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<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-06/">June, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-06-01T10:14:52+03:00">Thu Jun 01, 2017</time> by Alan Orth in
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<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/notes/" rel="tag">Notes</a>
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<h2 id="2017-06-01">2017-06-01</h2>
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<ul>
<li>After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes</li>
<li>The <code>cg.identifier.wletheme</code> field will be used for both Phase I and Phase II Research Themes</li>
2020-01-27 15:20:44 +01:00
<li>Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there</li>
2018-02-11 17:28:23 +01:00
<li>The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo;</li>
<li>Tagged all items in the current Phase I collections with their appropriate themes</li>
<li>Create pull request to add Phase II research themes to the submission form: <a href="https://github.com/ilri/DSpace/pull/328">#328</a></li>
<li>Add <code>cg.subject.system</code> to CGSpace metadata registry, for subject from the upcoming CGIAR Library migration</li>
</ul>
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<h2 id="2017-06-04">2017-06-04</h2>
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<ul>
<li>After adding <code>cg.identifier.wletheme</code> to 1106 WLE items I can see the field on XMLUI but not in REST!</li>
<li>Strangely it happens on DSpace Test AND on CGSpace!</li>
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<li>I tried to re-index Discovery but it didn&rsquo;t fix it</li>
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<li>Run all system updates on DSpace Test and reboot the server</li>
<li>After rebooting the server (and therefore restarting Tomcat) the new metadata field is available</li>
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<li>I&rsquo;ve sent a message to the dspace-tech mailing list to ask if this is a bug and whether I should file a Jira ticket</li>
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</ul>
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<h2 id="2016-06-05">2016-06-05</h2>
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<ul>
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<li>Rename WLE&rsquo;s &ldquo;Research Themes&rdquo; sub-community to &ldquo;WLE Phase I Research Themes&rdquo; on DSpace Test so Macaroni Bros can continue their testing</li>
<li>Macaroni Bros tested it and said it&rsquo;s fine, so I renamed it on CGSpace as well</li>
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<li>Working on how to automate the extraction of the CIAT Book chapters, doing some magic in OpenRefine to extract page fromto from cg.identifier.url and dc.format.extent, respectively:
<ul>
<li>cg.identifier.url: <code>value.split(&quot;page=&quot;, &quot;&quot;)[1]</code></li>
<li>dc.format.extent: <code>value.replace(&quot;p. &quot;, &quot;&quot;).split(&quot;-&quot;)[1].toNumber() - value.replace(&quot;p. &quot;, &quot;&quot;).split(&quot;-&quot;)[0].toNumber()</code></li>
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</ul>
</li>
<li>Finally, after some filtering to see which small outliers there were (based on dc.format.extent using &ldquo;p. 1-14&rdquo; vs &ldquo;29 p.&quot;), create a new column with last page number:
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<ul>
<li><code>cells[&quot;dc.page.from&quot;].value.toNumber() + cells[&quot;dc.format.pages&quot;].value.toNumber()</code></li>
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</ul>
</li>
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<li>Then create a new, unique file name to be used in the output, based on a SHA1 of the dc.title and with a description:
<ul>
<li>dc.page.to: <code>value.split(&quot; &quot;)[0].replace(&quot;,&quot;,&quot;&quot;).toLowercase() + &quot;-&quot; + sha1(value).get(1,9) + &quot;.pdf__description:&quot; + cells[&quot;dc.type&quot;].value</code></li>
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</ul>
</li>
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<li>Start processing 769 records after filtering the following (there are another 159 records that have some other format, or for example they have their own PDF which I will process later), using a modified <code>generate-thumbnails.py</code> script to read certain fields and then pass to GhostScript:
<ul>
<li>cg.identifier.url: <code>value.contains(&quot;page=&quot;)</code></li>
<li>dc.format.extent: <code>or(value.contains(&quot;p. &quot;),value.contains(&quot; p.&quot;))</code></li>
<li>Command like: <code>$ gs -dNOPAUSE -dBATCH -dFirstPage=14 -dLastPage=27 -sDEVICE=pdfwrite -sOutputFile=beans.pdf -f 12605-1.pdf</code></li>
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</ul>
</li>
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<li>17 of the items have issues with incorrect page number ranges, and upon closer inspection they do not appear in the referenced PDF</li>
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<li>I&rsquo;ve flagged them and proceeded without them (752 total) on DSpace Test:</li>
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</ul>
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<pre><code>$ JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot; [dspace]/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/93843 --source /home/aorth/src/CIAT-Books/SimpleArchiveFormat/ --mapfile=/tmp/ciat-books.map &amp;&gt; /tmp/ciat-books.log
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</code></pre><ul>
<li>I went and did some basic sanity checks on the remaining items in the CIAT Book Chapters and decided they are mostly fine (except one duplicate and the flagged ones), so I imported them to DSpace Test too (162 items)</li>
<li>Total items in CIAT Book Chapters is 914, with the others being flagged for some reason, and we should send that back to CIAT</li>
<li>Restart Tomcat on CGSpace so that the <code>cg.identifier.wletheme</code> field is available on REST API for Macaroni Bros</li>
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</ul>
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<h2 id="2017-06-07">2017-06-07</h2>
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<ul>
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<li>Testing <a href="https://github.com/ilri/DSpace/pull/319">Atmire&rsquo;s patch for the CUA Workflow Statistics again</a></li>
<li>Still doesn&rsquo;t seem to give results I&rsquo;d expect, like there are no results for Maria Garruccio, or for the ILRI community!</li>
<li>Then I&rsquo;ll file an update to the issue on Atmire&rsquo;s tracker</li>
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<li>Created a new branch with just the relevant changes, so I can send it to them</li>
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<li>One thing I noticed is that there is a failed database migration related to CUA:</li>
</ul>
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<pre><code>+----------------+----------------------------+---------------------+---------+
| Version | Description | Installed on | State |
+----------------+----------------------------+---------------------+---------+
| 1.1 | Initial DSpace 1.1 databas | | PreInit |
| 1.2 | Upgrade to DSpace 1.2 sche | | PreInit |
| 1.3 | Upgrade to DSpace 1.3 sche | | PreInit |
| 1.3.9 | Drop constraint for DSpace | | PreInit |
| 1.4 | Upgrade to DSpace 1.4 sche | | PreInit |
| 1.5 | Upgrade to DSpace 1.5 sche | | PreInit |
| 1.5.9 | Drop constraint for DSpace | | PreInit |
| 1.6 | Upgrade to DSpace 1.6 sche | | PreInit |
| 1.7 | Upgrade to DSpace 1.7 sche | | PreInit |
| 1.8 | Upgrade to DSpace 1.8 sche | | PreInit |
| 3.0 | Upgrade to DSpace 3.x sche | | PreInit |
| 4.0 | Initializing from DSpace 4 | 2015-11-20 12:42:52 | Success |
| 5.0.2014.08.08 | DS-1945 Helpdesk Request a | 2015-11-20 12:42:53 | Success |
| 5.0.2014.09.25 | DS 1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
| 5.0.2014.09.26 | DS-1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
| 5.0.2015.01.27 | MigrateAtmireExtraMetadata | 2015-11-20 12:43:29 | Success |
| 5.0.2017.04.28 | CUA eperson metadata migra | 2017-06-07 11:07:28 | OutOrde |
| 5.5.2015.12.03 | Atmire CUA 4 migration | 2016-11-27 06:39:05 | OutOrde |
| 5.5.2015.12.03 | Atmire MQM migration | 2016-11-27 06:39:06 | OutOrde |
| 5.6.2016.08.08 | CUA emailreport migration | 2017-01-29 11:18:56 | OutOrde |
+----------------+----------------------------+---------------------+---------+
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</code></pre><ul>
<li>Merge the pull request for <a href="https://github.com/ilri/DSpace/pull/328">WLE Phase II themes</a></li>
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</ul>
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<h2 id="2017-06-18">2017-06-18</h2>
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<ul>
<li>Redeploy CGSpace with latest changes from <code>5_x-prod</code>, run system updates, and reboot the server</li>
<li>Continue working on ansible infrastructure changes for CGIAR Library</li>
</ul>
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<h2 id="2017-06-20">2017-06-20</h2>
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<ul>
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<li>Import Abenet and Peter&rsquo;s changes to the CGIAR Library CRP community</li>
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<li>Due to them using Windows and renaming some columns there were formatting, encoding, and duplicate metadata value issues</li>
<li>I had to remove some fields from the CSV and rename some back to, ie, <code>dc.subject[en_US]</code> just so DSpace would detect changes properly</li>
<li>Now it looks much better: <a href="https://dspacetest.cgiar.org/handle/10947/2517">https://dspacetest.cgiar.org/handle/10947/2517</a></li>
<li>Removing the HTML tags and HTML/XML entities using the following GREL:
<ul>
<li><code>replace(value,/&lt;\/?\w+((\s+\w+(\s*=\s*(?:&quot;.*?&quot;|'.*?'|[^'&quot;&gt;\s]+))?)+\s*|\s*)\/?&gt;/,'')</code></li>
<li><code>value.unescape(&quot;html&quot;).unescape(&quot;xml&quot;)</code></li>
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</ul>
</li>
<li>Finally import 914 CIAT Book Chapters to CGSpace in two batches:</li>
</ul>
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<pre><code>$ JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot; [dspace]/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/35701 --source /home/aorth/CIAT-Books/SimpleArchiveFormat/ --mapfile=/tmp/ciat-books.map &amp;&gt; /tmp/ciat-books.log
$ JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot; [dspace]/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/35701 --source /home/aorth/CIAT-Books/SimpleArchiveFormat/ --mapfile=/tmp/ciat-books2.map &amp;&gt; /tmp/ciat-books2.log
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</code></pre><h2 id="2017-06-25">2017-06-25</h2>
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<ul>
<li>WLE has said that one of their Phase II research themes is being renamed from <code>Regenerating Degraded Landscapes</code> to <code>Restoring Degraded Landscapes</code></li>
<li>Pull request with the changes to <code>input-forms.xml</code>: <a href="https://github.com/ilri/DSpace/pull/329">#329</a></li>
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<li>As of now it doesn&rsquo;t look like there are any items using this research theme so we don&rsquo;t need to do any updates:</li>
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</ul>
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<pre><code>dspace=# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=237 and text_value like 'Regenerating Degraded Landscapes%';
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text_value
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------------
(0 rows)
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</code></pre><ul>
<li>Marianne from WLE asked if they can have both Phase I and II research themes together in the item submission form</li>
<li>Perhaps we can add them together in the same question for <code>cg.identifier.wletheme</code></li>
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</ul>
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<h2 id="2017-06-30">2017-06-30</h2>
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<ul>
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<li>CGSpace went down briefly, I see lots of these errors in the dspace logs:</li>
</ul>
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<pre><code>Java stacktrace: java.util.NoSuchElementException: Timeout waiting for idle object
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</code></pre><ul>
<li>After looking at the Tomcat logs, Munin graphs, and PostgreSQL connection stats, it seems there is just a high load</li>
2020-04-13 16:24:05 +02:00
<li>Might be a good time to adjust DSpace&rsquo;s database connection settings, like I first mentioned in April, 2017 after reading the <a href="https://wiki.lyrasis.org/display/cmtygp/DCAT+Meeting+April+2017">2017-04 DCAT comments</a></li>
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<li>I&rsquo;ve adjusted the following in CGSpace&rsquo;s config:
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<ul>
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<li><code>db.maxconnections</code> 30→70 (the default PostgreSQL config allows 100 connections, so DSpace&rsquo;s default of 30 is quite low)</li>
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<li><code>db.maxwait</code> 5000→10000</li>
<li><code>db.maxidle</code> 8→20 (DSpace default is -1, unlimited, but we had set it to 8 earlier)</li>
</ul>
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</li>
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<li>We will need to adjust this again (as well as the <code>pg_hba.conf</code> settings) when we deploy tsega&rsquo;s REST API</li>
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<li>Whip up a test for Marianne of WLE to be able to show both their Phase I and II research themes in the CGSpace item submission form:</li>
</ul>
<p><img src="/cgspace-notes/2017/06/wle-theme-test-a.png" alt="Test A for displaying the Phase I and II research themes">
<img src="/cgspace-notes/2017/06/wle-theme-test-b.png" alt="Test B for displaying the Phase I and II research themes"></p>
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2020-08-06 09:56:13 +02:00
<li><a href="/cgspace-notes/2020-08/">August, 2020</a></li>
2020-08-02 21:14:16 +02:00
2020-07-01 14:37:20 +02:00
<li><a href="/cgspace-notes/2020-07/">July, 2020</a></li>
2020-06-02 14:12:32 +02:00
<li><a href="/cgspace-notes/2020-06/">June, 2020</a></li>
2020-05-02 09:08:14 +02:00
2020-06-02 14:12:32 +02:00
<li><a href="/cgspace-notes/2020-05/">May, 2020</a></li>
2020-06-01 16:08:25 +02:00
2020-04-02 09:54:46 +02:00
<li><a href="/cgspace-notes/2020-04/">April, 2020</a></li>
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