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432 lines
17 KiB
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</head>
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<body>
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<div class="container">
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<a class="nav-link active" 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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</div>
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</header>
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<div class="container">
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<div class="row">
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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/2017-12/">December, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-12-01T13:53:54+03:00">Fri Dec 01, 2017</time> by Alan Orth 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="2017-12-01">2017-12-01</h2>
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<ul>
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<li>Uptime Robot noticed that CGSpace went down</li>
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<li>The logs say “Timeout waiting for idle object”</li>
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<li>PostgreSQL activity says there are 115 connections currently</li>
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<li>The list of connections to XMLUI and REST API for today:</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-12/'>Read more →</a>
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</article>
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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/2017-11/">November, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-11-02T09:37:54+02:00">Thu Nov 02, 2017</time> by Alan Orth 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="2017-11-01">2017-11-01</h2>
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<ul>
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<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
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</ul>
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<h2 id="2017-11-02">2017-11-02</h2>
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<ul>
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<li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li>
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</ul>
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<pre><code># grep -c "CORE" /var/log/nginx/access.log
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0
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</code></pre><ul>
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<li>Generate list of authors on CGSpace for Peter to go through and correct:</li>
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</ul>
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<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;
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COPY 54701
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a>
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</article>
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<article class="blog-post">
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth 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="2017-10-01">2017-10-01</h2>
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<ul>
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<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>
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</ul>
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<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
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</code></pre><ul>
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<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>
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<li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
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</article>
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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/cgiar-library-migration/">CGIAR Library Migration</a></h2>
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<p class="blog-post-meta"><time datetime="2017-09-18T16:38:35+03:00">Mon Sep 18, 2017</time> by Alan Orth 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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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/migration/" rel="tag">Migration</a>
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</p>
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</header>
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<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>
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<a href='https://alanorth.github.io/cgspace-notes/cgiar-library-migration/'>Read more →</a>
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</article>
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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/2017-09/">September, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-09-07T16:54:52+07:00">Thu Sep 07, 2017</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-09-06">2017-09-06</h2>
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<ul>
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<li>Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two hours</li>
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</ul>
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<h2 id="2017-09-07">2017-09-07</h2>
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<ul>
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<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>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-09/'>Read more →</a>
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</article>
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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/2017-08/">August, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-08-01T11:51:52+03:00">Tue Aug 01, 2017</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-08-01">2017-08-01</h2>
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<ul>
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<li>Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours</li>
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<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>
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<li>The good thing is that, according to <code>dspace.log.2017-08-01</code>, they are all using the same Tomcat session</li>
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<li>This means our Tomcat Crawler Session Valve is working</li>
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<li>But many of the bots are browsing dynamic URLs like:
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<ul>
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<li>/handle/10568/3353/discover</li>
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<li>/handle/10568/16510/browse</li>
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</ul>
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</li>
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<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>
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<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>
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<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>
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<li>Also, the bot has to successfully browse the page first so it can receive the HTTP header…</li>
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<li>We might actually have to <em>block</em> these requests with HTTP 403 depending on the user agent</li>
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<li>Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415</li>
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<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>
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<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>
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<li>Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-08/'>Read more →</a>
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</article>
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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/2017-07/">July, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-07-01T18:03:52+03:00">Sat Jul 01, 2017</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-07-01">2017-07-01</h2>
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<ul>
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<li>Run system updates and reboot DSpace Test</li>
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</ul>
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<h2 id="2017-07-04">2017-07-04</h2>
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<ul>
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<li>Merge changes for WLE Phase II theme rename (<a href="https://github.com/ilri/DSpace/pull/329">#329</a>)</li>
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<li>Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace</li>
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<li>We can use PostgreSQL’s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-07/'>Read more →</a>
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</article>
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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/2017-06/">June, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-06-01T10:14:52+03:00">Thu Jun 01, 2017</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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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.
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<a href='https://alanorth.github.io/cgspace-notes/2017-06/'>Read more →</a>
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</article>
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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/2017-05/">May, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-05-01T16:21:52+02:00">Mon May 01, 2017</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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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.
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<a href='https://alanorth.github.io/cgspace-notes/2017-05/'>Read more →</a>
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</article>
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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/2017-04/">April, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-04-02T17:08:52+02:00">Sun Apr 02, 2017</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-04-02">2017-04-02</h2>
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<ul>
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<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>
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<li>Quick proof-of-concept hack to add <code>dc.rights</code> to the input form, including some inline instructions/hints:</li>
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</ul>
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<p><img src="/cgspace-notes/2017/04/dc-rights.png" alt="dc.rights in the submission form"></p>
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<ul>
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<li>Remove redundant/duplicate text in the DSpace submission license</li>
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<li>Testing the CMYK patch on a collection with 650 items:</li>
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</ul>
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<pre><code>$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media-cmyk.txt
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</code></pre>
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<a href='https://alanorth.github.io/cgspace-notes/2017-04/'>Read more →</a>
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</article>
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<nav class="blog-pagination">
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<a class="btn btn-outline-primary" href="/cgspace-notes/page/3/" rel="prev" role="button">Previous page</a>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2020-05/">May, 2020</a></li>
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<li><a href="/cgspace-notes/2020-04/">April, 2020</a></li>
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<li><a href="/cgspace-notes/2020-03/">March, 2020</a></li>
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<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
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<li><a href="/cgspace-notes/2020-01/">January, 2020</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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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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