cgspace-notes/docs/page/7/index.html

452 lines
20 KiB
HTML
Raw Normal View History

2020-09-03 12:50:56 +02:00
<!DOCTYPE html>
<html lang="en" >
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
2020-12-06 15:53:29 +01:00
2020-09-03 12:50:56 +02:00
<meta property="og:title" content="CGSpace Notes" />
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
<meta property="og:type" content="website" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />
2022-05-13 09:28:23 +02:00
<meta property="og:updated_time" content="2022-05-13T08:39:15+03:00" />
2020-12-06 15:53:29 +01:00
2020-09-03 12:50:56 +02:00
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace Notes"/>
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
2022-05-04 10:09:45 +02:00
<meta name="generator" content="Hugo 0.98.0" />
2020-09-03 12:50:56 +02:00
<script type="application/ld+json">
{
"@context": "http://schema.org",
"@type": "Blog",
"headline": "CGSpace Notes",
"url" : "https://alanorth.github.io/cgspace-notes/",
"author": {
"@type": "Person",
"name": "Alan Orth"
},
2022-05-04 10:09:45 +02:00
"dateModified": "2022-05-04T09:13:39+03:00",
2020-11-16 09:54:00 +01:00
"keywords": "notes, migration, notes",
2020-09-03 12:50:56 +02:00
"description":"Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."
}
</script>
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/">
<title>CGSpace Notes</title>
<!-- combined, minified CSS -->
2021-01-24 08:46:27 +01:00
<link href="https://alanorth.github.io/cgspace-notes/css/style.beb8012edc08ba10be012f079d618dc243812267efe62e11f22fe49618f976a4.css" rel="stylesheet" integrity="sha256-vrgBLtwIuhC&#43;AS8HnWGNwkOBImfv5i4R8i/klhj5dqQ=" crossorigin="anonymous">
2020-09-03 12:50:56 +02:00
<!-- minified Font Awesome for SVG icons -->
2021-09-28 09:32:32 +02:00
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz&#43;lcnA=" crossorigin="anonymous"></script>
2020-09-03 12:50:56 +02:00
<!-- RSS 2.0 feed -->
<link rel="alternate" type="application/rss+xml" href="https://alanorth.github.io/cgspace-notes/index.xml" title="CGSpace Notes" />
</head>
<body>
<div class="blog-masthead">
<div class="container">
<nav class="nav blog-nav">
<a class="nav-link active" 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">
2022-05-04 10:09:45 +02:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-08/">August, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-08-01T11:51:52+03:00">Tue Aug 01, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-08-01">2017-08-01</h2>
<ul>
<li>Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours</li>
<li>I looked in the Activity pane of the Admin Control Panel and it seems that Google, Baidu, Yahoo, and Bing are all crawling with massive numbers of bots concurrently (~100 total, mostly Baidu and Google)</li>
<li>The good thing is that, according to <code>dspace.log.2017-08-01</code>, they are all using the same Tomcat session</li>
<li>This means our Tomcat Crawler Session Valve is working</li>
<li>But many of the bots are browsing dynamic URLs like:
<ul>
<li>/handle/10568/3353/discover</li>
<li>/handle/10568/16510/browse</li>
</ul>
</li>
<li>The <code>robots.txt</code> only blocks the top-level <code>/discover</code> and <code>/browse</code> URLs&hellip; we will need to find a way to forbid them from accessing these!</li>
<li>Relevant issue from DSpace Jira (semi resolved in DSpace 6.0): <a href="https://jira.duraspace.org/browse/DS-2962">https://jira.duraspace.org/browse/DS-2962</a></li>
<li>It turns out that we&rsquo;re already adding the <code>X-Robots-Tag &quot;none&quot;</code> HTTP header, but this only forbids the search engine from <em>indexing</em> the page, not crawling it!</li>
<li>Also, the bot has to successfully browse the page first so it can receive the HTTP header&hellip;</li>
<li>We might actually have to <em>block</em> these requests with HTTP 403 depending on the user agent</li>
<li>Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415</li>
<li>This was due to newline characters in the <code>dc.description.abstract</code> column, which caused OpenRefine to choke when exporting the CSV</li>
<li>I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using <code>g/^$/d</code></li>
<li>Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-08/'>Read more →</a>
</article>
2022-04-04 18:15:58 +02:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-07/">July, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-07-01T18:03:52+03:00">Sat Jul 01, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-07-01">2017-07-01</h2>
<ul>
<li>Run system updates and reboot DSpace Test</li>
</ul>
<h2 id="2017-07-04">2017-07-04</h2>
<ul>
<li>Merge changes for WLE Phase II theme rename (<a href="https://github.com/ilri/DSpace/pull/329">#329</a>)</li>
<li>Looking at extracting the metadata registries from ICARDA&rsquo;s MEL DSpace database so we can compare fields with CGSpace</li>
<li>We can use PostgreSQL&rsquo;s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-07/'>Read more →</a>
</article>
2022-03-01 15:48:40 +01:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-06/">June, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-06-01T10:14:52+03:00">Thu Jun 01, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg.
<a href='https://alanorth.github.io/cgspace-notes/2017-06/'>Read more →</a>
</article>
2022-02-10 18:35:40 +01:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-05/">May, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-05-01T16:21:52+02:00">Mon May 01, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace.
<a href='https://alanorth.github.io/cgspace-notes/2017-05/'>Read more →</a>
</article>
2022-01-01 14:21:47 +01:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-04/">April, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-04-02T17:08:52+02:00">Sun Apr 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-04-02">2017-04-02</h2>
<ul>
<li>Merge one change to CCAFS flagships that I had forgotten to remove last month (&ldquo;MANAGING CLIMATE RISK&rdquo;): <a href="https://github.com/ilri/DSpace/pull/317">https://github.com/ilri/DSpace/pull/317</a></li>
<li>Quick proof-of-concept hack to add <code>dc.rights</code> to the input form, including some inline instructions/hints:</li>
</ul>
<p><img src="/cgspace-notes/2017/04/dc-rights.png" alt="dc.rights in the submission form"></p>
<ul>
<li>Remove redundant/duplicate text in the DSpace submission license</li>
<li>Testing the CMYK patch on a collection with 650 items:</li>
</ul>
2022-03-04 13:30:06 +01:00
<pre tabindex="0"><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &#34;ImageMagick PDF Thumbnail&#34; -v &gt;&amp; /tmp/filter-media-cmyk.txt
2022-01-01 14:21:47 +01:00
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2017-04/'>Read more →</a>
</article>
2021-12-03 11:58:43 +01:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-03/">March, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-03-01T17:08:52+02:00">Wed Mar 01, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-03-01">2017-03-01</h2>
<ul>
<li>Run the 279 CIAT author corrections on CGSpace</li>
</ul>
<h2 id="2017-03-02">2017-03-02</h2>
<ul>
<li>Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace</li>
<li>CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles</li>
<li>They might come in at the top level in one &ldquo;CGIAR System&rdquo; community, or with several communities</li>
<li>I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?</li>
<li>Need to send Peter and Michael some notes about this in a few days</li>
<li>Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI</li>
<li>Filed an issue on DSpace issue tracker for the <code>filter-media</code> bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: <a href="https://jira.duraspace.org/browse/DS-3516">DS-3516</a></li>
<li>Discovered that the ImageMagic <code>filter-media</code> plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK</li>
<li>Interestingly, it seems DSpace 4.x&rsquo;s thumbnails were sRGB, but forcing regeneration using DSpace 5.x&rsquo;s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see <a href="https://cgspace.cgiar.org/handle/10568/51999">10568/51999</a>):</li>
</ul>
<pre tabindex="0"><code>$ identify ~/Desktop/alc_contrastes_desafios.jpg
/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2017-03/'>Read more →</a>
</article>
2021-11-01 09:49:21 +01:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-02/">February, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-02-07T07:04:52-08:00">Tue Feb 07, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-02-07">2017-02-07</h2>
<ul>
<li>An item was mapped twice erroneously again, so I had to remove one of the mappings manually:</li>
</ul>
2022-03-04 13:30:06 +01:00
<pre tabindex="0"><code>dspace=# select * from collection2item where item_id = &#39;80278&#39;;
2021-11-01 09:49:21 +01:00
id | collection_id | item_id
-------+---------------+---------
92551 | 313 | 80278
92550 | 313 | 80278
90774 | 1051 | 80278
(3 rows)
dspace=# delete from collection2item where id = 92551 and item_id = 80278;
DELETE 1
</code></pre><ul>
<li>Create issue on GitHub to track the addition of CCAFS Phase II project tags (<a href="https://github.com/ilri/DSpace/issues/301">#301</a>)</li>
<li>Looks like we&rsquo;ll be using <code>cg.identifier.ccafsprojectpii</code> as the field name</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-02/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-01/">January, 2017</a></h2>
<p class="blog-post-meta"><time datetime="2017-01-02T10:43:00+03:00">Mon Jan 02, 2017</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2017-01-02">2017-01-02</h2>
<ul>
<li>I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error</li>
<li>I tested on DSpace Test as well and it doesn&rsquo;t work there either</li>
<li>I asked on the dspace-tech mailing list because it seems to be broken, and actually now I&rsquo;m not sure if we&rsquo;ve ever had the sharding task run successfully over all these years</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2017-01/'>Read more →</a>
</article>
2021-09-02 16:21:48 +02:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-12/">December, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-12-02T10:43:00+03:00">Fri Dec 02, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-12-02">2016-12-02</h2>
<ul>
<li>CGSpace was down for five hours in the morning while I was sleeping</li>
<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
</ul>
2022-03-04 13:30:06 +01:00
<pre tabindex="0"><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&#34;dc.title&#34;, transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&#34;THUMBNAIL&#34;, transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&#34;-1&#34;, transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&#34;TX157907838689377964651674089851855413607&#34;)
2021-09-02 16:21:48 +02:00
</code></pre><ul>
<li>I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade</li>
<li>I&rsquo;ve raised a ticket with Atmire to ask</li>
<li>Another worrying error from dspace.log is:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-12/'>Read more →</a>
</article>
2021-08-01 15:19:05 +02:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-11/">November, 2016</a></h2>
<p class="blog-post-meta"><time datetime="2016-11-01T09:21:00+03:00">Tue Nov 01, 2016</time> by Alan Orth in
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
</p>
</header>
<h2 id="2016-11-01">2016-11-01</h2>
<ul>
<li>Add <code>dc.type</code> to the output options for Atmire&rsquo;s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
</ul>
<p><img src="/cgspace-notes/2016/11/listings-and-reports.png" alt="Listings and Reports with output type"></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-11/'>Read more →</a>
</article>
2020-09-03 12:50:56 +02:00
<nav class="blog-pagination">
<a class="btn btn-outline-primary" href="/cgspace-notes/page/6/" rel="prev" role="button">Previous page</a>
2021-06-03 20:54:49 +02:00
<a class="btn btn-outline-primary" href="/cgspace-notes/page/8/" rel="next" role="button">Next page</a>
2020-09-03 12:50:56 +02:00
</nav>
</div> <!-- /.blog-main -->
<aside class="col-sm-3 ml-auto blog-sidebar">
<section class="sidebar-module">
<h4>Recent Posts</h4>
<ol class="list-unstyled">
2022-05-04 10:09:45 +02:00
<li><a href="/cgspace-notes/2022-05/">May, 2022</a></li>
2022-04-27 08:58:45 +02:00
<li><a href="/cgspace-notes/2022-04/">April, 2022</a></li>
2022-03-01 15:48:40 +01:00
2022-04-27 08:58:45 +02:00
<li><a href="/cgspace-notes/2022-03/">March, 2022</a></li>
2022-04-04 18:15:58 +02:00
2022-02-10 18:35:40 +01:00
<li><a href="/cgspace-notes/2022-02/">February, 2022</a></li>
2022-01-01 14:21:47 +01:00
<li><a href="/cgspace-notes/2022-01/">January, 2022</a></li>
2020-09-03 12:50:56 +02:00
</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>