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<meta property="og:description" content="2018-03-02
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Export a CSV of the IITA community metadata for Martin Mueller
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" />
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<meta name="twitter:description" content="2018-03-02
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Export a CSV of the IITA community metadata for Martin Mueller
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<title>March, 2018 | CGSpace Notes</title>
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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">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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<article class="blog-post">
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<header>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-03/">March, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-03-02T16:07:54+02:00">Fri Mar 02, 2018</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <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="2018-03-02">2018-03-02</h2>
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<ul>
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<li>Export a CSV of the IITA community metadata for Martin Mueller</li>
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</ul>
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<p></p>
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<h2 id="2018-03-06">2018-03-06</h2>
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<ul>
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<li>Add three new CCAFS project tags to <code>input-forms.xml</code> (<a href="https://github.com/ilri/DSpace/pull/357">#357</a>)</li>
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<li>Andrea from Macaroni Bros had sent me an email that CCAFS needs them</li>
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<li>Give Udana more feedback on his WLE records from last month</li>
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<li>There were some records using a non-breaking space in their AGROVOC subject field</li>
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<li>I checked and tested some author corrections from Peter from last week, and then applied them on CGSpace</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i Correct-309-authors-2018-03-06.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3
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$ ./delete-metadata-values.py -i Delete-3-Authors-2018-03-06.csv -db dspace -u dspace-p 'fuuu' -f dc.contributor.author -m 3
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</code></pre>
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<ul>
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<li>This time there were no errors in whitespace but I did have to correct one incorrectly encoded accent character</li>
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<li>Add new CRP subject “GRAIN LEGUMES AND DRYLAND CEREALS” to <code>input-forms.xml</code> (<a href="https://github.com/ilri/DSpace/pull/358">#358</a>)</li>
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<li>Merge the ORCID integration stuff in to <code>5_x-prod</code> for deployment on CGSpace soon (<a href="https://github.com/ilri/DSpace/pull/359">#359</a>)</li>
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<li>Deploy ORCID changes on CGSpace (linode18), run all system updates, and reboot the server</li>
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<li>Run all system updates on DSpace Test and reboot server</li>
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<li>I ran the <a href="https://gist.github.com/alanorth/24d8081a5dc25e2a4e27e548e7e2389c">orcid-authority-to-item.py</a> script on CGSpace and mapped 2,864 ORCID identifiers from Solr to item metadata</li>
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</ul>
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<pre><code>$ ./orcid-authority-to-item.py -db dspace -u dspace -p 'fuuu' -s http://localhost:8081/solr -d
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</code></pre>
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<ul>
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<li>I ran the DSpace cleanup script on CGSpace and it threw an error (as always):</li>
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</ul>
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<pre><code>Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
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Detail: Key (bitstream_id)=(150659) is still referenced from table "bundle".
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</code></pre>
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<ul>
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<li><p>The solution is, as always:</p>
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<pre><code>$ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (150659);'
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UPDATE 1
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</code></pre></li>
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<li><p>Apply the proposed PostgreSQL indexes from DS-3636 (pull request <a href="https://github.com/DSpace/DSpace/pull/1791/">#1791</a> on CGSpace (linode18)</p></li>
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</ul>
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<h2 id="2018-03-07">2018-03-07</h2>
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<ul>
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<li>Add CIAT author Mauricio Efren Sotelo Cabrera to controlled vocabulary for ORCID identifiers (<a href="https://github.com/ilri/DSpace/pull/360">#360</a>)</li>
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<li>Help Sisay proof 200 IITA records on DSpace Test</li>
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<li>Finally import Udana’s 24 items to <a href="https://cgspace.cgiar.org/handle/10568/36185">IWMI Journal Articles</a> on CGSpace</li>
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<li>Skype with James Stapleton to discuss CGSpace, ILRI website, CKM staff issues, etc</li>
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</ul>
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<h2 id="2018-03-08">2018-03-08</h2>
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<ul>
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<li>Looking at a CSV dump of the CIAT community I see there are tons of stupid text languages people add for their metadata</li>
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<li>This makes the CSV have tons of columns, for example <code>dc.title</code>, <code>dc.title[]</code>, <code>dc.title[en]</code>, <code>dc.title[eng]</code>, <code>dc.title[en_US]</code> and so on!</li>
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<li>I think I can fix — or at least normalize — them in the database:</li>
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</ul>
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<pre><code>dspace=# select distinct text_lang from metadatavalue where resource_type_id=2;
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text_lang
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-----------
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ethnob
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en
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spa
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EN
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En
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en_
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en_US
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E.
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EN_US
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en_U
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eng
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fr
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es_ES
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es
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(16 rows)
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dspace=# update metadatavalue set text_lang='en_US' where resource_type_id=2 and text_lang in ('en','EN','En','en_','EN_US','en_U','eng');
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UPDATE 122227
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dspacetest=# select distinct text_lang from metadatavalue where resource_type_id=2;
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text_lang
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-----------
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ethnob
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en_US
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spa
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E.
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fr
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es_ES
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es
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(9 rows)
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</code></pre>
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<ul>
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<li>On second inspection it looks like <code>dc.description.provenance</code> fields use the text_lang “en” so that’s probably why there are over 100,000 fields changed…</li>
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<li>If I skip that, there are about 2,000, which seems more reasonably like the amount of fields users have edited manually, or fucked up during CSV import, etc:</li>
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</ul>
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<pre><code>dspace=# update metadatavalue set text_lang='en_US' where resource_type_id=2 and text_lang in ('EN','En','en_','EN_US','en_U','eng');
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UPDATE 2309
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</code></pre>
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<ul>
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<li>I will apply this on CGSpace right now</li>
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<li>In other news, I was playing with adding ORCID identifiers to a dump of CIAT’s community via CSV in OpenRefine</li>
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<li>Using a series of filters, flags, and GREL expressions to isolate items for a certain author, I figured out how to add ORCID identifiers to the <code>cg.creator.id</code> field</li>
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<li>For example, a GREL expression in a custom text facet to get all items with <code>dc.contributor.author[en_US]</code> of a certain author with several name variations (this is how you use a logical OR in OpenRefine):</li>
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</ul>
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<pre><code>or(value.contains('Ceballos, Hern'), value.contains('Hernández Ceballos'))
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</code></pre>
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<ul>
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<li>Then you can flag or star matching items and then use a conditional to either set the value directly or add it to an existing value:</li>
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</ul>
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<pre><code>if(isBlank(value), "Hernan Ceballos: 0000-0002-8744-7918", value + "||Hernan Ceballos: 0000-0002-8744-7918")
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</code></pre>
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<ul>
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<li>One thing that bothers me is that this won’t honor author order</li>
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<li>It might be better to do batches of these in PostgreSQL with a script that takes the <code>place</code> column of an author into account when setting the <code>cg.creator.id</code></li>
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<li>I wrote a Python script to read the author names and ORCID identifiers from CSV and create matching <code>cg.creator.id</code> fields: <a href="https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050">add-orcid-identifiers-csv.py </a></li>
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<li>The CSV should have two columns: author name and ORCID identifier:</li>
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</ul>
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<pre><code>dc.contributor.author,cg.creator.id
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"Orth, Alan",Alan S. Orth: 0000-0002-1735-7458
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"Orth, A.",Alan S. Orth: 0000-0002-1735-7458
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</code></pre>
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<ul>
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<li>I didn’t integrate the ORCID API lookup for author names in this script for now because I was only interested in “tagging” old items for a few given authors</li>
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<li>I added ORCID identifers for 187 items by CIAT’s Hernan Ceballos, because that is what Elizabeth was trying to do manually!</li>
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<li>Also, I decided to add ORCID identifiers for all records from Peter, Abenet, and Sisay as well</li>
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</ul>
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<h2 id="2018-03-09">2018-03-09</h2>
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<ul>
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<li>Give James Stapleton input on Sisay’s KRAs</li>
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<li>Create a pull request to disable ORCID authority integration for <code>dc.contributor.author</code> in the submission forms and XMLUI display (<a href="https://github.com/ilri/DSpace/pull/363">#363</a>)</li>
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</ul>
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<h2 id="2018-03-11">2018-03-11</h2>
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<ul>
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<li>Peter also wrote to say he is having issues with the Atmire Listings and Reports module</li>
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<li>When I logged in to try it I get a blank white page after continuing and I see this in dspace.log.2018-03-11:</li>
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</ul>
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<pre><code>2018-03-11 11:38:15,592 WARN org.dspace.app.webui.servlet.InternalErrorServlet @ :session_id=91C2C0C59669B33A7683570F6010603A:internal_error:-- URL Was: https://cgspace.cgiar.or
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g/jspui/listings-and-reports
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-- Method: POST
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-- Parameters were:
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-- selected_admin_preset: "ilri authors2"
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-- load: "normal"
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-- next: "NEXT STEP >>"
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-- step: "1"
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org.apache.jasper.JasperException: java.lang.NullPointerException
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</code></pre>
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<ul>
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<li>Looks like I needed to remove the Humidtropics subject from Listings and Reports because it was looking for the terms and couldn’t find them</li>
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<li>I made a quick fix and it’s working now (<a href="https://github.com/ilri/DSpace/pull/364">#364</a>)</li>
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</ul>
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<h2 id="2018-03-12">2018-03-12</h2>
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<ul>
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<li>Increase upload size on CGSpace’s nginx config to 85MB so Sisay can upload some data</li>
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</ul>
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<h2 id="2018-03-13">2018-03-13</h2>
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<ul>
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<li>I created a new Linode server for DSpace Test (linode6623840) so I could try the block storage stuff, but when I went to add a 300GB volume it said that block storage capacity was exceeded in that datacenter (Newark, NJ)</li>
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<li>I deleted the Linode and created another one (linode6624164) in the Fremont, CA region</li>
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<li>After that I deployed the Ubuntu 16.04 image and attached a 300GB block storage volume to the image</li>
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<li>Magdalena wrote to ask why there was no Altmetric donut for an item on CGSpace, but there was one on the related CCAFS publication page</li>
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<li>It looks the the CCAFS publications page fetches the donut using its DOI, whereas CGSpace queries via Handle</li>
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<li>I will write to Altmetric support and ask them, as perhaps its part of a larger issue</li>
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<li>CGSpace item: <a href="https://cgspace.cgiar.org/handle/10568/89643">https://cgspace.cgiar.org/handle/10568/89643</a></li>
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<li>CCAFS publication page: <a href="https://ccafs.cgiar.org/publications/can-scenario-planning-catalyse-transformational-change-evaluating-climate-change-policy">https://ccafs.cgiar.org/publications/can-scenario-planning-catalyse-transformational-change-evaluating-climate-change-policy</a></li>
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<li>Peter tweeted the Handle link and now Altmetric shows the donut for both the DOI and the Handle</li>
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</ul>
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<h2 id="2018-03-14">2018-03-14</h2>
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<ul>
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<li>Help Abenet with a troublesome Listings and Report question for CIAT author Steve Beebe</li>
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<li>Continue migrating DSpace Test to the new server (linode6624164)</li>
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<li>I emailed ILRI service desk to update the DNS records for dspacetest.cgiar.org</li>
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<li>Abenet was having problems saving Listings and Reports configurations or layouts but I tested it and it works</li>
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</ul>
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<h2 id="2018-03-15">2018-03-15</h2>
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<ul>
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<li>Help Abenet troubleshoot the Listings and Reports issue again</li>
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<li>It looks like it’s an issue with the layouts, if you create a new layout that only has one type (<code>dc.identifier.citation</code>):</li>
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</ul>
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<p><img src="/cgspace-notes/2018/03/layout-only-citation.png" alt="Listing and Reports layout" /></p>
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<ul>
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<li>The error in the DSpace log is:</li>
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</ul>
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<pre><code>org.apache.jasper.JasperException: java.lang.ArrayIndexOutOfBoundsException: -1
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</code></pre>
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<ul>
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<li>The full error is here: <a href="https://gist.github.com/alanorth/ea47c092725960e39610db9b0c13f6ca">https://gist.github.com/alanorth/ea47c092725960e39610db9b0c13f6ca</a></li>
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<li>If I do a report for “Orth, Alan” with the same custom layout it works!</li>
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<li>I submitted a ticket to Atmire: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=589">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=589</a></li>
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<li>Small fix to the example citation text in Listings and Reports (<a href="https://github.com/ilri/DSpace/pull/365">#365</a>)</li>
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</ul>
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<h2 id="2018-03-16">2018-03-16</h2>
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<ul>
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<li>ICT made the DNS updates for dspacetest.cgiar.org late last night</li>
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<li>I have removed the old server (linode02 aka linode578611) in favor of linode19 aka linode6624164</li>
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<li>Looking at the CRP subjects on CGSpace I see there is one blank one so I’ll just fix it:</li>
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</ul>
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<pre><code>dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=230 and text_value='';
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</code></pre>
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<ul>
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<li>Copy all CRP subjects to a CSV to do the mass updates:</li>
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</ul>
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<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=230 group by text_value order by count desc) to /tmp/crps.csv with csv header;
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COPY 21
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</code></pre>
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<ul>
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<li>Once I prepare the new input forms (<a href="https://github.com/ilri/DSpace/issues/362">#362</a>) I will need to do the batch corrections:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i Correct-21-CRPs-2018-03-16.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.crp -t correct -m 230 -n -d
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</code></pre>
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<ul>
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<li>Create a pull request to update the input forms for the new CRP subject style (<a href="https://github.com/ilri/DSpace/pull/366">#366</a>)</li>
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</ul>
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<h2 id="2018-03-19">2018-03-19</h2>
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<ul>
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<li>Tezira has been having problems accessing CGSpace from the ILRI Nairobi campus since last week</li>
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<li>She is getting an HTTPS error apparently</li>
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<li>It’s working outside, and Ethiopian users seem to be having no issues so I’ve asked ICT to have a look</li>
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<li>CGSpace crashed this morning for about seven minutes and Dani restarted Tomcat</li>
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<li>Around that time there were an increase of SQL errors:</li>
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</ul>
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<pre><code>2018-03-19 09:10:54,856 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error -
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...
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2018-03-19 09:10:54,862 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL query singleTable Error -
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</code></pre>
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||
<ul>
|
||
<li>But these errors, I don’t even know what they mean, because a handful of them happen every day:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ grep -c 'ERROR org.dspace.storage.rdbms.DatabaseManager' dspace.log.2018-03-1*
|
||
dspace.log.2018-03-10:13
|
||
dspace.log.2018-03-11:15
|
||
dspace.log.2018-03-12:13
|
||
dspace.log.2018-03-13:13
|
||
dspace.log.2018-03-14:14
|
||
dspace.log.2018-03-15:13
|
||
dspace.log.2018-03-16:13
|
||
dspace.log.2018-03-17:13
|
||
dspace.log.2018-03-18:15
|
||
dspace.log.2018-03-19:90
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>There wasn’t even a lot of traffic at the time (8–9 AM):</li>
|
||
</ul>
|
||
|
||
<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "19/Mar/2018:0[89]:" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
|
||
92 40.77.167.197
|
||
92 83.103.94.48
|
||
96 40.77.167.175
|
||
116 207.46.13.178
|
||
122 66.249.66.153
|
||
140 95.108.181.88
|
||
196 213.55.99.121
|
||
206 197.210.168.174
|
||
207 104.196.152.243
|
||
294 54.198.169.202
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Well there is a hint in Tomcat’s <code>catalina.out</code>:</li>
|
||
</ul>
|
||
|
||
<pre><code>Mon Mar 19 09:05:28 UTC 2018 | Query:id: 92032 AND type:2
|
||
Exception in thread "http-bio-127.0.0.1-8081-exec-280" java.lang.OutOfMemoryError: Java heap space
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>So someone was doing something heavy somehow… my guess is content and usage stats!</li>
|
||
<li>ICT responded that they “fixed” the CGSpace connectivity issue in Nairobi without telling me the problem</li>
|
||
<li>When I asked, Robert Okal said CGNET messed up when updating the DNS for cgspace.cgiar.org last week</li>
|
||
<li>I told him that my request last week was for dspacetest.cgiar.org, not cgspace.cgiar.org!</li>
|
||
<li>So they updated the wrong fucking DNS records</li>
|
||
<li>Magdalena from CCAFS wrote to ask about one record that has a bunch of metadata missing in her Listings and Reports export</li>
|
||
<li>It appears to be this one: <a href="https://cgspace.cgiar.org/handle/10568/83473?show=full">https://cgspace.cgiar.org/handle/10568/83473?show=full</a></li>
|
||
<li>The title is “Untitled” and there is some metadata but indeed the citation is missing</li>
|
||
<li>I don’t know what would cause that</li>
|
||
</ul>
|
||
|
||
<h2 id="2018-03-20">2018-03-20</h2>
|
||
|
||
<ul>
|
||
<li>DSpace Test has been down for a few hours with SQL and memory errors starting this morning:</li>
|
||
</ul>
|
||
|
||
<pre><code>2018-03-20 08:47:10,177 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error -
|
||
...
|
||
2018-03-20 08:53:11,624 ERROR org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter @ Serious Error Occurred Processing Request!
|
||
org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.OutOfMemoryError: Java heap space
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>I have no idea why it crashed</li>
|
||
<li>I ran all system updates and rebooted it</li>
|
||
<li>Abenet told me that one of Lance Robinson’s ORCID iDs on CGSpace is incorrect</li>
|
||
<li>I will remove it from the controlled vocabulary (<a href="https://github.com/ilri/DSpace/pull/367">#367</a>) and update any items using the old one:</li>
|
||
</ul>
|
||
|
||
<pre><code>dspace=# update metadatavalue set text_value='Lance W. Robinson: 0000-0002-5224-8644' where resource_type_id=2 and metadata_field_id=240 and text_value like '%0000-0002-6344-195X%';
|
||
UPDATE 1
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Communicate with DSpace editors on Yammer about being more careful about spaces and character editing when doing manual metadata edits</li>
|
||
<li>Merge the changes to CRP names to the <code>5_x-prod</code> branch and deploy on CGSpace (<a href="https://github.com/ilri/DSpace/pull/363">#363</a>)</li>
|
||
<li>Run corrections for CRP names in the database:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p 'fuuu'
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Run all system updates on CGSpace (linode18) and reboot the server</li>
|
||
<li>I started a full Discovery re-index on CGSpace because of the updated CRPs</li>
|
||
<li>I see this error in the DSpace log:</li>
|
||
</ul>
|
||
|
||
<pre><code>2018-03-20 19:03:14,844 ERROR com.atmire.dspace.discovery.AtmireSolrService @ No choices plugin was configured for field "dc_contributor_author".
|
||
java.lang.IllegalArgumentException: No choices plugin was configured for field "dc_contributor_author".
|
||
at org.dspace.content.authority.ChoiceAuthorityManager.getLabel(ChoiceAuthorityManager.java:261)
|
||
at org.dspace.content.authority.ChoiceAuthorityManager.getLabel(ChoiceAuthorityManager.java:249)
|
||
at org.dspace.browse.SolrBrowseCreateDAO.additionalIndex(SolrBrowseCreateDAO.java:215)
|
||
at com.atmire.dspace.discovery.AtmireSolrService.buildDocument(AtmireSolrService.java:662)
|
||
at com.atmire.dspace.discovery.AtmireSolrService.indexContent(AtmireSolrService.java:807)
|
||
at com.atmire.dspace.discovery.AtmireSolrService.updateIndex(AtmireSolrService.java:876)
|
||
at org.dspace.discovery.SolrServiceImpl.createIndex(SolrServiceImpl.java:370)
|
||
at org.dspace.discovery.IndexClient.main(IndexClient.java:117)
|
||
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
|
||
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||
at java.lang.reflect.Method.invoke(Method.java:498)
|
||
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226)
|
||
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78)
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>I have to figure that one out…</li>
|
||
</ul>
|
||
|
||
<h2 id="2018-03-21">2018-03-21</h2>
|
||
|
||
<ul>
|
||
<li>Looks like the indexing gets confused that there is still data in the <code>authority</code> column</li>
|
||
<li>Unfortunately this causes those items to simply not be indexed, which users noticed because item counts were cut in half and old items showed up in RSS!</li>
|
||
<li>Since we’ve migrated the ORCID identifiers associated with the authority data to the <code>cg.creator.id</code> field we can nullify the authorities remaining in the database:</li>
|
||
</ul>
|
||
|
||
<pre><code class="language-sql">dspace=# UPDATE metadatavalue SET authority=NULL WHERE resource_type_id=2 AND metadata_field_id=3 AND authority IS NOT NULL;
|
||
UPDATE 195463
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>After this the indexing works as usual and item counts and facets are back to normal</li>
|
||
<li>Send Peter a list of all authors to correct:</li>
|
||
</ul>
|
||
|
||
<pre><code class="language-sql">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 header;
|
||
COPY 56156
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Afterwards we’ll want to do some batch tagging of ORCID identifiers to these names</li>
|
||
<li>CGSpace crashed again this afternoon, I’m not sure of the cause but there are a lot of SQL errors in the DSpace log:</li>
|
||
</ul>
|
||
|
||
<pre><code>2018-03-21 15:11:08,166 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error -
|
||
java.sql.SQLException: Connection has already been closed.
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>I have no idea why so many connections were abandoned this afternoon:</li>
|
||
</ul>
|
||
|
||
<pre><code># grep 'Mar 21, 2018' /var/log/tomcat7/catalina.out | grep -c 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon'
|
||
268
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>DSpace Test crashed again due to Java heap space, this is from the DSpace log:</li>
|
||
</ul>
|
||
|
||
<pre><code>2018-03-21 15:18:48,149 ERROR org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter @ Serious Error Occurred Processing Request!
|
||
org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.OutOfMemoryError: Java heap space
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>And this is from the Tomcat Catalina log:</li>
|
||
</ul>
|
||
|
||
<pre><code>Mar 21, 2018 11:20:00 AM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
|
||
SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]]
|
||
java.lang.OutOfMemoryError: Java heap space
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>But there are tons of heap space errors on DSpace Test actually:</li>
|
||
</ul>
|
||
|
||
<pre><code># grep -c 'java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out
|
||
319
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>I guess we need to give it more RAM because it now has CGSpace’s large Solr core</li>
|
||
<li>I will increase the memory from 3072m to 4096m</li>
|
||
<li>Update <a href="https://github.com/ilri/rmg-ansible-public">Ansible playbooks</a> to use <a href="https://jdbc.postgresql.org/">PostgreSQL JBDC driver</a> 42.2.2</li>
|
||
<li>Deploy the new JDBC driver on DSpace Test</li>
|
||
<li>I’m also curious to see how long the <code>dspace index-discovery -b</code> takes on DSpace Test where the DSpace installation directory is on one of Linode’s new block storage volumes</li>
|
||
</ul>
|
||
|
||
<pre><code>$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
|
||
|
||
real 208m19.155s
|
||
user 8m39.138s
|
||
sys 2m45.135s
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>So that’s about three times as long as it took on CGSpace this morning</li>
|
||
<li>I should also check the raw read speed with <code>hdparm -tT /dev/sdc</code></li>
|
||
<li>Looking at Peter’s author corrections there are some mistakes due to Windows 1252 encoding</li>
|
||
<li>I need to find a way to filter these easily with OpenRefine</li>
|
||
<li>For example, Peter has inadvertantly introduced Unicode character 0xfffd into several fields</li>
|
||
<li>I can search for Unicode values by their hex code in OpenRefine using the following GREL expression:</li>
|
||
</ul>
|
||
|
||
<pre><code>isNotNull(value.match(/.*\ufffd.*/))
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>I need to be able to add many common characters though so that it is useful to copy and paste into a new project to find issues</li>
|
||
</ul>
|
||
|
||
<h2 id="2018-03-22">2018-03-22</h2>
|
||
|
||
<ul>
|
||
<li>Add ORCID identifier for Silvia Alonso</li>
|
||
<li>Update my Mirage 2 setup notes for Ubuntu 18.04: <a href="https://gist.github.com/alanorth/9bfd29feb7d2e836a9d417633319b3f5">https://gist.github.com/alanorth/9bfd29feb7d2e836a9d417633319b3f5</a></li>
|
||
</ul>
|
||
|
||
<h2 id="2018-03-24">2018-03-24</h2>
|
||
|
||
<ul>
|
||
<li>More work on the Ubuntu 18.04 readiness stuff for the <a href="https://github.com/ilri/rmg-ansible-public">Ansible playbooks</a></li>
|
||
<li>The playbook now uses the system’s Ruby and Node.js so I don’t have to manually install RVM and NVM after</li>
|
||
</ul>
|
||
|
||
<h2 id="2018-03-25">2018-03-25</h2>
|
||
|
||
<ul>
|
||
<li>Looking at Peter’s author corrections and trying to work out a way to find errors in OpenRefine easily</li>
|
||
<li>I can find all names that have acceptable characters using a GREL expression like:</li>
|
||
</ul>
|
||
|
||
<pre><code>isNotNull(value.match(/.*[a-zA-ZáÁéèïíñØøöóúü].*/))
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>But it’s probably better to just say which characters I know for sure are not valid (like parentheses, pipe, or weird Unicode characters):</li>
|
||
</ul>
|
||
|
||
<pre><code>or(
|
||
isNotNull(value.match(/.*[(|)].*/)),
|
||
isNotNull(value.match(/.*\uFFFD.*/)),
|
||
isNotNull(value.match(/.*\u00A0.*/)),
|
||
isNotNull(value.match(/.*\u200A.*/))
|
||
)
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>And here’s one combined GREL expression to check for items marked as to delete or check so I can flag them and export them to a separate CSV (though perhaps it’s time to add delete support to my <code>fix-metadata-values.py</code> script:</li>
|
||
</ul>
|
||
|
||
<pre><code>or(
|
||
isNotNull(value.match(/.*delete.*/i)),
|
||
isNotNull(value.match(/.*remove.*/i)),
|
||
isNotNull(value.match(/.*check.*/i))
|
||
)
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li><p>So I guess the routine is in OpenRefine is:</p>
|
||
|
||
<ul>
|
||
<li>Transform: trim leading/trailing whitespace</li>
|
||
<li>Transform: collapse consecutive whitespace</li>
|
||
<li>Custom text facet for items to delete/check</li>
|
||
<li>Custom text facet for illegal characters</li>
|
||
</ul></li>
|
||
|
||
<li><p>Test the corrections and deletions locally, then run them on CGSpace:</p></li>
|
||
</ul>
|
||
|
||
<pre><code>$ ./fix-metadata-values.py -i /tmp/Correct-2928-Authors-2018-03-21.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3
|
||
$ ./delete-metadata-values.py -i /tmp/Delete-8-Authors-2018-03-21.csv -f dc.contributor.author -m 3 -db dspacetest -u dspace -p 'fuuu'
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Afterwards I started a full Discovery reindexing on both CGSpace and DSpace Test</li>
|
||
<li>CGSpace took 76m28.292s</li>
|
||
<li>DSpace Test took 194m56.048s</li>
|
||
</ul>
|
||
|
||
<h2 id="2018-03-26">2018-03-26</h2>
|
||
|
||
<ul>
|
||
<li>Atmire got back to me about the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=589">Listings and Reports issue</a> and said it’s caused by items that have missing <code>dc.identifier.citation</code> fields</li>
|
||
<li>The will send a fix</li>
|
||
</ul>
|
||
|
||
<h2 id="2018-03-27">2018-03-27</h2>
|
||
|
||
<ul>
|
||
<li>Atmire got back with an updated quote about the DSpace 5.8 compatibility so I’ve forwarded it to Peter</li>
|
||
</ul>
|
||
|
||
<h2 id="2018-03-28">2018-03-28</h2>
|
||
|
||
<ul>
|
||
<li>DSpace Test crashed due to heap space so I’ve increased it from 4096m to 5120m</li>
|
||
<li>The error in Tomcat’s <code>catalina.out</code> was:</li>
|
||
</ul>
|
||
|
||
<pre><code>Exception in thread "RMI TCP Connection(idle)" java.lang.OutOfMemoryError: Java heap space
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>Add ISI Journal (cg.isijournal) as an option in Atmire’s Listing and Reports layout (<a href="https://github.com/ilri/DSpace/pull/370">#370</a>) for Abenet</li>
|
||
<li>I noticed a few hundred CRPs using the old capitalized formatting so I corrected them:</li>
|
||
</ul>
|
||
|
||
<pre><code>$ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db cgspace -u cgspace -p 'fuuu'
|
||
Fixed 29 occurences of: CLIMATE CHANGE, AGRICULTURE AND FOOD SECURITY
|
||
Fixed 7 occurences of: WATER, LAND AND ECOSYSTEMS
|
||
Fixed 19 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH
|
||
Fixed 100 occurences of: ROOTS, TUBERS AND BANANAS
|
||
Fixed 31 occurences of: HUMIDTROPICS
|
||
Fixed 21 occurences of: MAIZE
|
||
Fixed 11 occurences of: POLICIES, INSTITUTIONS, AND MARKETS
|
||
Fixed 28 occurences of: GRAIN LEGUMES
|
||
Fixed 3 occurences of: FORESTS, TREES AND AGROFORESTRY
|
||
Fixed 5 occurences of: GENEBANKS
|
||
</code></pre>
|
||
|
||
<ul>
|
||
<li>That’s weird because we just updated them last week…</li>
|
||
<li>Create a pull request to enable searching by ORCID identifier (<code>cg.creator.id</code>) in Discovery and Listings and Reports (<a href="https://github.com/ilri/DSpace/pull/371">#371</a>)</li>
|
||
<li>I will test it on DSpace Test first!</li>
|
||
<li>Fix one missing XMLUI string for “Access Status” (cg.identifier.status)</li>
|
||
<li>Run all system updates on DSpace Test and reboot the machine</li>
|
||
</ul>
|
||
|
||
|
||
|
||
|
||
|
||
</article>
|
||
|
||
|
||
|
||
</div> <!-- /.blog-main -->
|
||
|
||
<aside class="col-sm-3 ml-auto blog-sidebar">
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Recent Posts</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
|
||
<li><a href="/cgspace-notes/2018-06/">June, 2018</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-05/">May, 2018</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-04/">April, 2018</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-03/">March, 2018</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2018-02/">February, 2018</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Links</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
||
|
||
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
||
|
||
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
</aside>
|
||
|
||
|
||
</div> <!-- /.row -->
|
||
</div> <!-- /.container -->
|
||
|
||
|
||
|
||
<footer class="blog-footer">
|
||
<p>
|
||
|
||
Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
|
||
|
||
</p>
|
||
<p>
|
||
<a href="#">Back to top</a>
|
||
</p>
|
||
</footer>
|
||
|
||
|
||
</body>
|
||
|
||
</html>
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