
|
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1131)
|
|
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.visitEachStatisticShard(SourceFile:212)
|
|
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1104)
|
|
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1093)
|
|
at org.dspace.statistics.StatisticsLoggingConsumer.consume(SourceFile:104)
|
|
at org.dspace.event.BasicDispatcher.consume(BasicDispatcher.java:177)
|
|
at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:123)
|
|
at org.dspace.core.Context.dispatchEvents(Context.java:455)
|
|
at org.dspace.core.Context.commit(Context.java:424)
|
|
at org.dspace.core.Context.complete(Context.java:380)
|
|
at org.dspace.app.bulkedit.MetadataImport.main(MetadataImport.java:1399)
|
|
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
|
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
|
|
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
|
at java.lang.reflect.Method.invoke(Method.java:498)
|
|
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
|
|
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
|
|
</code></pre><ul>
|
|
<li>There are more in the DSpace log so I will raise it with Atmire immediately</li>
|
|
</ul>
|
|
<h2 id="2020-09-04">2020-09-04</h2>
|
|
<ul>
|
|
<li>I was checking the recent IITA data for duplicates when I noticed that one in CIFOR’s Archive and saw that CIFOR has updated a bunch of their website URLs, for example:
|
|
<ul>
|
|
<li><a href="http://www.cifor.org/nc/online-library/browse/view-publication/publication/151.html">http://www.cifor.org/nc/online-library/browse/view-publication/publication/151.html</a> → <a href="https://www.cifor.org/knowledge/publication/151">https://www.cifor.org/knowledge/publication/151</a></li>
|
|
<li><a href="https://www.cifor.org/library/4033">https://www.cifor.org/library/4033</a> → <a href="https://www.cifor.org/knowledge/publication/4033">https://www.cifor.org/knowledge/publication/4033</a></li>
|
|
<li><a href="https://www.cifor.org/pid/5087">https://www.cifor.org/pid/5087</a> → <a href="https://www.cifor.org/knowledge/publication/5087">https://www.cifor.org/knowledge/publication/5087</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>I will update our nearly 6,000 metadata values for CIFOR in the database accordingly:</li>
|
|
</ul>
|
|
<pre><code>dspace=# UPDATE metadatavalue SET text_value = regexp_replace(text_value, '^(http://)?www\.cifor\.org/(nc/)?online-library/browse/view-publication/publication/([[:digit:]]+)\.html$', 'https://www.cifor.org/knowledge/publication/\3') WHERE metadata_field_id=219 AND text_value ~ 'www\.cifor\.org/(nc/)?online-library/browse/view-publication/publication/[[:digit:]]+';
|
|
dspace=# UPDATE metadatavalue SET text_value = regexp_replace(text_value, '^https?://www\.cifor\.org/library/([[:digit:]]+)/?$', 'https://www.cifor.org/knowledge/publication/\1') WHERE metadata_field_id=219 AND text_value ~ 'https?://www\.cifor\.org/library/[[:digit:]]+/?';
|
|
dspace=# UPDATE metadatavalue SET text_value = regexp_replace(text_value, '^https?://www\.cifor\.org/pid/([[:digit:]]+)/?$', 'https://www.cifor.org/knowledge/publication/\1') WHERE metadata_field_id=219 AND text_value ~ 'https?://www\.cifor\.org/pid/[[:digit:]]+';
|
|
</code></pre><ul>
|
|
<li>I did some cleanup on the author affiliations of the IITA data our 2019-04 list using reconcile-csv and OpenRefine:
|
|
<ul>
|
|
<li><code>$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id</code></li>
|
|
<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>
|
|
</ul>
|
|
</li>
|
|
<li>I mapped one duplicated from the CIFOR Archives and re-uploaded the 94 IITA items to a new collection on <a href="https://dspacetest.cgiar.org/handle/10568/108453">DSpace Test</a></li>
|
|
</ul>
|
|
<h2 id="2020-09-08">2020-09-08</h2>
|
|
<ul>
|
|
<li>I noticed that the “share” link in AReS wasn’t working properly because it excludes the “explorer” part of the URI</li>
|
|
</ul>
|
|
<p><img src="/cgspace-notes/2020/09/ares-share-link.png" alt="AReS share link broken"></p>
|
|
<ul>
|
|
<li>I filed an issue on GitHub: <a href="https://github.com/ilri/OpenRXV/issues/41">https://github.com/ilri/OpenRXV/issues/41</a></li>
|
|
<li>I uploaded the 94 IITA items that I had been working on last week to CGSpace</li>
|
|
<li>RTB emailed to ask why they are getting HTTP 503 errors during harvesting to the RTB WordPress website
|
|
<ul>
|
|
<li>From the screenshot I can see they are requesting URLs like this:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code>https://cgspace.cgiar.org/bitstream/handle/10568/82745/Characteristics-Silage.JPG
|
|
</code></pre><ul>
|
|
<li>So they end up getting rate limited due to the XMLUI rate limits
|
|
<ul>
|
|
<li>I told them to use the REST API bitstream retrieve links, because we don’t have any rate limits there</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/2020-09/">September, 2020</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2020-07/">July, 2020</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2020-06/">June, 2020</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2020-05/">May, 2020</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>
|