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<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>
2019-02-01 20:45:50 +01:00
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2020-05-02 09:08:14 +02:00
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<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><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>
2020-04-02 09:54:46 +02:00
<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>
<pre><code>dspace=# select * from collection2item where item_id = '80278';
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>
2020-03-02 11:38:10 +01:00
<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>
2020-04-02 09:55:42 +02:00
<p class="blog-post-meta"><time datetime="2017-01-02T10:43:00+03:00">Mon Jan 02, 2017</time> by Alan Orth in
2020-03-02 11:38:10 +01:00
<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>
2020-02-02 16:15:48 +01:00
<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>
2020-04-02 09:55:42 +02:00
<p class="blog-post-meta"><time datetime="2016-12-02T10:43:00+03:00">Fri Dec 02, 2016</time> by Alan Orth in
2020-02-02 16:15:48 +01:00
<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>
<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;)
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;)
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;)
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;)
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;)
</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>
2020-01-06 10:14:44 +01:00
<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>
2020-04-02 09:55:42 +02:00
<p class="blog-post-meta"><time datetime="2016-11-01T09:21:00+03:00">Tue Nov 01, 2016</time> by Alan Orth in
2020-01-06 10:14:44 +01:00
2020-01-28 11:01:42 +01:00
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
2020-01-06 10:14:44 +01:00
</p>
</header>
<h2 id="2016-11-01">2016-11-01</h2>
<ul>
2020-01-27 15:20:44 +01:00
<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>
2020-01-06 10:14:44 +01:00
</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>
2019-12-01 10:29:49 +01:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-10/">October, 2016</a></h2>
2020-04-02 09:55:42 +02:00
<p class="blog-post-meta"><time datetime="2016-10-03T15:53:00+03:00">Mon Oct 03, 2016</time> by Alan Orth in
2019-12-01 10:29:49 +01:00
2020-01-28 11:01:42 +01:00
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
2019-12-01 10:29:49 +01:00
</p>
</header>
2019-12-17 13:49:24 +01:00
<h2 id="2016-10-03">2016-10-03</h2>
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<ul>
2020-04-13 16:24:05 +02:00
<li>Testing adding <a href="https://wiki.lyrasis.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>
2019-12-01 10:29:49 +01:00
<li>Need to test the following scenarios to see how author order is affected:
<ul>
<li>ORCIDs only</li>
<li>ORCIDs plus normal authors</li>
</ul>
</li>
2020-01-27 15:20:44 +01:00
<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>
2019-12-01 10:29:49 +01:00
</ul>
<pre><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2016-10/'>Read more →</a>
</article>
2019-11-04 15:41:19 +01:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-09/">September, 2016</a></h2>
2020-04-02 09:55:42 +02:00
<p class="blog-post-meta"><time datetime="2016-09-01T15:53:00+03:00">Thu Sep 01, 2016</time> by Alan Orth in
2019-11-04 15:41:19 +01:00
2020-01-28 11:01:42 +01:00
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
2019-11-04 15:41:19 +01:00
</p>
</header>
2019-12-17 13:49:24 +01:00
<h2 id="2016-09-01">2016-09-01</h2>
2019-11-04 15:41:19 +01:00
<ul>
<li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li>
2020-01-27 15:20:44 +01:00
<li>Discuss how the migration of CGIAR&rsquo;s Active Directory to a flat structure will break our LDAP groups in DSpace</li>
2019-11-04 15:41:19 +01:00
<li>We had been using <code>DC=ILRI</code> to determine whether a user was ILRI or not</li>
2019-11-28 16:30:45 +01:00
<li>It looks like we might be able to use OUs now, instead of DCs:</li>
2019-11-04 15:41:19 +01:00
</ul>
2019-11-28 16:30:45 +01:00
<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;
</code></pre>
2019-11-04 15:41:19 +01:00
<a href='https://alanorth.github.io/cgspace-notes/2016-09/'>Read more →</a>
</article>
2019-10-28 12:43:25 +01:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-08/">August, 2016</a></h2>
2020-04-02 09:55:42 +02:00
<p class="blog-post-meta"><time datetime="2016-08-01T15:53:00+03:00">Mon Aug 01, 2016</time> by Alan Orth in
2019-10-28 12:43:25 +01:00
2020-01-28 11:01:42 +01:00
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
2019-10-28 12:43:25 +01:00
</p>
</header>
2019-12-17 13:49:24 +01:00
<h2 id="2016-08-01">2016-08-01</h2>
2019-10-28 12:43:25 +01:00
<ul>
<li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li>
<li>Play with upgrading Mirage 2 dependencies in <code>bower.json</code> because most are several versions of out date</li>
<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>
<li>bower stuff is a dead end, waste of time, too many issues</li>
<li>Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of <code>fonts</code>)</li>
2019-11-28 16:30:45 +01:00
<li>Start working on DSpace 5.15.5 port:</li>
</ul>
2019-10-28 12:43:25 +01:00
<pre><code>$ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
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</code></pre>
2019-10-28 12:43:25 +01:00
<a href='https://alanorth.github.io/cgspace-notes/2016-08/'>Read more →</a>
</article>
2019-10-01 16:31:40 +02:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-07/">July, 2016</a></h2>
2020-04-02 09:55:42 +02:00
<p class="blog-post-meta"><time datetime="2016-07-01T10:53:00+03:00">Fri Jul 01, 2016</time> by Alan Orth in
2019-10-01 16:31:40 +02:00
2020-01-28 11:01:42 +01:00
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
2019-10-01 16:31:40 +02:00
</p>
</header>
2019-12-17 13:49:24 +01:00
<h2 id="2016-07-01">2016-07-01</h2>
2019-10-01 16:31:40 +02:00
<ul>
<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>
2019-11-28 16:30:45 +01:00
<li>I think this query should find and replace all authors that have &ldquo;,&rdquo; at the end of their names:</li>
</ul>
2019-10-01 16:31:40 +02:00
<pre><code>dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
UPDATE 95
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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------------
(0 rows)
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</code></pre><ul>
<li>In this case the select query was showing 95 results before the update</li>
2019-10-01 16:31:40 +02:00
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-07/'>Read more →</a>
</article>
2019-09-01 09:41:30 +02:00
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-06/">June, 2016</a></h2>
2020-04-02 09:55:42 +02:00
<p class="blog-post-meta"><time datetime="2016-06-01T10:53:00+03:00">Wed Jun 01, 2016</time> by Alan Orth in
2019-09-01 09:41:30 +02:00
2020-01-28 11:01:42 +01:00
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
2019-09-01 09:41:30 +02:00
</p>
</header>
2019-12-17 13:49:24 +01:00
<h2 id="2016-06-01">2016-06-01</h2>
2019-09-01 09:41:30 +02:00
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
2020-01-27 15:20:44 +01:00
<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>
2019-09-01 09:41:30 +02:00
<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>
<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>
<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>
<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>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2016-06/'>Read more →</a>
</article>
2019-02-01 20:45:50 +01:00
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<h4>Recent Posts</h4>
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2020-05-02 09:08:14 +02:00
<li><a href="/cgspace-notes/2020-05/">May, 2020</a></li>
2020-04-02 09:54:46 +02:00
<li><a href="/cgspace-notes/2020-04/">April, 2020</a></li>
2020-03-02 11:38:10 +01:00
<li><a href="/cgspace-notes/2020-03/">March, 2020</a></li>
2020-02-02 16:15:48 +01:00
<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
2020-01-14 19:40:41 +01:00
<li><a href="/cgspace-notes/2020-01/">January, 2020</a></li>
2019-02-01 20:45:50 +01:00
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<h4>Links</h4>
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<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>
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2019-02-01 20:45:50 +01:00
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