mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-12-27 15:34:30 +01:00
325 lines
17 KiB
HTML
325 lines
17 KiB
HTML
<!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="June, 2017" />
|
||
<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." />
|
||
<meta property="og:type" content="article" />
|
||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-06/" />
|
||
<meta property="article:published_time" content="2017-06-01T10:14:52+03:00" />
|
||
<meta property="article:modified_time" content="2020-04-13T15:30:24+03:00" />
|
||
|
||
|
||
|
||
<meta name="twitter:card" content="summary"/>
|
||
<meta name="twitter:title" content="June, 2017"/>
|
||
<meta name="twitter: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."/>
|
||
<meta name="generator" content="Hugo 0.125.0">
|
||
|
||
|
||
|
||
<script type="application/ld+json">
|
||
{
|
||
"@context": "http://schema.org",
|
||
"@type": "BlogPosting",
|
||
"headline": "June, 2017",
|
||
"url": "https://alanorth.github.io/cgspace-notes/2017-06/",
|
||
"wordCount": "1261",
|
||
"datePublished": "2017-06-01T10:14:52+03:00",
|
||
"dateModified": "2020-04-13T15:30:24+03:00",
|
||
"author": {
|
||
"@type": "Person",
|
||
"name": "Alan Orth"
|
||
},
|
||
"keywords": "Notes"
|
||
}
|
||
</script>
|
||
|
||
|
||
|
||
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2017-06/">
|
||
|
||
<title>June, 2017 | CGSpace Notes</title>
|
||
|
||
|
||
<!-- combined, minified CSS -->
|
||
|
||
<link href="https://alanorth.github.io/cgspace-notes/css/style.c6ba80bc50669557645abe05f86b73cc5af84408ed20f1551a267bc19ece8228.css" rel="stylesheet" integrity="sha256-xrqAvFBmlVdkWr4F+GtzzFr4RAjtIPFVGiZ7wZ7Ogig=" crossorigin="anonymous">
|
||
|
||
|
||
<!-- minified Font Awesome for SVG icons -->
|
||
|
||
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.f5072c55a0721857184db93a50561d7dc13975b4de2e19db7f81eb5f3fa57270.js" integrity="sha256-9QcsVaByGFcYTbk6UFYdfcE5dbTeLhnbf4HrXz+lcnA=" crossorigin="anonymous"></script>
|
||
|
||
<!-- RSS 2.0 feed -->
|
||
|
||
|
||
|
||
|
||
</head>
|
||
|
||
<body>
|
||
|
||
|
||
<div class="blog-masthead">
|
||
<div class="container">
|
||
<nav class="nav blog-nav">
|
||
<a class="nav-link " 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>
|
||
in
|
||
|
||
<span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a>
|
||
|
||
</p>
|
||
</header>
|
||
<h2 id="2017-06-01">2017-06-01</h2>
|
||
<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>
|
||
<li>Then we’ll create a new sub-community for Phase II and create collections for the research themes there</li>
|
||
<li>The current “Research Themes” community will be renamed to “WLE Phase I Research Themes”</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>
|
||
<h2 id="2017-06-04">2017-06-04</h2>
|
||
<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>
|
||
<li>I tried to re-index Discovery but it didn’t fix it</li>
|
||
<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>
|
||
<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>
|
||
</ul>
|
||
<h2 id="2016-06-05">2016-06-05</h2>
|
||
<ul>
|
||
<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>
|
||
<li>Macaroni Bros tested it and said it’s fine, so I renamed it on CGSpace as well</li>
|
||
<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:
|
||
<ul>
|
||
<li>cg.identifier.url: <code>value.split("page=", "")[1]</code></li>
|
||
<li>dc.format.extent: <code>value.replace("p. ", "").split("-")[1].toNumber() - value.replace("p. ", "").split("-")[0].toNumber()</code></li>
|
||
</ul>
|
||
</li>
|
||
<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:
|
||
<ul>
|
||
<li><code>cells["dc.page.from"].value.toNumber() + cells["dc.format.pages"].value.toNumber()</code></li>
|
||
</ul>
|
||
</li>
|
||
<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(" ")[0].replace(",","").toLowercase() + "-" + sha1(value).get(1,9) + ".pdf__description:" + cells["dc.type"].value</code></li>
|
||
</ul>
|
||
</li>
|
||
<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("page=")</code></li>
|
||
<li>dc.format.extent: <code>or(value.contains("p. "),value.contains(" p."))</code></li>
|
||
<li>Command like: <code>$ gs -dNOPAUSE -dBATCH -dFirstPage=14 -dLastPage=27 -sDEVICE=pdfwrite -sOutputFile=beans.pdf -f 12605-1.pdf</code></li>
|
||
</ul>
|
||
</li>
|
||
<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>
|
||
<li>I’ve flagged them and proceeded without them (752 total) on DSpace Test:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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
|
||
</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>
|
||
</ul>
|
||
<h2 id="2017-06-07">2017-06-07</h2>
|
||
<ul>
|
||
<li>Testing <a href="https://github.com/ilri/DSpace/pull/319">Atmire’s patch for the CUA Workflow Statistics again</a></li>
|
||
<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>
|
||
<li>Then I’ll file an update to the issue on Atmire’s tracker</li>
|
||
<li>Created a new branch with just the relevant changes, so I can send it to them</li>
|
||
<li>One thing I noticed is that there is a failed database migration related to CUA:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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 |
|
||
+----------------+----------------------------+---------------------+---------+
|
||
</code></pre><ul>
|
||
<li>Merge the pull request for <a href="https://github.com/ilri/DSpace/pull/328">WLE Phase II themes</a></li>
|
||
</ul>
|
||
<h2 id="2017-06-18">2017-06-18</h2>
|
||
<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>
|
||
<h2 id="2017-06-20">2017-06-20</h2>
|
||
<ul>
|
||
<li>Import Abenet and Peter’s changes to the CGIAR Library CRP community</li>
|
||
<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,/<\/?\w+((\s+\w+(\s*=\s*(?:".*?"|'.*?'|[^'">\s]+))?)+\s*|\s*)\/?>/,'')</code></li>
|
||
<li><code>value.unescape("html").unescape("xml")</code></li>
|
||
</ul>
|
||
</li>
|
||
<li>Finally import 914 CIAT Book Chapters to CGSpace in two batches:</li>
|
||
</ul>
|
||
<pre tabindex="0"><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
|
||
$ 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
|
||
</code></pre><h2 id="2017-06-25">2017-06-25</h2>
|
||
<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>
|
||
<li>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:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>dspace=# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=237 and text_value like 'Regenerating Degraded Landscapes%';
|
||
text_value
|
||
------------
|
||
(0 rows)
|
||
</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>
|
||
</ul>
|
||
<h2 id="2017-06-30">2017-06-30</h2>
|
||
<ul>
|
||
<li>CGSpace went down briefly, I see lots of these errors in the dspace logs:</li>
|
||
</ul>
|
||
<pre tabindex="0"><code>Java stacktrace: java.util.NoSuchElementException: Timeout waiting for idle object
|
||
</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>
|
||
<li>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.lyrasis.org/display/cmtygp/DCAT+Meeting+April+2017">2017-04 DCAT comments</a></li>
|
||
<li>I’ve adjusted the following in CGSpace’s config:
|
||
<ul>
|
||
<li><code>db.maxconnections</code> 30→70 (the default PostgreSQL config allows 100 connections, so DSpace’s default of 30 is quite low)</li>
|
||
<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>
|
||
</li>
|
||
<li>We will need to adjust this again (as well as the <code>pg_hba.conf</code> settings) when we deploy tsega’s REST API</li>
|
||
<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>
|
||
|
||
|
||
|
||
|
||
|
||
|
||
</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/2024-04/">April, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-03/">March, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-02/">February, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2024-01/">January, 2024</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-12/">December, 2023</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 dir="auto">
|
||
|
||
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>
|