428 lines
23 KiB
XML
428 lines
23 KiB
XML
<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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<channel>
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<title>Notes on CGSpace Notes</title>
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<link>https://alanorth.github.io/cgspace-notes/tags/notes/</link>
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<description>Recent content in Notes on CGSpace Notes</description>
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<generator>Hugo -- gohugo.io</generator>
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<language>en-us</language>
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<lastBuildDate>Sun, 02 Apr 2017 17:08:52 +0200</lastBuildDate>
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<atom:link href="https://alanorth.github.io/cgspace-notes/tags/notes/index.xml" rel="self" type="application/rss+xml" />
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<item>
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<title>April, 2017</title>
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<link>https://alanorth.github.io/cgspace-notes/2017-04/</link>
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<pubDate>Sun, 02 Apr 2017 17:08:52 +0200</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2017-04/</guid>
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<description><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 (&ldquo;MANAGING CLIMATE RISK&rdquo;): <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="https://alanorth.github.io/cgspace-notes/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 &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt
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</code></pre>
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<p></p></description>
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</item>
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<item>
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<title>March, 2017</title>
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<link>https://alanorth.github.io/cgspace-notes/2017-03/</link>
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<pubDate>Wed, 01 Mar 2017 17:08:52 +0200</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2017-03/</guid>
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<description><h2 id="2017-03-01">2017-03-01</h2>
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<ul>
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<li>Run the 279 CIAT author corrections on CGSpace</li>
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</ul>
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<h2 id="2017-03-02">2017-03-02</h2>
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<ul>
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<li>Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace</li>
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<li>CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles</li>
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<li>They might come in at the top level in one &ldquo;CGIAR System&rdquo; community, or with several communities</li>
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<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>
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<li>Need to send Peter and Michael some notes about this in a few days</li>
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<li>Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI</li>
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<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>
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<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>
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<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"><sup>10568</sup>&frasl;<sub>51999</sub></a>):</li>
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</ul>
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<pre><code>$ identify ~/Desktop/alc_contrastes_desafios.jpg
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/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000
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</code></pre>
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<p></p></description>
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</item>
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<item>
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<title>February, 2017</title>
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<link>https://alanorth.github.io/cgspace-notes/2017-02/</link>
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<pubDate>Tue, 07 Feb 2017 07:04:52 -0800</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2017-02/</guid>
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<description><h2 id="2017-02-07">2017-02-07</h2>
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<ul>
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<li>An item was mapped twice erroneously again, so I had to remove one of the mappings manually:</li>
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</ul>
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<pre><code>dspace=# select * from collection2item where item_id = '80278';
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id | collection_id | item_id
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-------+---------------+---------
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92551 | 313 | 80278
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92550 | 313 | 80278
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90774 | 1051 | 80278
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(3 rows)
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dspace=# delete from collection2item where id = 92551 and item_id = 80278;
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DELETE 1
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</code></pre>
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<ul>
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<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>
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<li>Looks like we&rsquo;ll be using <code>cg.identifier.ccafsprojectpii</code> as the field name</li>
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</ul>
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<p></p></description>
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</item>
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<item>
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<title>January, 2017</title>
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<link>https://alanorth.github.io/cgspace-notes/2017-01/</link>
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<pubDate>Mon, 02 Jan 2017 10:43:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2017-01/</guid>
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<description><h2 id="2017-01-02">2017-01-02</h2>
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<ul>
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<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>
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<li>I tested on DSpace Test as well and it doesn&rsquo;t work there either</li>
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<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>
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</ul>
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<p></p></description>
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</item>
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<item>
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<title>December, 2016</title>
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<link>https://alanorth.github.io/cgspace-notes/2016-12/</link>
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<pubDate>Fri, 02 Dec 2016 10:43:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-12/</guid>
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<description><h2 id="2016-12-02">2016-12-02</h2>
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<ul>
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<li>CGSpace was down for five hours in the morning while I was sleeping</li>
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<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
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</ul>
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<pre><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=&quot;TX157907838689377964651674089851855413607&quot;)
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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=&quot;dc.title&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
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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=&quot;THUMBNAIL&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
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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=&quot;-1&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
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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=&quot;TX157907838689377964651674089851855413607&quot;)
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</code></pre>
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<ul>
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<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>
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<li>I&rsquo;ve raised a ticket with Atmire to ask</li>
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<li>Another worrying error from dspace.log is:</li>
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</ul>
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<p></p></description>
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</item>
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<item>
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<title>November, 2016</title>
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<link>https://alanorth.github.io/cgspace-notes/2016-11/</link>
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<pubDate>Tue, 01 Nov 2016 09:21:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-11/</guid>
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<description><h2 id="2016-11-01">2016-11-01</h2>
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<ul>
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<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>
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</ul>
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<p><img src="https://alanorth.github.io/cgspace-notes/cgspace-notes/2016/11/listings-and-reports.png" alt="Listings and Reports with output type" /></p>
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<p></p></description>
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</item>
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<item>
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<title>October, 2016</title>
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<link>https://alanorth.github.io/cgspace-notes/2016-10/</link>
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<pubDate>Mon, 03 Oct 2016 15:53:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-10/</guid>
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<description><h2 id="2016-10-03">2016-10-03</h2>
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<ul>
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<li>Testing adding <a href="https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing">ORCIDs to a CSV</a> file for a single item to see if the author orders get messed up</li>
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<li>Need to test the following scenarios to see how author order is affected:
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<ul>
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<li>ORCIDs only</li>
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<li>ORCIDs plus normal authors</li>
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</ul></li>
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<li>I exported a random item&rsquo;s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</li>
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</ul>
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<pre><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
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</code></pre>
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<p></p></description>
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</item>
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<item>
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<title>September, 2016</title>
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<link>https://alanorth.github.io/cgspace-notes/2016-09/</link>
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<pubDate>Thu, 01 Sep 2016 15:53:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-09/</guid>
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<description><h2 id="2016-09-01">2016-09-01</h2>
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<ul>
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<li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li>
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<li>Discuss how the migration of CGIAR&rsquo;s Active Directory to a flat structure will break our LDAP groups in DSpace</li>
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<li>We had been using <code>DC=ILRI</code> to determine whether a user was ILRI or not</li>
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<li>It looks like we might be able to use OUs now, instead of DCs:</li>
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</ul>
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<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;
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</code></pre>
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<p></p></description>
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</item>
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<item>
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<title>August, 2016</title>
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<link>https://alanorth.github.io/cgspace-notes/2016-08/</link>
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<pubDate>Mon, 01 Aug 2016 15:53:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-08/</guid>
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<description><h2 id="2016-08-01">2016-08-01</h2>
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<ul>
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<li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li>
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<li>Play with upgrading Mirage 2 dependencies in <code>bower.json</code> because most are several versions of out date</li>
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<li>Bootstrap is at 3.3.0 but upstream is at 3.3.7, and upgrading to anything beyond 3.3.1 breaks glyphicons and probably more</li>
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<li>bower stuff is a dead end, waste of time, too many issues</li>
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<li>Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of <code>fonts</code>)</li>
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<li>Start working on DSpace 5.1 → 5.5 port:</li>
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</ul>
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<pre><code>$ git checkout -b 55new 5_x-prod
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$ git reset --hard ilri/5_x-prod
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$ git rebase -i dspace-5.5
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</code></pre>
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<p></p></description>
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</item>
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<item>
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<title>July, 2016</title>
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<link>https://alanorth.github.io/cgspace-notes/2016-07/</link>
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<pubDate>Fri, 01 Jul 2016 10:53:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-07/</guid>
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<description><h2 id="2016-07-01">2016-07-01</h2>
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<ul>
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<li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li>
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<li>I think this query should find and replace all authors that have &ldquo;,&rdquo; at the end of their names:</li>
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</ul>
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<pre><code>dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
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UPDATE 95
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dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
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text_value
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------------
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(0 rows)
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</code></pre>
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<ul>
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<li>In this case the select query was showing 95 results before the update</li>
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</ul>
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<p></p></description>
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</item>
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<item>
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<title>June, 2016</title>
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<link>https://alanorth.github.io/cgspace-notes/2016-06/</link>
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<pubDate>Wed, 01 Jun 2016 10:53:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-06/</guid>
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<description><h2 id="2016-06-01">2016-06-01</h2>
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<ul>
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<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
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<li>After reading the <a href="https://www.oclc.org/support/services/contentdm/help/server-admin-help/oai-support.en.html">ContentDM documentation</a> I found IFPRI&rsquo;s OAI endpoint: <a href="http://ebrary.ifpri.org/oai/oai.php">http://ebrary.ifpri.org/oai/oai.php</a></li>
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<li>After reading the <a href="https://www.openarchives.org/OAI/openarchivesprotocol.html">OAI documentation</a> and testing with an <a href="http://validator.oaipmh.com/">OAI validator</a> I found out how to get their publications</li>
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<li>This is their publications set: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc">http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&amp;from=2016-01-01&amp;set=p15738coll2&amp;metadataPrefix=oai_dc</a></li>
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<li>You can see the others by using the OAI <code>ListSets</code> verb: <a href="http://ebrary.ifpri.org/oai/oai.php?verb=ListSets">http://ebrary.ifpri.org/oai/oai.php?verb=ListSets</a></li>
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<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
|
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</ul>
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|
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<p></p></description>
|
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</item>
|
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<item>
|
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<title>May, 2016</title>
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<link>https://alanorth.github.io/cgspace-notes/2016-05/</link>
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<pubDate>Sun, 01 May 2016 23:06:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-05/</guid>
|
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<description><h2 id="2016-05-01">2016-05-01</h2>
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<ul>
|
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<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
|
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<li>I have blocked access to the API now</li>
|
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<li>There are 3,000 IPs accessing the REST API in a 24-hour period!</li>
|
||
</ul>
|
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<pre><code># awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l
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3168
|
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</code></pre>
|
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<p></p></description>
|
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</item>
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<item>
|
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<title>April, 2016</title>
|
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<link>https://alanorth.github.io/cgspace-notes/2016-04/</link>
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<pubDate>Mon, 04 Apr 2016 11:06:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-04/</guid>
|
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<description><h2 id="2016-04-04">2016-04-04</h2>
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<ul>
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<li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li>
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<li>We are backing up all logs in the log folder, including useless stuff like solr, cocoon, handle-plugin, etc</li>
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<li>After running DSpace for over five years I&rsquo;ve never needed to look in any other log file than dspace.log, leave alone one from last year!</li>
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<li>This will save us a few gigs of backup space we&rsquo;re paying for on S3</li>
|
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<li>Also, I noticed the <code>checker</code> log has some errors we should pay attention to:</li>
|
||
</ul>
|
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|
||
<p></p></description>
|
||
</item>
|
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|
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<item>
|
||
<title>March, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-03/</link>
|
||
<pubDate>Wed, 02 Mar 2016 16:50:00 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-03/</guid>
|
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<description><h2 id="2016-03-02">2016-03-02</h2>
|
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<ul>
|
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<li>Looking at issues with author authorities on CGSpace</li>
|
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<li>For some reason we still have the <code>index-lucene-update</code> cron job active on CGSpace, but I&rsquo;m pretty sure we don&rsquo;t need it as of the latest few versions of Atmire&rsquo;s Listings and Reports module</li>
|
||
<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
|
||
</ul>
|
||
|
||
<p></p></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>February, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-02/</link>
|
||
<pubDate>Fri, 05 Feb 2016 13:18:00 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-02/</guid>
|
||
<description><h2 id="2016-02-05">2016-02-05</h2>
|
||
|
||
<ul>
|
||
<li>Looking at some DAGRIS data for Abenet Yabowork</li>
|
||
<li>Lots of issues with spaces, newlines, etc causing the import to fail</li>
|
||
<li>I noticed we have a very <em>interesting</em> list of countries on CGSpace:</li>
|
||
</ul>
|
||
|
||
<p><img src="https://alanorth.github.io/cgspace-notes/cgspace-notes/2016/02/cgspace-countries.png" alt="CGSpace country list" /></p>
|
||
|
||
<ul>
|
||
<li>Not only are there 49,000 countries, we have some blanks (25)&hellip;</li>
|
||
<li>Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;</li>
|
||
</ul>
|
||
|
||
<p></p></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>January, 2016</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2016-01/</link>
|
||
<pubDate>Wed, 13 Jan 2016 13:18:00 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2016-01/</guid>
|
||
<description><h2 id="2016-01-13">2016-01-13</h2>
|
||
|
||
<ul>
|
||
<li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li>
|
||
<li>I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.</li>
|
||
<li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li>
|
||
</ul>
|
||
|
||
<p></p></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>December, 2015</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2015-12/</link>
|
||
<pubDate>Wed, 02 Dec 2015 13:18:00 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2015-12/</guid>
|
||
<description><h2 id="2015-12-02">2015-12-02</h2>
|
||
|
||
<ul>
|
||
<li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li>
|
||
</ul>
|
||
|
||
<pre><code># cd /home/dspacetest.cgiar.org/log
|
||
# ls -lh dspace.log.2015-11-18*
|
||
-rw-rw-r-- 1 tomcat7 tomcat7 2.0M Nov 18 23:59 dspace.log.2015-11-18
|
||
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
|
||
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
|
||
</code></pre>
|
||
|
||
<p></p></description>
|
||
</item>
|
||
|
||
<item>
|
||
<title>November, 2015</title>
|
||
<link>https://alanorth.github.io/cgspace-notes/2015-11/</link>
|
||
<pubDate>Mon, 23 Nov 2015 17:00:57 +0300</pubDate>
|
||
|
||
<guid>https://alanorth.github.io/cgspace-notes/2015-11/</guid>
|
||
<description><h2 id="2015-11-22">2015-11-22</h2>
|
||
|
||
<ul>
|
||
<li>CGSpace went down</li>
|
||
<li>Looks like DSpace exhausted its PostgreSQL connection pool</li>
|
||
<li>Last week I had increased the limit from 30 to 60, which seemed to help, but now there are many more idle connections:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
|
||
78
|
||
</code></pre>
|
||
|
||
<p></p></description>
|
||
</item>
|
||
|
||
</channel>
|
||
</rss> |