mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-20 13:45:02 +01:00
490 lines
17 KiB
HTML
490 lines
17 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="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/" />
|
|
|
|
|
|
|
|
<meta property="og:updated_time" content="2017-11-02T09:37:54+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."/>
|
|
<meta name="generator" content="Hugo 0.46" />
|
|
|
|
|
|
|
|
<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"
|
|
},
|
|
"dateModified": "2017-11-02T09:37:54+02:00",
|
|
"keywords": "notes,notes,",
|
|
"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 -->
|
|
<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-Upm5uY/SXdvbjuIGH6fBjF5vOYUr9DguqBskM+EQpLBzO9U+9fMVmWEt+TTlGrWQ" crossorigin="anonymous">
|
|
|
|
|
|
<!-- RSS 2.0 feed -->
|
|
<link href="https://alanorth.github.io/cgspace-notes/index.xml" rel="alternate" type="application/rss+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"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
|
|
<p class="lead blog-description">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"><a href="https://alanorth.github.io/cgspace-notes/2017-11/">November, 2017</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2017-11-02T09:37:54+02:00">Thu Nov 02, 2017</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2017-11-01">2017-11-01</h2>
|
|
|
|
<ul>
|
|
<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
|
|
</ul>
|
|
|
|
<h2 id="2017-11-02">2017-11-02</h2>
|
|
|
|
<ul>
|
|
<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
|
|
</ul>
|
|
|
|
<pre><code># grep -c "CORE" /var/log/nginx/access.log
|
|
0
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
|
|
</ul>
|
|
|
|
<pre><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
|
|
COPY 54701
|
|
</code></pre>
|
|
|
|
<p></p>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2017-10-01">2017-10-01</h2>
|
|
|
|
<ul>
|
|
<li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li>
|
|
</ul>
|
|
|
|
<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
|
|
</code></pre>
|
|
|
|
<ul>
|
|
<li>There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</li>
|
|
<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
|
|
</ul>
|
|
|
|
<p></p>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2017-09-18T16:38:35+03:00">Mon Sep 18, 2017</time> by Alan Orth in
|
|
<i class="fa fa-folder" aria-hidden="true"></i> <a href="/cgspace-notes/categories/notes" rel="category tag">Notes</a>
|
|
|
|
|
|
</p>
|
|
</header>
|
|
<p>Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called <em>CGIAR System Organization</em>.</p>
|
|
|
|
<p></p>
|
|
<a href='https://alanorth.github.io/cgspace-notes/cgiar-library-migration/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2017-09/">September, 2017</a></h2>
|
|
<p class="blog-post-meta"><time datetime="2017-09-07T16:54:52+07:00">Thu Sep 07, 2017</time> by Alan Orth in
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
|
|
|
</p>
|
|
</header>
|
|
<h2 id="2017-09-06">2017-09-06</h2>
|
|
|
|
<ul>
|
|
<li>Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two hours</li>
|
|
</ul>
|
|
|
|
<h2 id="2017-09-07">2017-09-07</h2>
|
|
|
|
<ul>
|
|
<li>Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account is both in the approvers step as well as the group</li>
|
|
</ul>
|
|
|
|
<p></p>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-09/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><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
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <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… 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’re already adding the <code>X-Robots-Tag "none"</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…</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>
|
|
|
|
<p></p>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-08/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><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
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <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’s MEL DSpace database so we can compare fields with CGSpace</li>
|
|
<li>We can use PostgreSQL’s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li>
|
|
</ul>
|
|
|
|
<p></p>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-07/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><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
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <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’ll create a new sub-community for Phase II and create collections for the research themes there The current “Research Themes” community will be renamed to “WLE Phase I Research Themes” 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>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><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
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <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’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’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>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><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
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <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 (“MANAGING CLIMATE RISK”): <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>
|
|
|
|
<pre><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media-cmyk.txt
|
|
</code></pre>
|
|
|
|
<p></p>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-04/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<article class="blog-post">
|
|
<header>
|
|
<h2 class="blog-post-title"><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
|
|
|
|
<i class="fa fa-tag" aria-hidden="true"></i> <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 “CGIAR System” 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’s thumbnails were sRGB, but forcing regeneration using DSpace 5.x’s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see <a href="https://cgspace.cgiar.org/handle/10568/51999"><sup>10568</sup>⁄<sub>51999</sub></a>):</li>
|
|
</ul>
|
|
|
|
<pre><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>
|
|
|
|
<p></p>
|
|
<a href='https://alanorth.github.io/cgspace-notes/2017-03/'>Read more →</a>
|
|
</article>
|
|
|
|
|
|
|
|
|
|
|
|
<nav class="blog-pagination">
|
|
|
|
<a class="btn btn-outline-primary" href="/cgspace-notes/" rel="prev" role="button">Previous page</a>
|
|
<a class="btn btn-outline-primary" href="/cgspace-notes/page/3/" rel="next" role="button">Next page</a>
|
|
|
|
|
|
|
|
</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">
|
|
|
|
|
|
<li><a href="/cgspace-notes/2018-09/">September, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-08/">August, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-07/">July, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-06/">June, 2018</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2018-05/">May, 2018</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>
|
|
|
|
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>
|