<!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="2020-08-05T15:00:06+03:00" /> <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 0.74.1" /> <script type="application/ld+json"> { "@context": "http://schema.org", "@type": "Blog", "headline": "CGSpace Notes", "url" : "https://alanorth.github.io/cgspace-notes/", "author": { "@type": 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href="https://alanorth.github.io/cgspace-notes/index.xml" title="CGSpace Notes" /> </head> <body> <div class="blog-masthead"> <div class="container"> <nav class="nav blog-nav"> <a class="nav-link active" href="https://alanorth.github.io/cgspace-notes/">Home</a> </nav> </div> </div> <header class="blog-header"> <div class="container"> <h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1> <p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p> </div> </header> <div class="container"> <div class="row"> <div class="col-sm-8 blog-main"> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-06/">June, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-06-01T10:14:52+03:00">Thu Jun 01, 2017</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <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" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-05/">May, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-05-01T16:21:52+02:00">Mon May 01, 2017</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <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" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-04/">April, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-04-02T17:08:52+02:00">Sun Apr 02, 2017</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <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> <a href='https://alanorth.github.io/cgspace-notes/2017-04/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-03/">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> <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">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> <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> <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’ll be using <code>cg.identifier.ccafsprojectpii</code> as the field name</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2017-02/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-01/">January, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-01-02T10:43:00+03:00">Mon Jan 02, 2017</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <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’t work there either</li> <li>I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’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> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-12/">December, 2016</a></h2> <p class="blog-post-meta"><time datetime="2016-12-02T10:43:00+03:00">Fri Dec 02, 2016</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <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="TX157907838689377964651674089851855413607") 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="dc.title", transactionID="TX157907838689377964651674089851855413607") 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="THUMBNAIL", transactionID="TX157907838689377964651674089851855413607") 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="-1", transactionID="TX157907838689377964651674089851855413607") 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="TX157907838689377964651674089851855413607") </code></pre><ul> <li>I see thousands of them in the logs for the last few months, so it’s not related to the DSpace 5.5 upgrade</li> <li>I’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> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2016-11/">November, 2016</a></h2> <p class="blog-post-meta"><time datetime="2016-11-01T09:21:00+03:00">Tue Nov 01, 2016</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a> </p> </header> <h2 id="2016-11-01">2016-11-01</h2> <ul> <li>Add <code>dc.type</code> to the output options for Atmire’s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li> </ul> <p><img src="/cgspace-notes/2016/11/listings-and-reports.png" alt="Listings and Reports with output type"></p> <a href='https://alanorth.github.io/cgspace-notes/2016-11/'>Read more →</a> </article> <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> <p class="blog-post-meta"><time datetime="2016-10-03T15:53:00+03:00">Mon Oct 03, 2016</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a> </p> </header> <h2 id="2016-10-03">2016-10-03</h2> <ul> <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> <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> <li>I exported a random item’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> </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> <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> <p class="blog-post-meta"><time datetime="2016-09-01T15:53:00+03:00">Thu Sep 01, 2016</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a> </p> </header> <h2 id="2016-09-01">2016-09-01</h2> <ul> <li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li> <li>Discuss how the migration of CGIAR’s Active Directory to a flat structure will break our LDAP groups in DSpace</li> <li>We had been using <code>DC=ILRI</code> to determine whether a user was ILRI or not</li> <li>It looks like we might be able to use OUs now, instead of DCs:</li> </ul> <pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)" </code></pre> <a href='https://alanorth.github.io/cgspace-notes/2016-09/'>Read more →</a> </article> <nav class="blog-pagination"> <a class="btn btn-outline-primary" href="/cgspace-notes/page/4/" rel="prev" role="button">Previous page</a> <a class="btn btn-outline-primary" href="/cgspace-notes/page/6/" 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/2020-07/">August, 2020</a></li> <li><a href="/cgspace-notes/2020-07/">July, 2020</a></li> <li><a href="/cgspace-notes/2020-06/">June, 2020</a></li> <li><a href="/cgspace-notes/2020-05/">May, 2020</a></li> <li><a href="/cgspace-notes/2020-04/">April, 2020</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 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