mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-22 22:55:04 +01:00
330 lines
15 KiB
HTML
330 lines
15 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="July, 2017" />
|
|
<meta property="og:description" content="2017-07-01
|
|
|
|
Run system updates and reboot DSpace Test
|
|
|
|
2017-07-04
|
|
|
|
Merge changes for WLE Phase II theme rename (#329)
|
|
Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
|
|
We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:
|
|
" />
|
|
<meta property="og:type" content="article" />
|
|
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-07/" />
|
|
<meta property="article:published_time" content="2017-07-01T18:03:52+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="July, 2017"/>
|
|
<meta name="twitter:description" content="2017-07-01
|
|
|
|
Run system updates and reboot DSpace Test
|
|
|
|
2017-07-04
|
|
|
|
Merge changes for WLE Phase II theme rename (#329)
|
|
Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
|
|
We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:
|
|
"/>
|
|
<meta name="generator" content="Hugo 0.112.3">
|
|
|
|
|
|
|
|
<script type="application/ld+json">
|
|
{
|
|
"@context": "http://schema.org",
|
|
"@type": "BlogPosting",
|
|
"headline": "July, 2017",
|
|
"url": "https://alanorth.github.io/cgspace-notes/2017-07/",
|
|
"wordCount": "1151",
|
|
"datePublished": "2017-07-01T18:03:52+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/2017-07/">
|
|
|
|
<title>July, 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/2017-07/">July, 2017</a></h2>
|
|
<p class="blog-post-meta">
|
|
<time datetime="2017-07-01T18:03:52+03:00">Sat Jul 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="2017-07-01">2017-07-01</h2>
|
|
<ul>
|
|
<li>Run system updates and reboot DSpace Test</li>
|
|
</ul>
|
|
<h2 id="2017-07-04">2017-07-04</h2>
|
|
<ul>
|
|
<li>Merge changes for WLE Phase II theme rename (<a href="https://github.com/ilri/DSpace/pull/329">#329</a>)</li>
|
|
<li>Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace</li>
|
|
<li>We can use PostgreSQL’s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ psql dspacenew -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=5 order by element, qualifier;' | sed -r 's:^-\[ RECORD (.*) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]*) +\| (.*): <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::'
|
|
</code></pre><ul>
|
|
<li>The <code>sed</code> script is from a post on the <a href="https://www.postgresql.org/message-id/437E44A5.508%40ultimeth.com">PostgreSQL mailing list</a></li>
|
|
<li>Abenet says the ILRI board wants to be able to have “lead author” for every item, so I’ve whipped up a WIP test in the <code>5_x-lead-author</code> branch</li>
|
|
<li>It works but is still very rough and we haven’t thought out the whole lifecycle yet</li>
|
|
</ul>
|
|
<p><img src="/cgspace-notes/2017/07/lead-author-test.png" alt="Testing lead author in submission form"></p>
|
|
<ul>
|
|
<li>I assume that “lead author” would actually be the first question on the item submission form</li>
|
|
<li>We also need to check to see which ORCID authority core this uses, because it seems to be using an entirely new one rather than the one for <code>dc.contributor.author</code> (which makes sense of course, but fuck, all the author problems aren’t bad enough?!)</li>
|
|
<li>Also would need to edit XMLUI item displays to incorporate this into authors list</li>
|
|
<li>And fuck, then anyone consuming our data via REST / OAI will not notice that we have an author outside of <code>dc.contributor.authors</code>… ugh</li>
|
|
<li>What if we modify the item submission form to use <a href="https://wiki.lyrasis.org/display/DSDOC5x/Submission+User+Interface#SubmissionUserInterface-ItemtypeBasedMetadataCollection"><code>type-bind</code> fields to show/hide certain fields depending on the type</a>?</li>
|
|
</ul>
|
|
<h2 id="2017-07-05">2017-07-05</h2>
|
|
<ul>
|
|
<li>Adjust WLE Research Theme to include both Phase I and II on the submission form according to editor feedback (<a href="https://github.com/ilri/DSpace/pull/330">#330</a>)</li>
|
|
<li>Generate list of fields in the current CGSpace <code>cg</code> scheme so we can record them properly in the metadata registry:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ psql dspace -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=2 order by element, qualifier;' | sed -r 's:^-\[ RECORD (.*) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]*) +\| (.*): <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::' > cg-types.xml
|
|
</code></pre><ul>
|
|
<li>CGSpace was unavailable briefly, and I saw this error in the DSpace log file:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>2017-07-05 13:05:36,452 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
|
|
org.postgresql.util.PSQLException: FATAL: remaining connection slots are reserved for non-replication superuser connections
|
|
</code></pre><ul>
|
|
<li>Looking at the <code>pg_stat_activity</code> table I saw there were indeed 98 active connections to PostgreSQL, and at this time the limit is 100, so that makes sense</li>
|
|
<li>Tsega restarted Tomcat and it’s working now</li>
|
|
<li>Abenet said she was generating a report with Atmire’s CUA module, so it could be due to that?</li>
|
|
<li>Looking in the logs I see this random error again that I should report to DSpace:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>2017-07-05 13:50:07,196 ERROR org.dspace.statistics.SolrLogger @ COUNTRY ERROR: EU
|
|
</code></pre><ul>
|
|
<li>Seems to come from <code>dspace-api/src/main/java/org/dspace/statistics/SolrLogger.java</code></li>
|
|
</ul>
|
|
<h2 id="2017-07-06">2017-07-06</h2>
|
|
<ul>
|
|
<li>Sisay tried to help by making a <a href="https://github.com/ilri/DSpace/pull/331">pull request for the RTB flagships</a> but there are formatting errors, unrelated changes, and the flagship names are not in the style I requested</li>
|
|
<li>Abenet talked to CIP and they said they are actually ok with using collection names rather than adding a new metadata field</li>
|
|
</ul>
|
|
<h2 id="2017-07-13">2017-07-13</h2>
|
|
<ul>
|
|
<li>Remove <code>UKaid</code> from the controlled vocabulary for <code>dc.description.sponsorship</code>, as <code>Department for International Development, United Kingdom</code> is the correct form and it is already present (<a href="https://github.com/ilri/DSpace/pull/334">#334</a>)</li>
|
|
</ul>
|
|
<h2 id="2017-07-14">2017-07-14</h2>
|
|
<ul>
|
|
<li>Sisay sent me a patch to add “Photo Report” to <code>dc.type</code> so I’ve added it to the <code>5_x-prod</code> branch</li>
|
|
</ul>
|
|
<h2 id="2017-07-17">2017-07-17</h2>
|
|
<ul>
|
|
<li>Linode shut down our seventeen (17) VMs due to nonpayment of the July 1st invoice</li>
|
|
<li>It took me a few hours to find the ICT/Finance contacts to pay the bill and boot all the servers back up</li>
|
|
<li>Since the server was down anyways, I decided to run all system updates and re-deploy CGSpace so that the latest changes to <code>input-forms.xml</code> and the sponsors controlled vocabulary</li>
|
|
</ul>
|
|
<h2 id="2017-07-20">2017-07-20</h2>
|
|
<ul>
|
|
<li>Skype chat with Addis team about the status of the CGIAR Library migration</li>
|
|
<li>Need to add the CGIAR System Organization subjects to Discovery Facets (test first)</li>
|
|
<li>Tentative list of dates for the migration:
|
|
<ul>
|
|
<li>August 4: aim to finish data cleanup and then give Peter a list of authors</li>
|
|
<li>August 18: ready to show System Office</li>
|
|
<li>September 4: all feedback and decisions (including workflows) from System Office</li>
|
|
<li>September 10/11: go live?</li>
|
|
</ul>
|
|
</li>
|
|
<li>Talk to Tsega and Danny about exporting/injesting the blog posts from Drupal into DSpace?</li>
|
|
<li>Followup meeting on August 8/9?</li>
|
|
<li>Sent Abenet the 2415 records from CGIAR Library’s Historical Archive (10947/1) after cleaning up the author authorities and HTML entities in <code>dc.contributor.author</code> and <code>dc.description.abstract</code> using OpenRefine:
|
|
<ul>
|
|
<li>Authors: <code>value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")</code></li>
|
|
<li>Abstracts: <code>replace(value,/<\/?\w+((\s+\w+(\s*=\s*(?:".*?"|'.*?'|[^'">\s]+))?)+\s*|\s*)\/?>/,'')</code></li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2017-07-24">2017-07-24</h2>
|
|
<ul>
|
|
<li>Move two top-level communities to be sub-communities of ILRI Projects</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ for community in 10568/2347 10568/25209; do /home/cgspace.cgiar.org/bin/dspace community-filiator --set --parent=10568/27629 --child="$community"; done
|
|
</code></pre><ul>
|
|
<li>Discuss CGIAR Library data cleanup with Sisay and Abenet</li>
|
|
</ul>
|
|
<h2 id="2017-07-27">2017-07-27</h2>
|
|
<ul>
|
|
<li>Help Sisay with some transforms to add descriptions to the <code>filename</code> column of some CIAT Presentations he’s working on in OpenRefine</li>
|
|
<li>Marianne emailed a few days ago to ask why “Integrating Ecosystem Solutions” was not in the list of WLE Phase I Research Themes on the input form</li>
|
|
<li>I told her that I only added the themes that I saw in the <a href="https://cgspace.cgiar.org/handle/10568/34508">WLE Phase I Research Themes</a> community</li>
|
|
<li>Then Mia from WLE also emailed to ask where some WLE focal regions went, and I said I didn’t understand what she was talking about, as all we did in our previous work was rename the old “Research Themes” subcommunity to “WLE Phase I Research Themes” and add a new subcommunity for “WLE Phase II Research Themes”.</li>
|
|
<li>Discuss some modifications to the CCAFS project tags in CGSpace submission form and in the database</li>
|
|
</ul>
|
|
<h2 id="2017-07-28">2017-07-28</h2>
|
|
<ul>
|
|
<li>Discuss updates to the Phase II CCAFS project tags with Andrea from Macaroni Bros</li>
|
|
<li>I will do the renaming and untagging of items in CGSpace database, and he will update his webservice with the latest project tags and I will get the XML from here for our <code>input-forms.xml</code>: <a href="https://ccafs.cgiar.org/export/ccafsproject">https://ccafs.cgiar.org/export/ccafsproject</a></li>
|
|
</ul>
|
|
<h2 id="2017-07-29">2017-07-29</h2>
|
|
<ul>
|
|
<li>Move some WLE items into appropriate Phase I Research Themes communities and delete some empty collections in WLE Regions community</li>
|
|
</ul>
|
|
<h2 id="2017-07-30">2017-07-30</h2>
|
|
<ul>
|
|
<li>Start working on CCAFS project tag cleanup</li>
|
|
<li>More questions about inconsistencies and spelling mistakes in their tags, so I’ve sent some questions for followup</li>
|
|
</ul>
|
|
<h2 id="2017-07-31">2017-07-31</h2>
|
|
<ul>
|
|
<li>Looks like the final list of metadata corrections for CCAFS project tags will be:</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-FP4_CRMWestAfrica';
|
|
update metadatavalue set text_value='FP3_VietnamLED' where resource_type_id=2 and metadata_field_id=134 and text_value='FP3_VeitnamLED';
|
|
update metadatavalue set text_value='PII-FP1_PIRCCA' where resource_type_id=2 and metadata_field_id=235 and text_value='PII-SEA_PIRCCA';
|
|
delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-WA_IntegratedInterventions';
|
|
</code></pre><ul>
|
|
<li>Now just waiting to run them on CGSpace, and then apply the modified input forms after Macaroni Bros give me an updated list</li>
|
|
<li>Temporarily increase the nginx upload limit to 200MB for Sisay to upload the CIAT presentations</li>
|
|
<li>Looking at CGSpace activity page, there are 52 Baidu bots concurrently crawling our website (I copied the activity page to a text file and grep it)!</li>
|
|
</ul>
|
|
<pre tabindex="0"><code>$ grep 180.76. /tmp/status | awk '{print $5}' | sort | uniq | wc -l
|
|
52
|
|
</code></pre><ul>
|
|
<li>From looking at the <code>dspace.log</code> I see they are all using the same session, which means our Crawler Session Manager Valve is working</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/2023-05/">May, 2023</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2023-04/">April, 2023</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2023-03/">March, 2023</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2023-02/">February, 2023</a></li>
|
|
|
|
<li><a href="/cgspace-notes/2023-01/">January, 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>
|