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<meta property="og:description" content="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." />
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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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<h2 class="blog-post-title"><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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<i class="fa fa-tag" aria-hidden="true"></i> <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>
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<li>After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes</li>
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<li>The <code>cg.identifier.wletheme</code> field will be used for both Phase I and Phase II Research Themes</li>
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<li>Then we’ll create a new sub-community for Phase II and create collections for the research themes there</li>
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<li>The current “Research Themes” community will be renamed to “WLE Phase I Research Themes”</li>
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<li>Tagged all items in the current Phase I collections with their appropriate themes</li>
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<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>
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<li>Add <code>cg.subject.system</code> to CGSpace metadata registry, for subject from the upcoming CGIAR Library migration</li>
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</ul>
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<h2 id="2017-06-04">2017-06-04</h2>
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<ul>
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<li>After adding <code>cg.identifier.wletheme</code> to 1106 WLE items I can see the field on XMLUI but not in REST!</li>
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<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’t fix it</li>
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<li>Run all system updates on DSpace Test and reboot the server</li>
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<li>After rebooting the server (and therefore restarting Tomcat) the new metadata field is available</li>
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<li>I’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’s “Research Themes” sub-community to “WLE Phase I Research Themes” on DSpace Test so Macaroni Bros can continue their testing</li>
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<li>Macaroni Bros tested it and said it’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 from–to from cg.identifier.url and dc.format.extent, respectively:
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<ul>
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<li>cg.identifier.url: <code>value.split("page=", "")[1]</code></li>
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<li>dc.format.extent: <code>value.replace("p. ", "").split("-")[1].toNumber() - value.replace("p. ", "").split("-")[0].toNumber()</code></li>
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</ul></li>
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<li>Finally, after some filtering to see which small outliers there were (based on dc.format.extent using “p. 1-14” vs “29 p.”), create a new column with last page number:
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<ul>
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<li><code>cells["dc.page.from"].value.toNumber() + cells["dc.format.pages"].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:
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<ul>
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<li>dc.page.to: <code>value.split(" ")[0].replace(",","").toLowercase() + "-" + sha1(value).get(1,9) + ".pdf__description:" + cells["dc.type"].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:
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<ul>
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<li>cg.identifier.url: <code>value.contains("page=")</code></li>
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<li>dc.format.extent: <code>or(value.contains("p. "),value.contains(" p."))</code></li>
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<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><p>I’ve flagged them and proceeded without them (752 total) on DSpace Test:</p>
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<pre><code>$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" [dspace]/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/93843 --source /home/aorth/src/CIAT-Books/SimpleArchiveFormat/ --mapfile=/tmp/ciat-books.map &> /tmp/ciat-books.log
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</code></pre></li>
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<li><p>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)</p></li>
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<li><p>Total items in CIAT Book Chapters is 914, with the others being flagged for some reason, and we should send that back to CIAT</p></li>
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<li><p>Restart Tomcat on CGSpace so that the <code>cg.identifier.wletheme</code> field is available on REST API for Macaroni Bros</p></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’s patch for the CUA Workflow Statistics again</a></li>
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<li>Still doesn’t seem to give results I’d expect, like there are no results for Maria Garruccio, or for the ILRI community!</li>
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<li>Then I’ll file an update to the issue on Atmire’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><p>One thing I noticed is that there is a failed database migration related to CUA:</p>
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<pre><code>+----------------+----------------------------+---------------------+---------+
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| Version | Description | Installed on | State |
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+----------------+----------------------------+---------------------+---------+
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| 1.1 | Initial DSpace 1.1 databas | | PreInit |
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| 1.2 | Upgrade to DSpace 1.2 sche | | PreInit |
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| 1.3 | Upgrade to DSpace 1.3 sche | | PreInit |
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| 1.3.9 | Drop constraint for DSpace | | PreInit |
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| 1.4 | Upgrade to DSpace 1.4 sche | | PreInit |
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| 1.5 | Upgrade to DSpace 1.5 sche | | PreInit |
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| 1.5.9 | Drop constraint for DSpace | | PreInit |
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| 1.6 | Upgrade to DSpace 1.6 sche | | PreInit |
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| 1.7 | Upgrade to DSpace 1.7 sche | | PreInit |
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| 1.8 | Upgrade to DSpace 1.8 sche | | PreInit |
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| 3.0 | Upgrade to DSpace 3.x sche | | PreInit |
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| 4.0 | Initializing from DSpace 4 | 2015-11-20 12:42:52 | Success |
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| 5.0.2014.08.08 | DS-1945 Helpdesk Request a | 2015-11-20 12:42:53 | Success |
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| 5.0.2014.09.25 | DS 1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
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| 5.0.2014.09.26 | DS-1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
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| 5.0.2015.01.27 | MigrateAtmireExtraMetadata | 2015-11-20 12:43:29 | Success |
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| 5.0.2017.04.28 | CUA eperson metadata migra | 2017-06-07 11:07:28 | OutOrde |
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| 5.5.2015.12.03 | Atmire CUA 4 migration | 2016-11-27 06:39:05 | OutOrde |
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| 5.5.2015.12.03 | Atmire MQM migration | 2016-11-27 06:39:06 | OutOrde |
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| 5.6.2016.08.08 | CUA emailreport migration | 2017-01-29 11:18:56 | OutOrde |
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+----------------+----------------------------+---------------------+---------+
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</code></pre></li>
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<li><p>Merge the pull request for <a href="https://github.com/ilri/DSpace/pull/328">WLE Phase II themes</a></p></li>
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</ul>
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<h2 id="2017-06-18">2017-06-18</h2>
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<ul>
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<li>Redeploy CGSpace with latest changes from <code>5_x-prod</code>, run system updates, and reboot the server</li>
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<li>Continue working on ansible infrastructure changes for CGIAR Library</li>
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</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’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>
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<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>
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<li>Now it looks much better: <a href="https://dspacetest.cgiar.org/handle/10947/2517">https://dspacetest.cgiar.org/handle/10947/2517</a></li>
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<li>Removing the HTML tags and HTML/XML entities using the following GREL:
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<ul>
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<li><code>replace(value,/<\/?\w+((\s+\w+(\s*=\s*(?:".*?"|'.*?'|[^'">\s]+))?)+\s*|\s*)\/?>/,'')</code></li>
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<li><code>value.unescape("html").unescape("xml")</code></li>
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</ul></li>
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<li><p>Finally import 914 CIAT Book Chapters to CGSpace in two batches:</p>
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<pre><code>$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" [dspace]/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/35701 --source /home/aorth/CIAT-Books/SimpleArchiveFormat/ --mapfile=/tmp/ciat-books.map &> /tmp/ciat-books.log
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$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" [dspace]/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/35701 --source /home/aorth/CIAT-Books/SimpleArchiveFormat/ --mapfile=/tmp/ciat-books2.map &> /tmp/ciat-books2.log
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</code></pre></li>
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</ul>
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<h2 id="2017-06-25">2017-06-25</h2>
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<ul>
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<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>
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<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><p>As of now it doesn’t look like there are any items using this research theme so we don’t need to do any updates:</p>
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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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------------
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(0 rows)
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</code></pre></li>
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<li><p>Marianne from WLE asked if they can have both Phase I and II research themes together in the item submission form</p></li>
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<li><p>Perhaps we can add them together in the same question for <code>cg.identifier.wletheme</code></p></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><p>CGSpace went down briefly, I see lots of these errors in the dspace logs:</p>
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<pre><code>Java stacktrace: java.util.NoSuchElementException: Timeout waiting for idle object
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</code></pre></li>
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<li><p>After looking at the Tomcat logs, Munin graphs, and PostgreSQL connection stats, it seems there is just a high load</p></li>
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<li><p>Might be a good time to adjust DSpace’s database connection settings, like I first mentioned in April, 2017 after reading the <a href="https://wiki.duraspace.org/display/cmtygp/DCAT+Meeting+April+2017">2017-04 DCAT comments</a></p></li>
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<li><p>I’ve adjusted the following in CGSpace’s config:</p>
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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’s default of 30 is quite low)</li>
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<li><code>db.maxwait</code> 5000→10000</li>
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<li><code>db.maxidle</code> 8→20 (DSpace default is -1, unlimited, but we had set it to 8 earlier)</li>
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</ul></li>
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<li><p>We will need to adjust this again (as well as the <code>pg_hba.conf</code> settings) when we deploy tsega’s REST API</p></li>
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<li><p>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:</p></li>
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</ul>
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<p><img src="/cgspace-notes/2017/06/wle-theme-test-a.png" alt="Test A for displaying the Phase I and II research themes" />
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<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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</article>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2019-05/">May, 2019</a></li>
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<li><a href="/cgspace-notes/posts/">Posts</a></li>
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<li><a href="/cgspace-notes/2019-05/">May, 2019</a></li>
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<li><a href="/cgspace-notes/2019-04/">April, 2019</a></li>
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<li><a href="/cgspace-notes/2019-03/">March, 2019</a></li>
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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